SDS@hd-Management

JabRef references

Author	Title	Year	Journal/Proceedings	Reftype	DOI/URL
Boffi, J.C., Knabbe, J., Kaiser, M. and Kuner, T.	KCC2-dependent Steady-state Intracellular Chloride Concentration and pH in Cortical Layer 2/3 Neurons of Anesthetized and Awake Mice [Abstract] [BibTeX]	2018	Frontiers in Cellular Neuroscience Vol. 12, pp. 7	article	DOI
Abstract: Neuronal intracellular Cl⁻ concentration ([Cl⁻]_i) influences a wide range of processes such as neuronal inhibition, membrane potential dynamics, intracellular pH (pH_i) or cell volume. Up to date, neuronal [Cl⁻]_i has predominantly been studied in model systems of reduced complexity. Here, we implemented the genetically encoded ratiometric Cl⁻ indicator Superclomeleon (SCLM) to estimate the steady-state [Cl⁻]_i in cortical neurons from anesthetized and awake mice using 2-photon microscopy. Additionally, we implemented superecliptic pHluorin (SE-pHluorin) as a ratiometric sensor to estimate the intracellular steady-state pH (pH_i) of mouse cortical neurons in vivo. We estimated an average resting [Cl⁻]_i of 6 textpm 2 mM with no evidence of subcellular gradients in the proximal somato-dendritic domain and an average somatic pH_i of 7.1 textpm 0.2. Neither [Cl⁻]_i nor pH_i were affected by isoflurane anesthesia. We deleted the cation-Cl⁻ co-transporter KCC2 in single identified neurons of adult mice and found an increase of [Cl⁻]_i to approximately 26 textpm 8 mM, demonstrating that under in vivo conditions KCC2 produces low [Cl⁻]_i in adult mouse neurons. In summary, neurons of the brain of awake adult mice exhibit a low and evenly distributed [Cl⁻]_i in the proximal somato-dendritic compartment that is independent of anesthesia and requires KCC2 expression for its maintenance.
BibTeX: @article{10.3389/fncel.2018.00007, author = {Boffi, Juan C. and Knabbe, Johannes and Kaiser, Michaela and Kuner, Thomas}, title = {KCC2-dependent Steady-state Intracellular Chloride Concentration and pH in Cortical Layer 2/3 Neurons of Anesthetized and Awake Mice}, journal = {Frontiers in Cellular Neuroscience}, year = {2018}, volume = {12}, pages = {7}, doi = {https://doi.org/10.3389/fncel.2018.00007} }
Knabbe, J., Joris Paul Nassal, Verhage, M. and Kuner, T.	Secretory vesicle trafficking in awake and anaesthetized mice: differential speeds in axons versus synapses [Abstract] [BibTeX]	2018	Journal of Physiology - London Vol. 596(16), pp. 3759-3773	article	DOI
Abstract: Key points Despite their immense physiological and pathophysiological importance, we know very little about the biology of dense core vesicle (DCV) trafficking in the intact mammalian brain. DCVs are transported at similar average speeds in the anaesthetized and awake mouse brain compared to neurons in culture, yet maximal speed and pausing fraction of transport were higher. Microtubule plus (+)-end extension imaging visualized microtubular growth at 0.12 μm/s and revealed that DCVs were transported faster in the anterograde direction. DCV transport slowed down upon presynaptic bouton approach, possibly promoting synaptic localization and cargo release. Our work provides a basis to extrapolate DCV transport properties determined in cultured neurons to the intact mouse brain and reveals novel features such as slowing upon bouton approach and brain state-dependent trafficking directionality. Abstract Neuronal dense core vesicles (DCVs) transport many cargo molecules like neuropeptides and neurotrophins to their release sites in dendrites or axons. The transport properties of DCVs in axons of the intact mammalian brain are unknown. We used viral expression of a DCV cargo reporter (NPY-Venus/Cherry) in the thalamus and two-photon in vivo imaging to visualize axonal DCV trafficking in thalamocortical projections of anaesthetized and awake mice. We found an average speed of 1 μm/s, maximal speeds of up to 5 μm/s and a pausing fraction of ∼11%. Directionality of transport differed between anaesthetized and awake mice. In vivo microtubule +-end extension imaging using MACF18-GFP revealed microtubular growth at 0.12 μm/s and provided positive identification of antero- and retrograde axonal transport. Consistent with previous reports, anterograde transport was faster (∼2.1 μm/s) than retrograde transport (∼1.4 μm/s). In summary, DCVs are transported with faster maximal speeds and lower pausing fraction in vivo compared to previous results obtained in vitro. Finally, we found that DCVs slowed down upon presynaptic bouton approach. We propose that this mechanism promotes synaptic localization and cargo release.
BibTeX: @article{1c38634724e94c29ac83a91d5498cc60, author = {Johannes Knabbe and Joris Paul Nassal, and Matthijs Verhage and Thomas Kuner}, title = {Secretory vesicle trafficking in awake and anaesthetized mice: differential speeds in axons versus synapses}, journal = {Journal of Physiology - London}, publisher = {Wiley-Blackwell}, year = {2018}, volume = {596}, number = {16}, pages = {3759--3773}, doi = {https://doi.org/10.1113/JP276022} }
	Photobiomodulation of the response to exercise-induced damage in murine skeletal muscle [BibTeX]	2019		book	DOI
BibTeX: @book{2019a,, title = {Photobiomodulation of the response to exercise-induced damage in murine skeletal muscle}, publisher = {Universitätsbibliothek Heidelberg}, year = {2019}, doi = {https://doi.org/10.11588/heidok.00027217} }
	Influence of photobiomodulation with blue light on the metabolism, proliferation and gene expression of human fibroblasts [BibTeX]	2019		book	DOI
BibTeX: @book{2019b,, title = {Influence of photobiomodulation with blue light on the metabolism, proliferation and gene expression of human fibroblasts}, publisher = {Universitätsbibliothek Heidelberg}, year = {2019}, doi = {https://doi.org/10.11588/heidok.00027187} }
	The Survival of Pharaonic Ostraca: Coincidence or Meaningful Patterns? [BibTeX]	2020	Using Ostraca in the Ancient World, pp. 89-108	incollection	DOI
BibTeX: @incollection{2020,, title = {The Survival of Pharaonic Ostraca: Coincidence or Meaningful Patterns?}, booktitle = {Using Ostraca in the Ancient World}, publisher = {De Gruyter}, year = {2020}, pages = {89--108}, doi = {https://doi.org/10.1515/9783110712902-005} }
Abd El Hay, M.Y.	The role of TRPV1 and TRPM2 in warm temperature detection [BibTeX]	2021		article	DOI
BibTeX: @article{AbdElHay2021, author = {Abd El Hay, Muad Yusuf}, title = {The role of TRPV1 and TRPM2 in warm temperature detection}, publisher = {Heidelberg University Library}, year = {2021}, doi = {https://doi.org/10.11588/HEIDOK.00030387} }
Abderhalden-Raba, A., Della Casa, P., Kothieringer, K., Lambers, K., Mächtle, B., Ranzinger, M. and Röpke, A.	Neue Untersuchungen zu den (prä-) historischen Terrassen von Ramosch [BibTeX]	2021	Archäologie in Graubünden Vol. 4, pp. 27-36	article
BibTeX: @article{AbderhaldenRaba2021, author = {Abderhalden-Raba, Angelika and Della Casa, Philippe and Kothieringer, Katja and Lambers, Karsten and Mächtle, Bertil and Ranzinger, Mario and Röpke, Astrid}, title = {Neue Untersuchungen zu den (prä-) historischen Terrassen von Ramosch}, journal = {Archäologie in Graubünden}, publisher = {Somedia Buchverlag}, year = {2021}, volume = {4}, pages = {27--36} }
Acuna, C., Liu, X. and Südhof, T.C.	How to Make an Active Zone: Unexpected Universal Functional Redundancy between RIMs and RIM-BPs [BibTeX]	2016	Neuron Vol. 91(4), pp. 792-807	article	DOI
BibTeX: @article{Acuna2016, author = {Claudio Acuna and Xinran Liu and Thomas C. Südhof}, title = {How to Make an Active Zone: Unexpected Universal Functional Redundancy between RIMs and RIM-BPs}, journal = {Neuron}, publisher = {Elsevier BV}, year = {2016}, volume = {91}, number = {4}, pages = {792--807}, doi = {https://doi.org/10.1016/j.neuron.2016.07.042} }
Agarwal, B., Cullen, F., Khochfar, S., Ceverino, D. and Klessen, R.S.	Optimal neighbourhood to nurture giants: a fundamental link between star-forming galaxies and direct collapse black holes [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 488(3), pp. 3268-3273	article	DOI
BibTeX: @article{Agarwal2019, author = {Bhaskar Agarwal and Fergus Cullen and Sadegh Khochfar and Daniel Ceverino and Ralf S Klessen}, title = {Optimal neighbourhood to nurture giants: a fundamental link between star-forming galaxies and direct collapse black holes}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {488}, number = {3}, pages = {3268--3273}, doi = {https://doi.org/10.1093/mnras/stz1347} }
Aggarwal, A., Frey, H., McDowell, G., Drenkhan, F., Nüsser, M., Racoviteanu, A. and Hoelzle, M.	Adaptation to climate change induced water stress in major glacierized mountain regions [BibTeX]	2021	Climate and Development, pp. 1-13	article	DOI
BibTeX: @article{Aggarwal2021, author = {Anubha Aggarwal and Holger Frey and Graham McDowell and Fabian Drenkhan and Marcus Nüsser and Adina Racoviteanu and Martin Hoelzle}, title = {Adaptation to climate change induced water stress in major glacierized mountain regions}, journal = {Climate and Development}, publisher = {Informa UK Limited}, year = {2021}, pages = {1--13}, doi = {https://doi.org/10.1080/17565529.2021.1971059} }
Ahmed, Y.L., Schleich, S., Bohlen, J., Mandel, N., Simon, B., Sinning, I. and Teleman, A.A.	DENR--MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation [Abstract] [BibTeX]	2018	PLOS Biology Vol. 16(6), pp. 1-21	article	DOI
Abstract: Author summary Usually, eukaryotic ribosomes translate only a single open reading frame (ORF) on an mRNA and then dissociate from the mRNA. In some cases, when there is a short upstream open reading frame (uORF) that precedes the main ORF, ribosomes can translate the uORF, terminate translation, and then undergo a poorly understood process called ``translation reinitiation'' whereby they resume scanning for another AUG initiation codon and then translate the main ORF. The molecular functions required for translation reinitiation are not known. We previously showed that two noncanonical initiation factors, density-regulated reinitiation and release factor (DENR) and multiple copies in T-cell lymphoma-1 (MCTS1), are involved in this process. We show here, based on a structure of MCTS1 bound to a fragment of DENR, that in order to successfully promote translation reinitiation, DENR and MCTS1 need to dimerize, and they need to bind tRNA. We thereby identify two molecular functions needed for translation reinitiation.
BibTeX: @article{Ahmed2018, author = {Ahmed, Yasar Luqman and Schleich, Sibylle and Bohlen, Jonathan and Mandel, Nicolas and Simon, Bernd and Sinning, Irmgard and Teleman, Aurelio A.}, title = {DENR--MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation}, journal = {PLOS Biology}, publisher = {Public Library of Science}, year = {2018}, volume = {16}, number = {6}, pages = {1--21}, doi = {https://doi.org/10.1371/journal.pbio.2005160} }
Ahmed, Y.L., Thoms, M., Mitterer, V., Sinning, I. and Hurt, E.	Crystal structures of Rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin--ligand-type complexes [Abstract] [BibTeX]	2019	Nature Communications Vol. 10(1), pp. 3050	article	DOI
Abstract: The Rea1 AAA+-ATPase dislodges assembly factors from pre-60S ribosomes upon ATP hydrolysis, thereby driving ribosome biogenesis. Here, we present crystal structures of Rea1-MIDAS, the conserved domain at the tip of the flexible Rea1 tail, alone and in complex with its substrate ligands, the UBL domains of Rsa4 or Ytm1. These complexes have structural similarity to integrin α-subunit domains when bound to extracellular matrix ligands, which for integrin biology is a key determinant for force-bearing cell--cell adhesion. However, the presence of additional motifs equips Rea1-MIDAS for its tasks in ribosome maturation. One loop insert cofunctions as an NLS and to activate the mechanochemical Rea1 cycle, whereas an additional β-hairpin provides an anchor to hold the ligand UBL domains in place. Our data show the versatility of the MIDAS fold for mechanical force transmission in processes as varied as integrin-mediated cell adhesion and mechanochemical removal of assembly factors from pre-ribosomes.
BibTeX: @article{Ahmed2019, author = {Ahmed, Yasar Luqman and Thoms, Matthias and Mitterer, Valentin and Sinning, Irmgard and Hurt, Ed}, title = {Crystal structures of Rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin--ligand-type complexes}, journal = {Nature Communications}, year = {2019}, volume = {10}, number = {1}, pages = {3050}, doi = {https://doi.org/10.1038/s41467-019-10922-6} }
Albrecht, M., Sticht, C., Wagner, T., Hettler, S.A., Torre, C.D.L., Qiu, J., Gretz, N., Albrecht, T., Yard, B., Sleeman, J.P. and Garvalov, B.K.	The crosstalk between glomerular endothelial cells and podocytes controls their responses to metabolic stimuli in diabetic nephropathy [BibTeX]	2023	Scientific Reports Vol. 13(1)	article	DOI
BibTeX: @article{Albrecht2023, author = {Michael Albrecht and Carsten Sticht and Tabea Wagner and Steffen A. Hettler and Carolina De La Torre and Jiedong Qiu and Norbert Gretz and Thomas Albrecht and Benito Yard and Jonathan P. Sleeman and Boyan K. Garvalov}, title = {The crosstalk between glomerular endothelial cells and podocytes controls their responses to metabolic stimuli in diabetic nephropathy}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2023}, volume = {13}, number = {1}, doi = {https://doi.org/10.1038/s41598-023-45139-7} }
Allert, C., Waclawiczek, A., Zimmermann, S.M.N., Göllner, S., Heid, D., Janssen, M., Renders, S., Rohde, C., Bauer, M., Bruckmann, M., Zinz, R., Pauli, C., Besenbeck, B., Wickenhauser, C., Trumpp, A., Krijgsveld, J., Müller-Tidow, C. and Blank, M.F.	Protein tyrosine kinase 2b inhibition reverts niche-associated resistance to tyrosine kinase inhibitors in AML [Abstract] [BibTeX]	2022	Leukemia Vol. 36(10), pp. 2418-2429	article	DOI URL
Abstract: AbstractFLT3 tyrosine kinase inhibitor (TKI) therapy evolved into a standard therapy in FLT3-mutated AML. TKI resistance, however, develops frequently with poor outcomes. We analyzed acquired TKI resistance in AML cell lines by multilayered proteome analyses. Leupaxin (LPXN), a regulator of cell migration and adhesion, was induced during early resistance development, alongside the tyrosine kinase PTK2B which phosphorylated LPXN. Resistant cells differed in cell adhesion and migration, indicating altered niche interactions. PTK2B and LPXN were highly expressed in leukemic stem cells in FLT3-ITD patients. PTK2B/FAK inhibition abrogated resistance-associated phenotypes, such as enhanced cell migration. Altered pathways in resistant cells, assessed by nascent proteomics, were largely reverted upon PTK2B/FAK inhibition. PTK2B/FAK inhibitors PF-431396 and defactinib synergized with different TKIs or daunorubicin in FLT3-mutated AML. Midostaurin-resistant and AML cells co-cultured with mesenchymal stroma cells responded particularly well to PTK2B/FAK inhibitor addition. Xenograft mouse models showed significant longer time to leukemia symptom-related endpoint upon gilteritinib/defactinib combination treatment in comparison to treatment with either drug alone. Our data suggest that the leupaxin-PTK2B axis plays an important role in acquired TKI resistance in AML. PTK2B/FAK inhibitors act synergistically with currently used therapeutics and may overcome emerging TKI resistance in FLT3-mutated AML at an early timepoint.
BibTeX: @article{Allert2022, author = {Catana Allert, Alexander Waclawiczek, Sarah Miriam Naomi Zimmermann, Stefanie Göllner, Daniel Heid, Maike Janssen, Simon Renders, Christian Rohde, Marcus Bauer, Margarita Bruckmann, Rafael Zinz, Cornelius Pauli, Birgit Besenbeck, Claudia Wickenhauser, Andreas Trumpp, Jeroen Krijgsveld, Carsten Müller-Tidow, Maximilian Felix Blank}, title = {Protein tyrosine kinase 2b inhibition reverts niche-associated resistance to tyrosine kinase inhibitors in AML}, journal = {Leukemia}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {36}, number = {10}, pages = {2418--2429}, url = {https://www.nature.com/articles/s41375-022-01687-x.pdf}, doi = {https://doi.org/10.1038/s41375-022-01687-x} }
Amirian, M., Azizi, H., Karoii, D.H. and Skutella, T.	VASA protein and gene expression analysis of human non-obstructive azoospermia and normal by immunohistochemistry, immunocytochemistry, and bioinformatics analysis [Abstract] [BibTeX]	2022	Scientific Reports Vol. 12(1)	article	DOI URL
Abstract: AbstractVASA, also known as DDX4, is a member of the DEAD-box proteins and an RNA binding protein with an ATP-dependent RNA helicase. The VASA gene expression, which is required for human germ cell development, may lead to infertility. Immunocytochemistry and immunohistochemistry were used to examine the expression of VASA protein in the human testis sections of azoospermic patients, in-vitro and in-silico models. Some studies of fertile humans showed VASA expression in the basal and adluminal compartments of seminiferous tubules. Our Immunocytochemistry and immunohistochemistry in infertile humans showed expression of VASA in the luminal compartments of the seminiferous tubule. The immunohistochemical analysis of three human cases with different levels of non-obstructive azoospermia revealed a higher expression of VASA-positive cells. For this purpose, Enrichr and Shiny Gene Ontology databases were used for pathway enrichment analysis and gene ontology. STRING and Cytoscape online evaluation were applied to predict proteins' functional and molecular interactions and performed to recognize the master genes, respectively. According to the obtained results, the main molecular functions of the up-regulated and downregulated genes include the meiotic cell cycle, RNA binding, and differentiation. STRING and Cytoscape analyses presented seven genes, i.e., DDX5, TNP2, DDX3Y, TDRD6, SOHL2, DDX31, and SYCP3, as the hub genes involved in infertility with VASA co-function and protein–protein interaction. Our findings suggest that VASA and its interacting hub proteins could help determine the pathophysiology of germ cell abnormalities and infertility.
BibTeX: @article{Amirian2022, author = {Mehdi Amirian, Hossein Azizi, Danial Hashemi Karoii, Thomas Skutella}, title = {VASA protein and gene expression analysis of human non-obstructive azoospermia and normal by immunohistochemistry, immunocytochemistry, and bioinformatics analysis}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {12}, number = {1}, url = {https://www.nature.com/articles/s41598-022-22137-9.pdf}, doi = {https://doi.org/10.1038/s41598-022-22137-9} }
Amr, A., Hinderer, M., Griebel, L., Deuber, D., Egger, C., Sedaghat-Hamedani, F., Kayvanpour, E., Huhn, D., Haas, J., Frese, K., Schweig, M., Marnau, N., Krämer, A., Durand, C., Battke, F., Prokosch, H.-U., Backes, M., Keller, A., Schröder, D., Katus, H.A., Frey, N. and Meder, B.	Controlling my genome with my smartphone: first clinical experiences of the PROMISE system [Abstract] [BibTeX]	2021	Clinical Research in Cardiology Vol. 111(6), pp. 638-650	article	DOI
Abstract: Abstract Background The development of Precision Medicine strategies requires high-dimensional phenotypic and genomic data, both of which are highly privacy-sensitive data types. Conventional data management systems lack the capabilities to sufficiently handle the expected large quantities of such sensitive data in a secure manner. PROMISE is a genetic data management concept that implements a highly secure platform for data exchange while preserving patient interests, privacy, and autonomy. Methods The concept of PROMISE to democratize genetic data was developed by an interdisciplinary team. It integrates a sophisticated cryptographic concept that allows only the patient to grant selective access to defined parts of his genetic information with single DNA base-pair resolution cryptography. The PROMISE system was developed for research purposes to evaluate the concept in a pilot study with nineteen cardiomyopathy patients undergoing genotyping, questionnaires, and longitudinal follow-up. Results The safety of genetic data was very important to 79%, and patients generally regarded the data as highly sensitive. More than half the patients reported that their attitude towards the handling of genetic data has changed after using the PROMISE app for 4 months (median). The patients reported higher confidence in data security and willingness to share their data with commercial third parties, including pharmaceutical companies (increase from 5 to 32%). Conclusion PROMISE democratizes genomic data by a transparent, secure, and patient-centric approach. This clinical pilot study evaluating a genetic data infrastructure is unique and shows that patient’s acceptance of data sharing can be increased by patient-centric decision-making. Graphic abstract
BibTeX: @article{Amr2021, author = {Ali Amr, Marc Hinderer, Lena Griebel, Dominic Deuber, Christoph Egger, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Daniel Huhn, Jan Haas, Karen Frese, Marc Schweig, Ninja Marnau, Annika Krämer, Claudia Durand, Florian Battke, Hans-Ulrich Prokosch, Michael Backes, Andreas Keller, Dominique Schröder, Hugo A. Katus, Norbert Frey, Benjamin Meder}, title = {Controlling my genome with my smartphone: first clinical experiences of the PROMISE system}, journal = {Clinical Research in Cardiology}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {111}, number = {6}, pages = {638--650}, doi = {https://doi.org/10.1007/s00392-021-01942-8} }
Aprupe, L., Litjens, G., Brinker, T.J., van der Laak, J. and Grabe, N.	Robust and accurate quantification of biomarkers of immune cells in lung cancer micro-environment using deep convolutional neural networks [Abstract] [BibTeX]	2019	PeerJ Vol. 7, pp. e6335	article	DOI
Abstract: Recent years have seen a growing awareness of the role the immune system plays in successful cancer treatment, especially in novel therapies like immunotherapy. The characterization of the immunological composition of tumors and their micro-environment is thus becoming a necessity. In this paper we introduce a deep learning-based immune cell detection and quantification method, which is based on supervised learning, i.e., the input data for training comprises labeled images. Our approach objectively deals with staining variation and staining artifacts in immunohistochemically stained lung cancer tissue and is as precise as humans. This is evidenced by the low cell count difference to humans of 0.033 cells on average. This method, which is based on convolutional neural networks, has the potential to provide a new quantitative basis for research on immunotherapy.
BibTeX: @article{Aprupe2019, author = {Aprupe, Lilija and Litjens, Geert and Brinker, Titus J. and van der Laak, Jeroen and Grabe, Niels}, title = {Robust and accurate quantification of biomarkers of immune cells in lung cancer micro-environment using deep convolutional neural networks}, journal = {PeerJ}, year = {2019}, volume = {7}, pages = {e6335}, doi = {https://doi.org/10.7717/peerj.6335} }
Argelaguet, R., Velten, B., Arnol, D., Dietrich, S., Zenz, T., Marioni, J.C., Buettner, F., Huber, W. and Stegle, O.	Multi-Omics Factor Analysis---a framework for unsupervised integration of multi-omics data sets [Abstract] [BibTeX]	2018	Molecular Systems Biology Vol. 14(6), pp. e8124	article	DOI
Abstract: Abstract Multi-omics studies promise the improved characterization of biological processes across molecular layers. However, methods for the unsupervised integration of the resulting heterogeneous data sets are lacking. We present Multi-Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi-omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities. The learnt factors enable a variety of downstream analyses, including identification of sample subgroups, data imputation and the detection of outlier samples. We applied MOFA to a cohort of 200 patient samples of chronic lymphocytic leukaemia, profiled for somatic mutations, RNA expression, DNA methylation and ex vivo drug responses. MOFA identified major dimensions of disease heterogeneity, including immunoglobulin heavy-chain variable region status, trisomy of chromosome 12 and previously underappreciated drivers, such as response to oxidative stress. In a second application, we used MOFA to analyse single-cell multi-omics data, identifying coordinated transcriptional and epigenetic changes along cell differentiation.
BibTeX: @article{Argelaguet2018, author = {Argelaguet, Ricard and Velten, Britta and Arnol, Damien and Dietrich, Sascha and Zenz, Thorsten and Marioni, John C. and Buettner, Florian and Huber, Wolfgang and Stegle, Oliver}, title = {Multi-Omics Factor Analysis---a framework for unsupervised integration of multi-omics data sets}, journal = {Molecular Systems Biology}, year = {2018}, volume = {14}, number = {6}, pages = {e8124}, doi = {https://doi.org/10.15252/msb.20178124} }
Armbruster, L., Linster, E., Boyer, J.-B., Brünje, A., Eirich, J., Stephan, I., Bienvenut, W.V., Weidenhausen, J., Meinnel, T., Hell, R., Sinning, I., Finkemeier, I., Giglione, C. and Wirtz, M.	NAA50 Is an Enzymatically Active Nupalpha-Acetyltransferase That Is Crucial for Development and Regulation of Stress Responses [BibTeX]	2020	Plant Physiology Vol. 183(4), pp. 1502-1516	article	DOI
BibTeX: @article{Armbruster2020, author = {Laura Armbruster and Eric Linster and Jean-Baptiste Boyer and Annika Brünje and Jürgen Eirich and Iwona Stephan and Willy V. Bienvenut and Jonas Weidenhausen and Thierry Meinnel and Ruediger Hell and Irmgard Sinning and Iris Finkemeier and Carmela Giglione and Markus Wirtz}, title = {NAA50 Is an Enzymatically Active Nupalpha-Acetyltransferase That Is Crucial for Development and Regulation of Stress Responses}, journal = {Plant Physiology}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {183}, number = {4}, pages = {1502--1516}, doi = {https://doi.org/10.1104/pp.20.00222} }
Arnold, M. and Hessel, L.	Transforming data silos into knowledge: Early Chinese Periodicals Online (ECPO) [BibTeX]	2020	E-Science-Tage 2019	article	DOI
BibTeX: @article{Arnold2020, author = {Arnold, Matthias and Hessel, Lena}, title = {Transforming data silos into knowledge: Early Chinese Periodicals Online (ECPO)}, journal = {E-Science-Tage 2019}, publisher = {University Library Heidelberg}, year = {2020}, doi = {https://doi.org/10.11588/HEIBOOKS.598.C8420} }
Arnold, M., Heckmann, D., Gietz, P., Frank, A., Ursinus, M., Roth, C., Chitavong, A., Hansche, J., Bellm, N. and Dolata, M.	Turkology Annual Online – Full bibliographic records [BibTeX]	2021		misc	DOI
BibTeX: @misc{Arnold2021, author = {Arnold, Matthias and Heckmann, Dustin and Gietz, Peter and Frank, Anette and Ursinus, Michael and Roth, Christian and Chitavong, Arina and Hansche, Jens and Bellm, Nicolas and Dolata, Mateusz}, title = {Turkology Annual Online – Full bibliographic records}, publisher = {heiDATA}, year = {2021}, doi = {https://doi.org/10.11588/DATA/GH511N} }
Arnold, M. and Henke, K.	Building and Improving an OCR Classifier for Republican Chinese Newspaper Text [BibTeX]	2022		article	DOI
BibTeX: @article{Arnold2022, author = {Arnold, Matthias and Henke, Konstantin}, title = {Building and Improving an OCR Classifier for Republican Chinese Newspaper Text}, publisher = {Zenodo}, year = {2022}, doi = {https://doi.org/10.5281/ZENODO.6327919} }
Arnold, M., Paterson, D. and Xie, J.	Procedural challenges: the FAIR principles and PRC electronic resources - a case study of Chinese republican newspapers [Abstract] [BibTeX]	2022	International Journal of Digital Humanities	article	DOI
Abstract: AbstractIt is tempting to assume that FAIR data principles effectively apply globally. In practice, digital research platforms play a central role in ensuring the applicability of these principles to research exchange, where General Data Protection Regulation (EU) and Multi Level Protection Scheme 2.0 (PRC) provide the overarching legal frameworks. For this article, we conduct a systematic review of research into Chinese Republican newspapers as it appears in Chinese academic journal databases. We experimentally compare the results of repeated search runs using different interfaces and with different points of origin. We then analyze our results regarding the practical and technical accessibility conditions. Concluding with an analysis of conceptual mismatches surrounding the classification of items as “full-text“, and of a case of total data loss that is nevertheless symptomatic of the limited degree of data re-usability. Our results show structural challenges preventing Findability, Accessibility, Interoperability, and Re-usability from being put into practice. Since these experiments draw upon our Digital Humanities (DH) research, we include a state-of-the-field overview of historical Periodicals and digitization research in the PRC. Our research on the one hand addresses DH practitioners interested in digital collections, and technical aspects of document processing with a focus on historical Chinese sources. On the other hand, our experience is helpful to researchers irrespective of the topic. Our article is accompanied by a data publication containing sources and results of our experiments, as well as an online bibliography of the research articles we collected.
BibTeX: @article{Arnold2022a, author = {Matthias Arnold, Duncan Paterson, Jia Xie}, title = {Procedural challenges: the FAIR principles and PRC electronic resources - a case study of Chinese republican newspapers}, journal = {International Journal of Digital Humanities}, publisher = {Springer Science and Business Media LLC}, year = {2022}, doi = {https://doi.org/10.1007/s42803-022-00055-6} }
Asan, L., Falfán-Melgoza, C., Beretta, C.A., Sack, M., Zheng, L., Weber-Fahr, W., Kuner, T. and Knabbe, J.	Cellular correlates of gray matter volume changes in magnetic resonance morphometry identified by two-photon microscopy [BibTeX]	2021	Scientific Reports Vol. 11	article	DOI
BibTeX: @article{Asan2021, author = {Livia Asan and Claudia Falfán-Melgoza and Carlo A. Beretta and Markus Sack and Lei Zheng and Wolfgang Weber-Fahr and Thomas Kuner and Johannes Knabbe}, title = {Cellular correlates of gray matter volume changes in magnetic resonance morphometry identified by two-photon microscopy}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {11}, doi = {https://doi.org/10.1038/s41598-021-83491-8} }
Awwad, M.H.S., Kriegsmann, K., Plaumann, J., Benn, M., Hillengass, J., Raab, M.S., Bertsch, U., Munder, M., Weisel, K., Salwender, H.J., Hänel, M., Fenk, R., Dürig, J., Müller-Tidow, C., Goldschmidt, H. and Hundemer, M.	The prognostic and predictive value of IKZF1 and IKZF3 expression in T-cells in patients with multiple myeloma [BibTeX]	2018	OncoImmunology Vol. 7(10), pp. e1486356	article	DOI
BibTeX: @article{Awwad2018, author = {Mohamed H. S. Awwad and Katharina Kriegsmann and Julian Plaumann and Michael Benn and Jens Hillengass and Marc S. Raab and Uta Bertsch and Markus Munder and Katja Weisel and Hans Jürgen Salwender and Mathias Hänel and Roland Fenk and Jan Dürig and Carsten Müller-Tidow and Hartmut Goldschmidt and Michael Hundemer}, title = {The prognostic and predictive value of IKZF1 and IKZF3 expression in T-cells in patients with multiple myeloma}, journal = {OncoImmunology}, publisher = {Informa UK Limited}, year = {2018}, volume = {7}, number = {10}, pages = {e1486356}, doi = {https://doi.org/10.1080/2162402x.2018.1486356} }
Awwad, M.H.S., Mahmoud, A., Bruns, H., Echchannaoui, H., Kriegsmann, K., Lutz, R., Raab, M.S., Bertsch, U., Munder, M., Jauch, A., Weisel, K., Maier, B., Weinhold, N., Salwender, H.J., Eckstein, V., Hänel, M., Fenk, R., Dürig, J., Brors, B., Benner, A., Müller-Tidow, C., Goldschmidt, H. and Hundemer, M.	Selective elimination of immunosuppressive T cells in patients with multiple myeloma [BibTeX]	2021	Leukemia	article	DOI
BibTeX: @article{Awwad2021, author = {Mohamed H. S. Awwad and Abdelrahman Mahmoud and Heiko Bruns and Hakim Echchannaoui and Katharina Kriegsmann and Raphael Lutz and Marc S. Raab and Uta Bertsch and Markus Munder and Anna Jauch and Katja Weisel and Bettina Maier and Niels Weinhold and Hans Jürgen Salwender and Volker Eckstein and Mathias Hänel and Roland Fenk and Jan Dürig and Benedikt Brors and Axel Benner and Carsten Müller-Tidow and Hartmut Goldschmidt and Michael Hundemer}, title = {Selective elimination of immunosuppressive T cells in patients with multiple myeloma}, journal = {Leukemia}, publisher = {Springer Science and Business Media LLC}, year = {2021}, doi = {https://doi.org/10.1038/s41375-021-01172-x} }
Azizi, H., Karoii, D.H. and Skutella, T.	Whole Exome Sequencing and In Silico Analysis of Human Sertoli in Patients with Non-Obstructive Azoospermia [Abstract] [BibTeX]	2022	International Journal of Molecular Sciences Vol. 23(20), pp. 12570	article	DOI URL
Abstract: Non-obstructive azoospermia (NOA) is a serious cause of male infertility. The Sertoli cell responds to androgens and takes on roles supporting spermatogenesis, which may cause infertility. This work aims to enhance the genetic diagnosis of NOA via the discovery of new and hub genes implicated in human NOA and to better assess the odds of successful sperm extraction according to the individual’s genotype. Whole exome sequencing (WES) was done on three NOA patients to find key genes involved in NOA. We evaluated genome-wide transcripts (about 50,000 transcripts) by microarray between the Sertoli of non-obstructive azoospermia and normal cells. The microarray analysis of three human cases with different non-obstructive azoospermia revealed that 32 genes were upregulated, and the expressions of 113 genes were downregulated versus the normal case. For this purpose, Enrich Shiny GO, STRING, and Cytoscape online evaluations were applied to predict the functional and molecular interactions of proteins and then recognize the master pathways. The functional enrichment analysis demonstrated that the biological process (BP) terms “inositol lipid-mediated signaling”, “positive regulation of transcription by RNA polymerase II”, and “positive regulation of DNA-templated transcription” significantly changed in upregulated differentially expressed genes (DEGs). The BP investigation of downregulated DEGs highlighted “mitotic cytokinesis”, “regulation of protein-containing complex assembly”, “cytoskeleton-dependent cytokinesis”, and the “peptide metabolic process”. Overrepresented molecular function (MF) terms in upregulated DEGs included “ubiquitin-specific protease binding”, “protease binding”, “phosphatidylinositol trisphosphate phosphatase activity”, and “clathrin light chain binding”. Interestingly, the MF analysis of the downregulated DEGs revealed overexpression in “ATPase inhibitor activity”, “glutathione transferase activity”, and “ATPase regulator activity”. Our findings suggest that these genes and their interacting hub proteins could help determine the pathophysiologies of germ cell abnormalities and infertility.
BibTeX: @article{Azizi2022, author = {Hossein Azizi, Danial Hashemi Karoii, Thomas Skutella}, title = {Whole Exome Sequencing and In Silico Analysis of Human Sertoli in Patients with Non-Obstructive Azoospermia}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2022}, volume = {23}, number = {20}, pages = {12570}, url = {https://www.mdpi.com/1422-0067/23/20/12570/pdf}, doi = {https://doi.org/10.3390/ijms232012570} }
Ballesteros-Paredes, J., Vázquez-Semadeni, E., Palau, A. and Klessen, R.S.	Gravity or turbulence? - IV. Collapsing cores in out-of-virial disguise [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 479(2), pp. 2112-2125	article	DOI
BibTeX: @article{BallesterosParedes2018, author = {Ballesteros-Paredes, Javier and Vázquez-Semadeni, Enrique and Palau, Aina and Klessen, Ralf S.}, title = {Gravity or turbulence? - IV. Collapsing cores in out-of-virial disguise}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {479}, number = {2}, pages = {2112--2125}, doi = {https://doi.org/10.1093/mnras/sty1515} }
Ballesteros-Paredes, J., Vázquez-Semadeni, E., Palau, A. and Klessen, R.S.	Erratum: Gravity or turbulence? - IV. Collapsing cores in out of virial disguise [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 487(2), pp. 2730-2731	article	DOI
BibTeX: @article{BallesterosParedes2019, author = {Javier Ballesteros-Paredes and Enrique Vázquez-Semadeni and Aina Palau and Ralf S Klessen}, title = {Erratum: Gravity or turbulence? - IV. Collapsing cores in out of virial disguise}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {487}, number = {2}, pages = {2730--2731}, doi = {https://doi.org/10.1093/mnras/stz1384} }
Bamberg, L.V., Heigwer, F., Wandmacher, A.M., Singh, A., Betge, J., Rindtorff, N., Werner, J., Josten, J., Skabkina, O.V., Hinsenkamp, I., Erdmann, G., Röcken, C., Ebert, M.P., Burgermeister, E., Zhan, T. and Boutros, M.	Targeting euchromatic histone lysine methyltransferases sensitizes colorectal cancer to histone deacetylase inhibitors [BibTeX]	2022	International Journal of Cancer Vol. 151(9), pp. 1586-1601	article	DOI
BibTeX: @article{Bamberg2022, author = {Leonhard Valentin Bamberg, Florian Heigwer, Anna Maxi Wandmacher, Ambika Singh, Johannes Betge, Niklas Rindtorff, Johannes Werner, Julia Josten, Olga Valerievna Skabkina, Isabel Hinsenkamp, Gerrit Erdmann, Christoph Röcken, Matthias P Ebert, Elke Burgermeister, Tianzuo Zhan, Michael Boutros}, title = {Targeting euchromatic histone lysine methyltransferases sensitizes colorectal cancer to histone deacetylase inhibitors}, journal = {International Journal of Cancer}, publisher = {Wiley}, year = {2022}, volume = {151}, number = {9}, pages = {1586--1601}, doi = {https://doi.org/10.1002/ijc.34155} }
Baranov, V., Engel, M., Hammel, J., Hörnig, M., van de Kamp, T., Zuber, M. and Haug, J.	Synchrotron-radiation computed tomography uncovers ecosystem functions of fly larvae in an Eocene forest [BibTeX]	2021	Palaeontologia Electronica	article	DOI
BibTeX: @article{Baranov2021, author = {Viktor Baranov and Michael Engel and Jörg Hammel and Marie Hörnig and Thomas van de Kamp and Marcus Zuber and Joachim Haug}, title = {Synchrotron-radiation computed tomography uncovers ecosystem functions of fly larvae in an Eocene forest}, journal = {Palaeontologia Electronica}, publisher = {Coquina Press}, year = {2021}, doi = {https://doi.org/10.26879/1129} }
	Deutsche Ostasienstudien 37 - China and the World—the World and China: Transcultural Perspectives (Essays in Honor of Rudolf G. Wagner) [BibTeX]	2019	Vol. 3 Transcultural Perspectives on Modern China	book
BibTeX: @book{BarbaraMittler2019,, title = {Deutsche Ostasienstudien 37 - China and the World—the World and China: Transcultural Perspectives (Essays in Honor of Rudolf G. Wagner)}, publisher = {OSTASIEN Verlag}, year = {2019}, volume = {3 Transcultural Perspectives on Modern China} }
	Deutsche Ostasienstudien 37 - China and the World—the World and China: Transcultural Perspectives (Essays in Honor of Rudolf G. Wagner) [BibTeX]	2019	Vol. 4 Transcultural Perspectives on Global China	book
BibTeX: @book{BarbaraMittler2019a,, title = {Deutsche Ostasienstudien 37 - China and the World—the World and China: Transcultural Perspectives (Essays in Honor of Rudolf G. Wagner)}, publisher = {OSTASIEN Verlag}, year = {2019}, volume = {4 Transcultural Perspectives on Global China} }
Barf, M.-M., Benneckendorf, F.S., Reiser, P., Bäuerle, R., Köntges, W., Müller, L., Pfannmöller, M., Beck, S., Mankel, E., Freudenberg, J., Jänsch, D., Tisserant, J.-N., Lovrincic, R., Schröder, R.R., Bunz, U.H.F., Pucci, A., Jaegermann, W., Kowalsky, W. and Müllen, K.	Compensation of Oxygen Doping in p-Type Organic Field-Effect Transistors Utilizing Immobilized n-Dopants [BibTeX]	2020	Advanced Materials Technologies, pp. 2000556	article	DOI
BibTeX: @article{Barf2020, author = {Marc-Michael Barf and Frank S. Benneckendorf and Patrick Reiser and Rainer Bäuerle and Wolfgang Köntges and Lars Müller and Martin Pfannmöller and Sebastian Beck and Eric Mankel and Jan Freudenberg and Daniel Jänsch and Jean-Nicolas Tisserant and Robert Lovrincic and Rasmus R. Schröder and Uwe H. F. Bunz and Annemarie Pucci and Wolfram Jaegermann and Wolfgang Kowalsky and Klaus Müllen}, title = {Compensation of Oxygen Doping in p-Type Organic Field-Effect Transistors Utilizing Immobilized n-Dopants}, journal = {Advanced Materials Technologies}, publisher = {Wiley}, year = {2020}, pages = {2000556}, doi = {https://doi.org/10.1002/admt.202000556} }
Barro, A.V., Stöckle, D., Thellmann, M., Ruiz-Duarte, P., Bald, L., Louveaux, M., von Born, P., Denninger, P., Goh, T., Fukaki, H., Vermeer, J.E. and Maizel, A.	Cytoskeleton Dynamics Are Necessary for Early Events of Lateral Root Initiation in Arabidopsis [Abstract] [BibTeX]	2019	Current Biology Vol. 29(15), pp. 2443-2454.e5	article	DOI URL
Abstract: Summary How plant cells re-establish differential growth to initiate organs is poorly understood. Morphogenesis of lateral roots relies on the asymmetric cell division of initially symmetric founder cells. This division is preceded by the tightly controlled asymmetric radial expansion of these cells. The cellular mechanisms that license and ensure the coordination of these events are unknown. Here, we quantitatively analyze microtubule and F-actin dynamics during lateral root initiation. Using mutants and pharmacological and tissue-specific genetic perturbations, we show that dynamic reorganization of both microtubule and F-actin networks is necessary for the asymmetric expansion of the founder cells. This cytoskeleton remodeling intertwines with auxin signaling in the pericycle and endodermis in order for founder cells to acquire a basic polarity required for initiating lateral root development. Our results reveal the conservation of cell remodeling and polarization strategies between the Arabidopsis zygote and lateral root founder cells. We propose that coordinated, auxin-driven reorganization of the cytoskeleton licenses asymmetric cell growth and divisions during embryonic and post-embryonic organogenesis.
BibTeX: @article{Barro2019, author = {Barro, Amaya Vilches and Stöckle, Dorothee and Thellmann, Martha and Ruiz-Duarte, Paola and Bald, Lotte and Louveaux, Marion and von Born, Patrick and Denninger, Philipp and Goh, Tatsuaki and Fukaki, Hidehiro and Vermeer, Joop E.M. and Maizel, Alexis}, title = {Cytoskeleton Dynamics Are Necessary for Early Events of Lateral Root Initiation in Arabidopsis}, journal = {Current Biology}, publisher = {Elsevier BV}, year = {2019}, volume = {29}, number = {15}, pages = {2443--2454.e5}, url = {http://www.sciencedirect.com/science/article/pii/S0960982219307663}, doi = {https://doi.org/10.1016/j.cub.2019.06.039} }
Barulina, E., Khodr, A., Dkhil, S.B., Perkhun, P., Quiroz, Y.A.A., Koganezawa, T., Yoshimoto, N., Köntges, W., Schröder, R.R., Pfammöller, M., Margeat, O., Ackermann, J. and Videlot-Ackermann, C.	Improved ultraviolet stability of fullerene-based organic solar cells through light-induced enlargement and crystallization of fullerene domains [BibTeX]	2022	Thin Solid Films Vol. 757, pp. 139394	article	DOI URL
BibTeX: @article{Barulina2022, author = {Elena Barulina, Anass Khodr, Sadok Ben Dkhil, Pavlo Perkhun, Yatzil Alejandra Avalos Quiroz, Tomoyuki Koganezawa, Noriyuki Yoshimoto, Wolfgang Köntges, Rasmus R. Schröder, Martin Pfammöller, Olivier Margeat, Jörg Ackermann, Christine Videlot-Ackermann}, title = {Improved ultraviolet stability of fullerene-based organic solar cells through light-induced enlargement and crystallization of fullerene domains}, journal = {Thin Solid Films}, publisher = {Elsevier BV}, year = {2022}, volume = {757}, pages = {139394}, url = {https://api.elsevier.com/content/article/PII:S004060902200308X?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.tsf.2022.139394} }
Bas-Orth, C., Koch, M., Lau, D., Buchthal, B. and Bading, H.	A microRNA signature of toxic extrasynaptic N-methyl-D-aspartate (NMDA) receptor signaling [BibTeX]	2020	Molecular Brain Vol. 13(1)	article	DOI
BibTeX: @article{BasOrth2020, author = {Carlos Bas-Orth and Mirja Koch and David Lau and Bettina Buchthal and Hilmar Bading}, title = {A microRNA signature of toxic extrasynaptic N-methyl-D-aspartate (NMDA) receptor signaling}, journal = {Molecular Brain}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {13}, number = {1}, doi = {https://doi.org/10.1186/s13041-020-0546-0} }
Baßler, J., Ahmed, Y.L., Kallas, M., Kornprobst, M., Calviño, F.R., Gnädig, M., Thoms, M., Stier, G., Ismail, S., Kharde, S., Castillo, N., Griesel, S., Bastuck, S., Bradatsch, B., Thomson, E., Flemming, D., Sinning, I. and Hurt, E.	Interaction network of the ribosome assembly machinery from a eukaryotic thermophile [Abstract] [BibTeX]	2017	Protein Science Vol. 26(2), pp. 327-342	article	DOI
Abstract: Abstract Ribosome biogenesis in eukaryotic cells is a highly dynamic and complex process innately linked to cell proliferation. The assembly of ribosomes is driven by a myriad of biogenesis factors that shape pre-ribosomal particles by processing and folding the ribosomal RNA and incorporating ribosomal proteins. Biochemical approaches allowed the isolation and characterization of pre-ribosomal particles from Saccharomyces cerevisiae, which lead to a spatiotemporal map of biogenesis intermediates along the path from the nucleolus to the cytoplasm. Here, we cloned almost the entire set (∼180) of ribosome biogenesis factors from the thermophilic fungus Chaetomium thermophilum in order to perform an in-depth analysis of their protein--protein interaction network as well as exploring the suitability of these thermostable proteins for structural studies. First, we performed a systematic screen, testing about 80 factors for crystallization and structure determination. Next, we performed a yeast 2-hybrid analysis and tested about 32,000 binary combinations, which identified more than 1000 protein--protein contacts between the thermophilic ribosome assembly factors. To exemplary verify several of these interactions, we performed biochemical reconstitution with the focus on the interaction network between 90S pre-ribosome factors forming the ctUTP-A and ctUTP-B modules, and the Brix-domain containing assembly factors of the pre-60S subunit. Our work provides a rich resource for biochemical reconstitution and structural analyses of the conserved ribosome assembly machinery from a eukaryotic thermophile.
BibTeX: @article{Bassler2017, author = {Baßler, Jochen and Ahmed, Yasar Luqman and Kallas, Martina and Kornprobst, Markus and Calviño, Fabiola R. and Gnädig, Marén and Thoms, Matthias and Stier, Gunter and Ismail, Sherif and Kharde, Satyavati and Castillo, Nestor and Griesel, Sabine and Bastuck, Sonja and Bradatsch, Bettina and Thomson, Emma and Flemming, Dirk and Sinning, Irmgard and Hurt, Ed}, title = {Interaction network of the ribosome assembly machinery from a eukaryotic thermophile}, journal = {Protein Science}, year = {2017}, volume = {26}, number = {2}, pages = {327--342}, doi = {https://doi.org/10.1002/pro.3085} }
Bauer, T.A., Horvat, N.K., Marques, O., Chocarro, S., Mertens, C., Colucci, S., Schmitt, S., Carrella, L.M., Morsbach, S., Koynov, K., Fenaroli, F., Blümler, P., Jung, M., Sotillo, R., Hentze, M.W., Muckenthaler, M.U. and Barz, M.	Core Cross-Linked Polymeric Micelles for Specific Iron Delivery: Inducing Sterile Inflammation in Macrophages [BibTeX]	2021	Advanced Healthcare Materials Vol. 10(19), pp. 2100385	article	DOI
BibTeX: @article{Bauer2021, author = {Tobias A. Bauer and Natalie K. Horvat and Oriana Marques and Sara Chocarro and Christina Mertens and Silvia Colucci and Sascha Schmitt and Luca M. Carrella and Svenja Morsbach and Kaloian Koynov and Federico Fenaroli and Peter Blümler and Michaela Jung and Rocio Sotillo and Matthias W. Hentze and Martina U. Muckenthaler and Matthias Barz}, title = {Core Cross-Linked Polymeric Micelles for Specific Iron Delivery: Inducing Sterile Inflammation in Macrophages}, journal = {Advanced Healthcare Materials}, publisher = {Wiley}, year = {2021}, volume = {10}, number = {19}, pages = {2100385}, doi = {https://doi.org/10.1002/adhm.202100385} }
Baumann, M., Heuveline, V., Mattes, O., Richling, S. and Siebler, S.	SDS@hd -- Scientific Data Storage [BibTeX]	2018	Proceedings of the bwHPC Symposium 2017, pp. 32-36	inproceedings	DOI
BibTeX: @inproceedings{Baumann2018, author = {Baumann, Martin and Heuveline, Vincent and Mattes, Oliver and Richling, Sabine and Siebler, Sven}, title = {SDS@hd -- Scientific Data Storage}, booktitle = {Proceedings of the bwHPC Symposium 2017}, publisher = {Universität Tübingen}, year = {2018}, pages = {32--36}, doi = {https://doi.org/10.15496/publikation-25204} }
Baumann, M., Mattes, O., Richling, S., Siebler, S. and Balz, A.	SDS@hd - Scientific Data Storage [BibTeX]	2019	E-Science-Tage 2019, pp. 1 S.	incollection	DOI
BibTeX: @incollection{Baumann2019, author = {Baumann, Martin and Mattes, Oliver and Richling, Sabine and Siebler, Sven and Balz, Alexander}, title = {SDS@hd - Scientific Data Storage}, booktitle = {E-Science-Tage 2019}, publisher = {heiDOK}, year = {2019}, pages = {1 S.}, doi = {https://doi.org/10.11588/heidok.00026851} }
Baumann, M., Mattes, O., Richling, S., Siebler, S. and Balz, A.	SDS@hd - Scientific Data Storage [BibTeX]	2020	E-Science-Tage 2019, pp. 4 S.	incollection	DOI
BibTeX: @incollection{Baumann2020, author = {Baumann, Martin and Mattes, Oliver and Richling, Sabine and Siebler, Sven and Balz, Alexander}, title = {SDS@hd - Scientific Data Storage}, booktitle = {E-Science-Tage 2019}, publisher = {heiBOOKS}, year = {2020}, pages = {4 S.}, note = {Gesehen am 01.04.2020}, doi = {https://doi.org/10.11588/HEIBOOKS.598.C8444} }
Baumann, M., Heß, F., Maylein, L., Mechler, T., Scherbaum, B. and Volkmann, E.	heiARCHIVE, a long-term preservation service at Heidelberg University [BibTeX]	2022		article	DOI
BibTeX: @article{Baumann2022, author = {Baumann, Martin and Heß, Florian and Maylein, Leonhard and Mechler, Tatjana and Scherbaum, Benjamin and Volkmann, Eric}, title = {heiARCHIVE, a long-term preservation service at Heidelberg University}, publisher = {heiBOOKS}, year = {2022}, doi = {https://doi.org/10.11588/HEIBOOKS.979.C13740} }
Beattie, J.R., Federrath, C., Klessen, R.S. and Schneider, N.	The relation between the turbulent Mach number and observed fractal dimensions of turbulent clouds [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 488(2), pp. 2493-2502	article	DOI
BibTeX: @article{Beattie2019, author = {James R Beattie and Christoph Federrath and Ralf S Klessen and Nicola Schneider}, title = {The relation between the turbulent Mach number and observed fractal dimensions of turbulent clouds}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {488}, number = {2}, pages = {2493--2502}, doi = {https://doi.org/10.1093/mnras/stz1853} }
Beattie, J.R., Federrath, C. and Klessen, R.S.	The relation between the true and observed fractal dimensions of turbulent clouds [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 487(2), pp. 2070-2081	article	DOI
BibTeX: @article{Beattie2019a, author = {James R Beattie and Christoph Federrath and Ralf S Klessen}, title = {The relation between the true and observed fractal dimensions of turbulent clouds}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {487}, number = {2}, pages = {2070--2081}, doi = {https://doi.org/10.1093/mnras/stz1416} }
Becker, M.M.M., Lapouge, K., Segnitz, B., Wild, K. and Sinning, I.	Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction [Abstract] [BibTeX]	2017	Nucleic acids research Vol. 45(1), pp. 470-481	article	DOI URL
Abstract: Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The two largest proteins SRP68 and SRP72 form a heterodimer and bind to a regulatory site of the SRP RNA. Despite their essential roles in the SRP pathway, structural information has been available only for the SRP68 RNA-binding domain (RBD). Here we present the crystal structures of the SRP68 protein-binding domain (PBD) in complex with SRP72-PBD and of the SRP72-RBD bound to the SRP S domain (SRP RNA, SRP19 and SRP68) detailing all interactions of SRP72 within SRP. The SRP72-PBD is a tetratricopeptide repeat, which binds an extended linear motif of SRP68 with high affinity. The SRP72-RBD is a flexible peptide crawling along the 5e- and 5f-loops of SRP RNA. A conserved tryptophan inserts into the 5e-loop forming a novel type of RNA kink-turn stabilized by a potassium ion, which we define as K(+)-turn. In addition, SRP72-RBD remodels the 5f-loop involved in ribosome binding and visualizes SRP RNA plasticity. Docking of the S domain structure into cryo-electron microscopy density maps reveals multiple contact sites between SRP68/72 and the ribosome, and explains the role of SRP72 in the SRP pathway.
BibTeX: @article{Becker2017, author = {Becker, Matthias M. M. and Lapouge, Karine and Segnitz, Bernd and Wild, Klemens and Sinning, Irmgard}, title = {Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction}, journal = {Nucleic acids research}, publisher = {Oxford University Press}, year = {2017}, volume = {45}, number = {1}, pages = {470--481}, note = {27899666[pmid]}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27899666}, doi = {https://doi.org/10.1093/nar/gkw1124} }
Becker, A.	Influence of photobiomodulation with blue light on the metabolism, proliferation and gene expression of human keratinocytes [BibTeX]	2017		book
BibTeX: @book{Becker2017a, author = {Becker, Anja}, title = {Influence of photobiomodulation with blue light on the metabolism, proliferation and gene expression of human keratinocytes}, year = {2017} }
Ben Dkhil, S., Pfannmöller, M., Schröder, R.R., Alkarsifi, R., Gaceur, M., Köntges, W., Heidari, H., Bals, S., Margeat, O., Ackermann, J. and Videlot-Ackermann, C.	Interplay of Interfacial Layers and Blend Composition To Reduce Thermal Degradation of Polymer Solar Cells at High Temperature [BibTeX]	2018	ACS Applied Materials & Interfaces Vol. 10(4), pp. 3874-3884	article	DOI
BibTeX: @article{BenDkhil2018, author = {Ben Dkhil, Sadok and Pfannmöller, Martin and Schröder, Rasmus R. and Alkarsifi, Riva and Gaceur, Meriem and Köntges, Wolfgang and Heidari, Hamed and Bals, Sara and Margeat, Olivier and Ackermann, Jörg and Videlot-Ackermann, Christine}, title = {Interplay of Interfacial Layers and Blend Composition To Reduce Thermal Degradation of Polymer Solar Cells at High Temperature}, journal = {ACS Applied Materials & Interfaces}, publisher = {American Chemical Society}, year = {2018}, volume = {10}, number = {4}, pages = {3874--3884}, doi = {https://doi.org/10.1021/acsami.7b17021} }
Berthet, B., Bald, L., Louveaux, M. and Maizel, A.	Progressive maturation of the root apical meristem in Arabidopsis thaliana lateral roots [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: AbstractMeristems are stem cells niches that support the formation of all plant organs and are either set during embryogenesis and maintained throughout the plant life or specified de novo, post-embryonically. The embryo-derived root apical meristem is organized around a group of infrequently dividing cells, the quiescent centre, that maintains the stem cells, organizes growth along two axes and owing to its resistance to 3ic stress can replace damaged stem cells. In most cases, lateral roots post-embryonically branch off the primary and establish a new root meristem which organization is identical to the primary root one. The cellular and molecular processes underpinning the emergence of new stem cell niches are not well known. Here, we characterize the de novo establishment of the root apical meristem in lateral roots. While the position of the new stem cell niche is set early during morphogenesis, its cellular layout, unique gene expression profile and mitotic quiescence are only acquired after emergence concomitant to the establishment of two diverging growth axis. Our results show that the intertwined attributes of the mature root stem cell niche are progressively acquired during lateral root formation, and support a model in which the position of the stem cell niche emerges from the establishment of diverging growth axis.HighlightAnalyze of the ontogeny of the quiescent center during lateral root ontogeny reveal its late formation and supports that its emergence results from the establishment of two diverging growth axis.
BibTeX: @article{Berthet2022, author = {Béatrice Berthet, Lotte Bald, Marion Louveaux, Alexis Maizel}, title = {Progressive maturation of the root apical meristem in Arabidopsis thaliana lateral roots}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.02.18.481036} }
	Writing Matters [BibTeX]	2017		book	DOI
BibTeX: @book{Berti2017,, title = {Writing Matters}, publisher = {De Gruyter}, year = {2017}, doi = {https://doi.org/10.1515/9783110534597} }
Betge, J., Rindtorff, N., Sauer, J., Rauscher, B., Dingert, C., Gaitantzi, H., Herweck, F., Srour-Mhanna, K., Miersch, T., Valentini, E., Boonekamp, K.E., Hauber, V., Gutting, T., Frank, L., Belle, S., Gaiser, T., Buchholz, I., Jesenofsky, R., Härtel, N., Zhan, T., Fischer, B., Breitkopf-Heinlein, K., Burgermeister, E., Ebert, M.P. and Boutros, M.	The drug-induced phenotypic landscape of colorectal cancer organoids [Abstract] [BibTeX]	2022	Nature Communications Vol. 13(1)	article	DOI URL
Abstract: AbstractPatient-derived organoids resemble the biology of tissues and tumors, enabling ex vivo modeling of human diseases. They have heterogeneous morphologies with unclear biological causes and relationship to treatment response. Here, we use high-throughput, image-based profiling to quantify phenotypes of over 5 million individual colorectal cancer organoids after treatment with >500 small molecules. Integration of data using multi-omics modeling identifies axes of morphological variation across organoids: Organoid size is linked to IGF1 receptor signaling, and cystic vs. solid organoid architecture is associated with LGR5 + stemness. Treatment-induced organoid morphology reflects organoid viability, drug mechanism of action, and is biologically interpretable. Inhibition of MEK leads to cystic reorganization of organoids and increases expression ofLGR5, while inhibition of mTOR induces IGF1 receptor signaling. In conclusion, we identify shared axes of variation for colorectal cancer organoid morphology, their underlying biological mechanisms, and pharmacological interventions with the ability to move organoids along them.
BibTeX: @article{Betge2022, author = {Johannes Betge, Niklas Rindtorff, Jan Sauer, Benedikt Rauscher, Clara Dingert, Haristi Gaitantzi, Frank Herweck, Kauthar Srour-Mhanna, Thilo Miersch, Erica Valentini, Kim E. Boonekamp, Veronika Hauber, Tobias Gutting, Larissa Frank, Sebastian Belle, Timo Gaiser, Inga Buchholz, Ralf Jesenofsky, Nicolai Härtel, Tianzuo Zhan, Bernd Fischer, Katja Breitkopf-Heinlein, Elke Burgermeister, Matthias P. Ebert, Michael Boutros}, title = {The drug-induced phenotypic landscape of colorectal cancer organoids}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {13}, number = {1}, url = {https://www.nature.com/articles/s41467-022-30722-9.pdf}, doi = {https://doi.org/10.1038/s41467-022-30722-9} }
Betzler, A.M., Nanduri, L.K., Hissa, B., Blickensdörfer, L., Muders, M.H., Roy, J., Jesinghaus, M., Steiger, K., Weichert, W., Kloor, M., Klink, B., Schroeder, M., Mazzone, M., Weitz, J., Reissfelder, C., Rahbari, N.N. and Schölch, S.	Differential Effects of Trp53 Alterations in Murine Colorectal Cancer [BibTeX]	2021	Cancers Vol. 13(4), pp. 808	article	DOI
BibTeX: @article{Betzler2021, author = {Alexander M. Betzler and Lahiri K. Nanduri and Barbara Hissa and Linda Blickensdörfer and Michael H. Muders and Janine Roy and Moritz Jesinghaus and Katja Steiger and Wilko Weichert and Matthias Kloor and Barbara Klink and Michael Schroeder and Massimiliano Mazzone and Jürgen Weitz and Christoph Reissfelder and Nuh N. Rahbari and Sebastian Schölch}, title = {Differential Effects of Trp53 Alterations in Murine Colorectal Cancer}, journal = {Cancers}, publisher = {MDPI AG}, year = {2021}, volume = {13}, number = {4}, pages = {808}, doi = {https://doi.org/10.3390/cancers13040808} }
Beuther, H., Walsh, A., Wang, Y., Rugel, M., Soler, J., Linz, H., Klessen, R.S., Anderson, L.D., Urquhart, J.S., Glover, S.C.O., Billington, S.J., Kainulainen, J., Menten, K.M., Roy, N., Longmore, S.N. and Bigiel, F.	OH maser emission in the THOR survey of the northern Milky Way [BibTeX]	2019	Astronomy & Astrophysics Vol. 628, pp. A90	article	DOI
BibTeX: @article{Beuther2019, author = {H. Beuther and A. Walsh and Y. Wang and M. Rugel and J. Soler and H. Linz and R. S. Klessen and L. D. Anderson and J. S. Urquhart and S. C. O. Glover and S. J. Billington and J. Kainulainen and K. M. Menten and N. Roy and S. N. Longmore and F. Bigiel}, title = {OH maser emission in the THOR survey of the northern Milky Way}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2019}, volume = {628}, pages = {A90}, doi = {https://doi.org/10.1051/0004-6361/201935936} }
Bhambri, R., Schmidt, S., Chand, P., Nüsser, M., Haritashya, U., Sain, K., Tiwari, S.K. and Yadav, J.S.	Heterogeneity in glacier thinning and slowdown of ice movement in the Garhwal Himalaya, India [BibTeX]	2023	Science of The Total Environment Vol. 875, pp. 162625	article	DOI
BibTeX: @article{Bhambri2023, author = {Rakesh Bhambri and Susanne Schmidt and Pritam Chand and Marcus Nüsser and Umesh Haritashya and Kalachand Sain and Sameer K. Tiwari and Jairam Singh Yadav}, title = {Heterogeneity in glacier thinning and slowdown of ice movement in the Garhwal Himalaya, India}, journal = {Science of The Total Environment}, publisher = {Elsevier BV}, year = {2023}, volume = {875}, pages = {162625}, doi = {https://doi.org/10.1016/j.scitotenv.2023.162625} }
Blandino, A., Scherer, D., Rounge, T.B., Umu, S.U., Boekstegers, F., Ponce, C.B., Marcelain, K., Gárate-Calderón, V., Waldenberger, M., Morales, E., Rojas, A., Munoz, C., Retamales, J., de Toro, G., Barajas, O., Rivera, M.T., Cortés, A., Loader, D., Saavedra, J., Gutiérrez, L., Ortega, A., Bertrán, M.E., Gabler, F., Campos, M., Alvarado, J., Moisán, F., Spencer, L., Nervi, B., Carvajal-Hausdorf, D.E., Losada, H., Almau, M., Fernández, P., Gallegos, I., Olloquequi, J., Fuentes-Guajardo, M., Gonzalez-Jose, R., Bortolini, M.C., Gallo, C., Linares, A.R., Rothhammer, F. and Bermejo, J.L.	Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression [Abstract] [BibTeX]	2022	Cancers Vol. 14(3), pp. 634	article	DOI URL
Abstract: Long noncoding RNAs (lncRNAs) play key roles in cell processes and are good candidates for cancer risk prediction. Few studies have investigated the association between individual genotypes and lncRNA expression. Here we integrate three separate datasets with information on lncRNA expression only, both lncRNA expression and genotype, and genotype information only to identify circulating lncRNAs associated with the risk of gallbladder cancer (GBC) using robust linear and logistic regression techniques. In the first dataset, we preselect lncRNAs based on expression changes along the sequence “gallstones → dysplasia → GBC”. In the second dataset, we validate associations between genetic variants and serum expression levels of the preselected lncRNAs (cis-lncRNA-eQTLs) and build lncRNA expression prediction models. In the third dataset, we predict serum lncRNA expression based on individual genotypes and assess the association between genotype-based expression and GBC risk. AC084082.3 and LINC00662 showed increasing expression levels (p-value = 0.009), while C22orf34 expression decreased in the sequence from gallstones to GBC (p-value = 0.04). We identified and validated two cis-LINC00662-eQTLs (r2 = 0.26) and three cis-C22orf34-eQTLs (r2 = 0.24). Only LINC00662 showed a genotyped-based serum expression associated with GBC risk (OR = 1.25 per log2 expression unit, 95% CI 1.04–1.52, p-value = 0.02). Our results suggest that preselection of lncRNAs based on tissue samples and exploitation of cis-lncRNA-eQTLs may facilitate the identification of circulating noncoding RNAs linked to cancer risk.
BibTeX: @article{Blandino2022, author = {Alice Blandino, Dominique Scherer, Trine B. Rounge, Sinan U. Umu, Felix Boekstegers, Carol Barahona Ponce, Katherine Marcelain, Valentina Gárate-Calderón, Melanie Waldenberger, Erik Morales, Armando Rojas, César Munoz, Javier Retamales, Gonzalo de Toro, Olga Barajas, María Teresa Rivera, Analía Cortés, Denisse Loader, Javiera Saavedra, Lorena Gutiérrez, Alejandro Ortega, Maria Enriqueta Bertrán, Fernando Gabler, Mónica Campos, Juan Alvarado, Fabrizio Moisán, Loreto Spencer, Bruno Nervi, Daniel E. Carvajal-Hausdorf, Héctor Losada, Mauricio Almau, Plinio Fernández, Ivan Gallegos, Jordi Olloquequi, Macarena Fuentes-Guajardo, Rolando Gonzalez-Jose, Maria Cátira Bortolini, Carla Gallo, Andres Ruiz Linares, Francisco Rothhammer, Justo Lorenzo Bermejo}, title = {Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression}, journal = {Cancers}, publisher = {MDPI AG}, year = {2022}, volume = {14}, number = {3}, pages = {634}, url = {https://www.mdpi.com/2072-6694/14/3/634/pdf}, doi = {https://doi.org/10.3390/cancers14030634} }
Bodmer, B.S., Breithaupt, A., Heung, M., Brunetti, J.E., Henkel, C., Müller-Guhl, J., Rodr\iguez, E., Wendt, L., Winter, S.L., Vallbracht, M., Müller, A., Römer, S., Chlanda, P., Muñoz-Fontela, C., Hoenen, T. and Escudero-Pérez, B.	lessigreaterIn vivoless/igreater characterization of the novel ebolavirus Bombali virus suggests a low pathogenic potential for humans [BibTeX]	2023	Emerging Microbes &ampmathsemicolon Infections Vol. 12(1)	article	DOI
BibTeX: @article{Bodmer2023, author = {B. S. Bodmer and A. Breithaupt and M. Heung and J. E. Brunetti and C. Henkel and J. Müller-Guhl and E. Rodr\iguez and L. Wendt and S. L. Winter and M. Vallbracht and A. Müller and S. Römer and P. Chlanda and C. Muñoz-Fontela and T. Hoenen and B. Escudero-Pérez}, title = {lessigreaterIn vivoless/igreater characterization of the novel ebolavirus Bombali virus suggests a low pathogenic potential for humans}, journal = {Emerging Microbes &ampmathsemicolon Infections}, publisher = {Informa UK Limited}, year = {2023}, volume = {12}, number = {1}, doi = {https://doi.org/10.1080/22221751.2022.2164216} }
Böhler, A., Vermeulen, B.J., Würtz, M., Zupa, E., Pfeffer, S. and Schiebel, E.	The gamma‐tubulin ring complex: Deciphering the molecular organization and assembly mechanism of a major vertebrate microtubule nucleator [BibTeX]	2021	BioEssays Vol. 43(8), pp. 2100114	article	DOI
BibTeX: @article{Boehler2021, author = {Anna Böhler, Bram J.A. Vermeulen, Martin Würtz, Erik Zupa, Stefan Pfeffer, Elmar Schiebel}, title = {The gamma‐tubulin ring complex: Deciphering the molecular organization and assembly mechanism of a major vertebrate microtubule nucleator}, journal = {BioEssays}, publisher = {Wiley}, year = {2021}, volume = {43}, number = {8}, pages = {2100114}, doi = {https://doi.org/10.1002/bies.202100114} }
Boekholt, T.C.N., Schleicher, D.R.G., Fellhauer, M., Klessen, R.S., Reinoso, B., Stutz, A.M. and Haemmerlé, L.	Formation of massive seed black holes via collisions and accretion [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 476(1), pp. 366-380	article	DOI
BibTeX: @article{Boekholt2018, author = {Boekholt, T. C. N. and Schleicher, D. R. G. and Fellhauer, M. and Klessen, R. S. and Reinoso, B. and Stutz, A. M. and Haemmerlé, L.}, title = {Formation of massive seed black holes via collisions and accretion}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {476}, number = {1}, pages = {366--380}, doi = {https://doi.org/10.1093/mnras/sty208} }
Boekstegers, F., Scherer, D., Ponce, C.B., Marcelain, K., Gárate-Calderón, V., Waldenberger, M., Morales, E., Rojas, A., Munoz, C., Retamales, J., de Toro, G., Barajas, O., Rivera, M.T., Cortés, A., Loader, D., Saavedra, J., Gutiérrez, L., Ortega, A., Bertrán, M.E., Bartolotti, L., Gabler, F., Campos, M., Alvarado, J., Moisán, F., Spencer, L., Nervi, B., Carvajal-Hausdorf, D., Losada, H., Almau, M., Fernández, P., Olloquequi, J., Fuentes-Guajardo, M., Gonzalez-Jose, R., Bortolini, M.C., Acuña-Alonzo, V., Gallo, C., Linares, A.R., Rothhammer, F. and Bermejo, J.L.	Development and internal validation of a multifactorial risk prediction model for gallbladder cancer in a high-incidence country [BibTeX]	2023	International Journal of Cancer Vol. 153(6), pp. 1151-1161	article	DOI
BibTeX: @article{Boekstegers2023, author = {Felix Boekstegers and Dominique Scherer and Carol Barahona Ponce and Katherine Marcelain and Valentina Gárate-Calderón and Melanie Waldenberger and Erik Morales and Armando Rojas and César Munoz and Javier Retamales and Gonzalo de Toro and Olga Barajas and Mar\ia Teresa Rivera and Anal\ia Cortés and Denisse Loader and Javiera Saavedra and Lorena Gutiérrez and Alejandro Ortega and Maria Enriqueta Bertrán and Leonardo Bartolotti and Fernando Gabler and Mónica Campos and Juan Alvarado and Fabricio Moisán and Loreto Spencer and Bruno Nervi and Daniel Carvajal-Hausdorf and Héctor Losada and Mauricio Almau and Plinio Fernández and Jordi Olloquequi and Macarena Fuentes-Guajardo and Rolando Gonzalez-Jose and Maria Cátira Bortolini and Victor Acuña-Alonzo and Carla Gallo and Andres Ruiz Linares and Francisco Rothhammer and Justo Lorenzo Bermejo}, title = {Development and internal validation of a multifactorial risk prediction model for gallbladder cancer in a high-incidence country}, journal = {International Journal of Cancer}, publisher = {Wiley}, year = {2023}, volume = {153}, number = {6}, pages = {1151--1161}, doi = {https://doi.org/10.1002/ijc.34607} }
Bolle, K.	Materialität und Präsenz spätantiker Inschriften [BibTeX]	2019		book	DOI
BibTeX: @book{Bolle2019, author = {Katharina Bolle}, title = {Materialität und Präsenz spätantiker Inschriften}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110633566} }
	Inschriftenkulturen im kommunalen Italien [BibTeX]	2019		book	DOI
BibTeX: @book{Bolle2019a,, title = {Inschriftenkulturen im kommunalen Italien}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110642261} }
Bonea, A.	"Contagion by Telephone": Print Media and Knowledge about Infectious Diseases in Britain, 1880s–1914 [BibTeX]	2021	Technology and Culture Vol. 62(4), pp. 1063-1086	article	DOI
BibTeX: @article{Bonea2021, author = {Amelia Bonea}, title = {"Contagion by Telephone": Print Media and Knowledge about Infectious Diseases in Britain, 1880s–1914}, journal = {Technology and Culture}, publisher = {Project Muse}, year = {2021}, volume = {62}, number = {4}, pages = {1063--1086}, doi = {https://doi.org/10.1353/tech.2021.0154} }
Bonifacio, P., Caffau, E., Spite, M., Spite, F., Sbordone, L., Monaco, L., François, P., Plez, B., Molaro, P., Gallagher, A.J., Cayrel, R., Christlieb, N., Klessen, R.S., Koch, A., Ludwig, H.-G., Steffen, M., Zaggia, S. and Abate, C.	TOPoS. IV. Chemical abundances from high-resolution observations of seven extremely metal-poor stars [BibTeX]	2018	Astronomy & Astrophysics Vol. 612, pp. A65	article	DOI
BibTeX: @article{Bonifacio2018, author = {Bonifacio, P. and Caffau, E. and Spite, M. and Spite, F. and Sbordone, L. and Monaco, L. and François, P. and Plez, B. and Molaro, P. and Gallagher, A. J. and Cayrel, R. and Christlieb, N. and Klessen, R. S. and Koch, A. and Ludwig, H.-G. and Steffen, M. and Zaggia, S. and Abate, C.}, title = {TOPoS. IV. Chemical abundances from high-resolution observations of seven extremely metal-poor stars}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {612}, pages = {A65}, doi = {https://doi.org/10.1051/0004-6361/201732320} }
Bragado Alonso, S., Reinert, J.K., Marichal, N., Massalini, S., Berninger, B., Kuner, T. and Calegari, F.	An increase in neural stem cells and olfactory bulb adult neurogenesis improves discrimination of highly similar odorants [Abstract] [BibTeX]	2019	The EMBO Journal Vol. 38(6), pp. e98791	article	DOI
Abstract: Abstract Adult neurogenesis is involved in cognitive performance but studies that manipulated this process to improve brain function are scarce. Here, we characterized a genetic mouse model in which neural stem cells (NSC) of the subventricular zone (SVZ) were temporarily expanded by conditional expression of the cell cycle regulators Cdk4/cyclinD1, thus increasing neurogenesis. We found that supernumerary neurons matured and integrated in the olfactory bulb similarly to physiologically generated newborn neurons displaying a correct expression of molecular markers, morphology and electrophysiological activity. Olfactory performance upon increased neurogenesis was unchanged when mice were tested on relatively easy tasks using distinct odor stimuli. In contrast, intriguingly, increasing neurogenesis improved the discrimination ability of mice when challenged with a difficult task using mixtures of highly similar odorants. Together, our study provides a mammalian model to control the expansion of somatic stem cells that can in principle be applied to any tissue for basic research and models of therapy. By applying this to NSC of the SVZ, we highlighted the importance of adult neurogenesis to specifically improve performance in a challenging olfactory task.
BibTeX: @article{BragadoAlonso2019, author = {Bragado Alonso, Sara and Reinert, Janine K. and Marichal, Nicolas and Massalini, Simone and Berninger, Benedikt and Kuner, Thomas and Calegari, Federico}, title = {An increase in neural stem cells and olfactory bulb adult neurogenesis improves discrimination of highly similar odorants}, journal = {The EMBO Journal}, year = {2019}, volume = {38}, number = {6}, pages = {e98791}, doi = {https://doi.org/10.15252/embj.201798791} }
Brenna, C., ul Maula Khan, A., Picascia, T., Sun, Q., Heuveline, V. and Gretz, N.	New technical approaches for 3D morphological imaging and quantification of measurements [BibTeX]	2020	The Anatomical Record Vol. 303(10), pp. 2702-2715	article	DOI
BibTeX: @article{Brenna2020, author = {Cinzia Brenna and Arif ul Maula Khan and Tiziana Picascia and Quanchao Sun and Vincent Heuveline and Norbert Gretz}, title = {New technical approaches for 3D morphological imaging and quantification of measurements}, journal = {The Anatomical Record}, publisher = {Wiley}, year = {2020}, volume = {303}, number = {10}, pages = {2702--2715}, doi = {https://doi.org/10.1002/ar.24463} }
Brinster, R., Scherer, D. and Bermejo, J.L.	Optimal selection of genetic variants for adjustment of population stratification in European association studies [BibTeX]	2019	Briefings in Bioinformatics Vol. 21(3), pp. 753-761	article	DOI
BibTeX: @article{Brinster2019, author = {Regina Brinster and Dominique Scherer and Justo Lorenzo Bermejo}, title = {Optimal selection of genetic variants for adjustment of population stratification in European association studies}, journal = {Briefings in Bioinformatics}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {21}, number = {3}, pages = {753--761}, doi = {https://doi.org/10.1093/bib/bbz023} }
Brombierstäudl, D., Schmidt, S. and Nüsser, M.	Distribution and relevance of aufeis (icing) in the Upper Indus Basin [BibTeX]	2021	Science of The Total Environment Vol. 780, pp. 146604	article	DOI
BibTeX: @article{Brombierstaeudl2021, author = {Dagmar Brombierstäudl and Susanne Schmidt and Marcus Nüsser}, title = {Distribution and relevance of aufeis (icing) in the Upper Indus Basin}, journal = {Science of The Total Environment}, publisher = {Elsevier BV}, year = {2021}, volume = {780}, pages = {146604}, doi = {https://doi.org/10.1016/j.scitotenv.2021.146604} }
Brombierstäudl, D., Schmidt, S. and Nüsser, M.	Spatial and temporal dynamics of aufeis in the Tso Moriri basin, eastern Ladakh, India [BibTeX]	2022	Permafrost and Periglacial Processes Vol. 34(1), pp. 81-93	article	DOI
BibTeX: @article{Brombierstaeudl2022, author = {Dagmar Brombierstäudl, Susanne Schmidt, Marcus Nüsser}, title = {Spatial and temporal dynamics of aufeis in the Tso Moriri basin, eastern Ladakh, India}, journal = {Permafrost and Periglacial Processes}, publisher = {Wiley}, year = {2022}, volume = {34}, number = {1}, pages = {81--93}, doi = {https://doi.org/10.1002/ppp.2173} }
Brosius, C. and Michaels, A.	Vernacular Heritage as Urban Place-Making. Activities and Positions in the Reconstruction of Monuments after the Gorkha Earthquake in Nepal, 2015–2020: The Case of Patan [BibTeX]	2020	Sustainability Vol. 12(20), pp. 8720	article	DOI
BibTeX: @article{Brosius2020, author = {Christiane Brosius and Axel Michaels}, title = {Vernacular Heritage as Urban Place-Making. Activities and Positions in the Reconstruction of Monuments after the Gorkha Earthquake in Nepal, 2015–2020: The Case of Patan}, journal = {Sustainability}, publisher = {MDPI AG}, year = {2020}, volume = {12}, number = {20}, pages = {8720}, doi = {https://doi.org/10.3390/su12208720} }
Brown, M., Miglus, P., Rasheed, K. and Ahmad, M.	PORTRAITS OF A PARTHIAN KING: ROCK-RELIEFS AND THE MOUNTAIN FORTRESSES OF RABANA-MERQULY IN IRAQI KURDISTAN [BibTeX]	2018	Iraq Vol. 80, pp. 1-15	article	DOI
BibTeX: @article{Brown2018, author = {Brown, Michael and Miglus, Peter and Rasheed, Kamal and Ahmad, Mustafa}, title = {PORTRAITS OF A PARTHIAN KING: ROCK-RELIEFS AND THE MOUNTAIN FORTRESSES OF RABANA-MERQULY IN IRAQI KURDISTAN}, journal = {Iraq}, year = {2018}, volume = {80}, pages = {1--15}, doi = {https://doi.org/10.1017/irq.2018.5} }
Brown, M., Raheem, K.R. and Abdullah, H.H.	Rabana-Merquly: a fortress in the kingdom of Adiabene in the Zagros Mountains [Abstract] [BibTeX]	2022	Antiquity Vol. 96(388), pp. 920-936	article	DOI URL
Abstract: The mountain fortress of Rabana-Merquly was a major regional centre of the Parthian period (first century BC) in the Zagros Mountains of Iraqi Kurdistan. The iconography of two rock-reliefs that show an unnamed ruler suggests an association with the vassal kingdom of Adiabene. The exceptional preservation of the fortress's stone walls, undamaged by later agriculture in this highland location, provides an almost complete example of a large, fortified site with two main intramural settlements. Through its ability to control the surrounding landscape, Rabana-Merquly highlights the role of client states on the peripheries of the Parthian and Roman Empires and illuminates the practicalities of territorial control by state authorities in hinterland regions.
BibTeX: @article{Brown2022, author = {Michael Brown, Kamal Rasheed Raheem, Hashim Hama Abdullah}, title = {Rabana-Merquly: a fortress in the kingdom of Adiabene in the Zagros Mountains}, journal = {Antiquity}, publisher = {Antiquity Publications}, year = {2022}, volume = {96}, number = {388}, pages = {920--936}, url = {https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0003598X22000746}, doi = {https://doi.org/10.15184/aqy.2022.74} }
Bubenzer, O., Jäger, S., Ludwig, R., Mächtle, B., Schöneweis, T., von der Osten-Woldenburg, H. and Wieland, G.	Neue geoarchäologische Forschungen auf dem Heiligenberg: Sondage einer Podiengruppe am Osthang des Berges. [BibTeX]	2022	Arch. Ausgr. Baden-Württemberg 2021, pp. 140-145	incollection
BibTeX: @incollection{Bubenzer2022, author = {Olaf Bubenzer, Sven Jäger, Renate Ludwig, Bertil Mächtle, Tobias Schöneweis, Harald von der Osten-Woldenburg, Günther Wieland}, title = {Neue geoarchäologische Forschungen auf dem Heiligenberg: Sondage einer Podiengruppe am Osthang des Berges.}, booktitle = {Arch. Ausgr. Baden-Württemberg 2021}, publisher = {wbg Theiss}, year = {2022}, pages = {140--145} }
Buchmuller, B.C., Herbst, K., Meurer, M., Kirrmaier, D., Sass, E., Levy, E.D. and Knop, M.	Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast [Abstract] [BibTeX]	2019	Nature Communications Vol. 10(1), pp. 2960	article	DOI
Abstract: Clone collections of modified strains (``libraries'') are a major resource for systematic studies with the yeast Saccharomyces cerevisiae. Construction of such libraries is time-consuming, costly and confined to the genetic background of a specific yeast strain. To overcome these limitations, we present CRISPR-Cas12a (Cpf1)-assisted tag library engineering (CASTLING) for multiplexed strain construction. CASTLING uses microarray-synthesized oligonucleotide pools and in vitro recombineering to program the genomic insertion of long DNA constructs via homologous recombination. One simple transformation yields pooled libraries with >90% of correctly tagged clones. Up to several hundred genes can be tagged in a single step and, on a genomic scale, approximately half of all genes are tagged with only 10-fold oversampling. We report several parameters that affect tagging success and provide a quantitative targeted next-generation sequencing method to analyze such pooled collections. Thus, CASTLING unlocks avenues for increasing throughput in functional genomics and cell biology research.
BibTeX: @article{Buchmuller2019, author = {Buchmuller, Benjamin C. and Herbst, Konrad and Meurer, Matthias and Kirrmaier, Daniel and Sass, Ehud and Levy, Emmanuel D. and Knop, Michael}, title = {Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast}, journal = {Nature Communications}, year = {2019}, volume = {10}, number = {1}, pages = {2960}, doi = {https://doi.org/10.1038/s41467-019-10816-7} }
Bürger, U.	Cultural Encounters and Local Traditions. [BibTeX]	2020	Zagros Studies, pp. 67-92	incollection	DOI
BibTeX: @incollection{Buerger2020, author = {Ulrike Bürger}, title = {Cultural Encounters and Local Traditions.}, booktitle = {Zagros Studies}, publisher = {Peeters Publishers}, year = {2020}, pages = {67--92}, doi = {https://doi.org/10.2307/j.ctv1q26j2t.8} }
Bürger, U.	Tell Mohammed und seine Gräber – Eine Näherung [BibTeX]	2021	Altorientalische Variationen zum 90. Geburtstag von Eva Strommenger, Heidelberger Studien zum Alten Orient 17, pp. 21-38	incollection
BibTeX: @incollection{Buerger2021, author = {Ulrike Bürger}, title = {Tell Mohammed und seine Gräber – Eine Näherung}, booktitle = {Altorientalische Variationen zum 90. Geburtstag von Eva Strommenger, Heidelberger Studien zum Alten Orient 17}, year = {2021}, pages = {21--38} }
Bunse, L., Pusch, S., Bunse, T., Sahm, F., Sanghvi, K., Friedrich, M., Alansary, D., Sonner, J.K., Green, E., Deumelandt, K., Kilian, M., Neftel, C., Uhlig, S., Kessler, T., von Landenberg, A., Berghoff, A.S., Marsh, K., Steadman, M., Zhu, D., Nicolay, B., Wiestler, B., Breckwoldt, M.O., Al-Ali, R., Karcher-Bausch, S., Bozza, M., Oezen, I., Kramer, M., Meyer, J., Habel, A., Eisel, J., Poschet, G., Weller, M., Preusser, M., Nadji-Ohl, M., Thon, N., Burger, M.C., Harter, P.N., Ratliff, M., Harbottle, R., Benner, A., Schrimpf, D., Okun, J., Herold-Mende, C., Turcan, S., Kaulfuss, S., Hess‐Stumpp, H., Bieback, K., Cahill, D.P., Plate, K.H., Hänggi, D., Dorsch, M., Suvà, M.L., Niemeyer, B.A., von Deimling, A., Wick, W. and Platten, M.	Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate [Abstract] [BibTeX]	2018	Nature Medicine Vol. 24(8), pp. 1192-1203	article	DOI
Abstract: The oncometabolite (R)-2-hydroxyglutarate (R-2-HG) produced by isocitrate dehydrogenase (IDH) mutations promotes gliomagenesis via DNA and histone methylation. Here, we identify an additional activity of R-2-HG: tumor cell--derived R-2-HG is taken up by T cells where it induces a perturbation of nuclear factor of activated T cells transcriptional activity and polyamine biosynthesis, resulting in suppression of T cell activity. IDH1-mutant gliomas display reduced T cell abundance and altered calcium signaling. Antitumor immunity to experimental syngeneic IDH1-mutant tumors induced by IDH1-specific vaccine or checkpoint inhibition is improved by inhibition of the neomorphic enzymatic function of mutant IDH1. These data attribute a novel, non-tumor cell-autonomous role to an oncometabolite in shaping the tumor immune microenvironment.
BibTeX: @article{Bunse2018, author = {Bunse, Lukas and Pusch, Stefan and Bunse, Theresa and Sahm, Felix and Sanghvi, Khwab and Friedrich, Mirco and Alansary, Dalia and Sonner, Jana K. and Green, Edward and Deumelandt, Katrin and Kilian, Michael and Neftel, Cyril and Uhlig, Stefanie and Kessler, Tobias and von Landenberg, Anna and Berghoff, Anna S. and Marsh, Kelly and Steadman, Mya and Zhu, Dongwei and Nicolay, Brandon and Wiestler, Benedikt and Breckwoldt, Michael O. and Al-Ali, Ruslan and Karcher-Bausch, Simone and Bozza, Matthias and Oezen, Iris and Kramer, Magdalena and Meyer, Jochen and Habel, Antje and Eisel, Jessica and Poschet, Gernot and Weller, Michael and Preusser, Matthias and Nadji-Ohl, Minou and Thon, Niklas and Burger, Michael C. and Harter, Patrick N. and Ratliff, Miriam and Harbottle, Richard and Benner, Axel and Schrimpf, Daniel and Okun, Jürgen and Herold-Mende, Christel and Turcan, Sevin and Kaulfuss, Stefan and Hess‐Stumpp, Holger and Bieback, Karen and Cahill, Daniel P. and Plate, Karl H. and Hänggi, Daniel and Dorsch, Marion and Suvà, Mario L. and Niemeyer, Barbara A. and von Deimling, Andreas and Wick, Wolfgang and Platten, Michael}, title = {Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate}, journal = {Nature Medicine}, year = {2018}, volume = {24}, number = {8}, pages = {1192--1203}, doi = {https://doi.org/10.1038/s41591-018-0095-6} }
Burgermeister, E., Battaglin, F., Eladly, F., Wu, W., Herweck, F., Schulte, N., Betge, J., Härtel, N., Kather, J.N., Weis, C.-A., Gaiser, T., Marx, A., Weiss, C., Hofheinz, R., Miller, I.S., Loupakis, F., Lenz, H.-J., Byrne, A.T. and Ebert, M.P.	Aryl hydrocarbon receptor nuclear translocator-like (ARNTL/BMAL1) is associated with bevacizumab resistance in colorectal cancer via regulation of vascular endothelial growth factor A [Abstract] [BibTeX]	2019	EBioMedicine Vol. 45, pp. 139-154	article	DOI URL
Abstract: Background The identification of new biomarkers and the development of novel, targetable contexts of vulnerability are of urgent clinical need in drug-resistant metastatic colorectal cancer (mCRC). Aryl-Hydrocarbon-Receptor-Nuclear-Translocator-Like (ARNTL/BMAL1) is a circadian clock-regulated transcription factor promoting expression of genes involved in angiogenesis and tumour progression. We hypothesised that BMAL1 increases expression of the vascular endothelial growth factor A VEGFA gene and, thereby, confers resistance to anti-angiogenic therapy with bevacizumab (Beva), a clinically used antibody for neutralization of VEGFA. Methods PCR and immunohistochemistry were employed to assess BMAL1 expression in mice (C57BL/6 J Apcmin/+; BALB/c nu/nu xenografts) and CRC patients under combination chemotherapy with Beva. BMAL1 single nucleotide gene polymorphisms (SNPs) were analysed by DNA-microarray in clinical samples. BMAL1 functions were studied in human CRC cell lines using colorimetric growth, DNA-binding and reporter assays. Findings In murine CRCs, high BMAL1 expression correlated with poor preclinical response to Beva treatment. In CRC patients' tumours (n = 74), high BMAL1 expression was associated with clinical non-response to combination chemotherapy with Beva (p = .0061) and reduced progression-free survival (PFS) [p = .0223, Hazard Ratio (HR) = 1.69]. BMAL1 SNPs also correlated with shorter PFS (rs7396943, rs7938307, rs2279287) and overall survival (OS) [rs11022780, *p = .014, HR = 1.61]. Mechanistically, Nuclear-Receptor-Subfamily-1-Group-D-Member-1 (NR1D1/REVERBA) bound a − 672 bp Retinoic-Acid-Receptor-Related-Orphan-Receptor-Alpha-responsive-element (RORE) adjacent to a BMAL1 DNA-binding motif (E-box) in the VEGFA gene promoter, resulting in increased VEGFA synthesis and proliferation of human CRC cell lines. Interpretation BMAL1 was associated with Beva resistance in CRC. Inhibition of REVERBA-BMAL1 signalling may prevent resistance to anti-angiogenic therapy. Fund This work was in part supported by the European Commission Seventh Framework Programme (Contract No. 278981 [ANGIOPREDICT]).
BibTeX: @article{Burgermeister2019, author = {Burgermeister, Elke and Battaglin, Francesca and Eladly, Fagr and Wu, Wen and Herweck, Frank and Schulte, Nadine and Betge, Johannes and Härtel, Nicolai and Kather, Jakob N. and Weis, Cleo-Aron and Gaiser, Timo and Marx, Alexander and Weiss, Christel and Hofheinz, Ralf and Miller, Ian S. and Loupakis, Fotios and Lenz, Heinz-Josef and Byrne, Annette T. and Ebert, Matthias P.}, title = {Aryl hydrocarbon receptor nuclear translocator-like (ARNTL/BMAL1) is associated with bevacizumab resistance in colorectal cancer via regulation of vascular endothelial growth factor A}, journal = {EBioMedicine}, year = {2019}, volume = {45}, pages = {139--154}, url = {http://www.sciencedirect.com/science/article/pii/S2352396419304396}, doi = {https://doi.org/10.1016/j.ebiom.2019.07.004} }
Calviño, F.R., Kornprobst, M., Schermann, G., Birkle, F., Wild, K., Fischer, T., Hurt, E., Ahmed, Y.L. and Sinning, I.	Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis [Abstract] [BibTeX]	2017	PloS one Vol. 12(6), pp. e0178752-e0178752	article	DOI URL
Abstract: Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The 'U three protein' (UTP) complexes and snoRNP particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5'-end of the pre-ribosomal RNA (5'-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2.15 Å resolution and analyze its function by UV RNA-crosslinking (CRAC) and in context of a recent cryo-EM structure of the 90S pre-ribosome. Utp4 consists of two orthogonal and highly basic β-propellers that perfectly fit the EM-data. The Utp4 structure highlights an unusual Velcro-closure of its C-terminal β-propeller as relevant for protein integrity and potentially Utp8 recognition in the context of the pre-ribosome. We provide a first model of the 5'-ETS RNA from the internally hidden 5'-end up to the region that hybridizes to the 3'-hinge sequence of U3 snoRNA and validate a specific Utp4/5'-ETS interaction by CRAC analysis.
BibTeX: @article{Calvino2017, author = {Calviño, Fabiola R. and Kornprobst, Markus and Schermann, Géza and Birkle, Fabienne and Wild, Klemens and Fischer, Tamas and Hurt, Ed and Ahmed, Yasar Luqman and Sinning, Irmgard}, title = {Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis}, journal = {PloS one}, publisher = {Public Library of Science}, year = {2017}, volume = {12}, number = {6}, pages = {e0178752--e0178752}, note = {28575120[pmid]}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28575120}, doi = {https://doi.org/10.1371/journal.pone.0178752} }
Cao, Z., Sugimura, N., Burgermeister, E., Ebert, M.P., Zuo, T. and Lan, P.	The gut virome: A new microbiome component in health and disease [BibTeX]	2022	eBioMedicine Vol. 81, pp. 104113	article	DOI URL
BibTeX: @article{Cao2022, author = {Zhirui Cao, Naoki Sugimura, Elke Burgermeister, Matthias P. Ebert, Tao Zuo, Ping Lan}, title = {The gut virome: A new microbiome component in health and disease}, journal = {eBioMedicine}, publisher = {Elsevier BV}, year = {2022}, volume = {81}, pages = {104113}, url = {https://api.elsevier.com/content/article/PII:S2352396422002948?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.ebiom.2022.104113} }
	Using Ostraca in the Ancient World [BibTeX]	2020		book	DOI
BibTeX: @book{Caputo2020,, title = {Using Ostraca in the Ancient World}, publisher = {De Gruyter}, year = {2020}, doi = {https://doi.org/10.1515/9783110712902} }
Cardoso-Moreira, M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascenção, K., Rummel, C., Ovchinnikova, S., Mazin, P.V., Xenarios, I., Harshman, K., Mort, M., Cooper, D.N., Sandi, C., Soares, M.J., Ferreira, P.G., Afonso, S., Carneiro, M., Turner, J.M.A., VandeBerg, J.L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y.E. and Kaessmann, H.	Gene expression across mammalian organ development [Abstract] [BibTeX]	2019	Nature Vol. 571(7766), pp. 505-509	article	DOI
Abstract: The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.
BibTeX: @article{CardosoMoreira2019, author = {Margarida Cardoso-Moreira and Jean Halbert and Delphine Valloton and Britta Velten and Chunyan Chen and Yi Shao and Angélica Liechti and Kelly Ascenção and Coralie Rummel and Svetlana Ovchinnikova and Pavel V. Mazin and Ioannis Xenarios and Keith Harshman and Matthew Mort and David N. Cooper and Carmen Sandi and Michael J. Soares and Paula G. Ferreira and Sandra Afonso and Miguel Carneiro and James M. A. Turner and John L. VandeBerg and Amir Fallahshahroudi and Per Jensen and Rüdiger Behr and Steven Lisgo and Susan Lindsay and Philipp Khaitovich and Wolfgang Huber and Julie Baker and Simon Anders and Yong E. Zhang and Henrik Kaessmann}, title = {Gene expression across mammalian organ development}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {571}, number = {7766}, pages = {505--509}, doi = {https://doi.org/10.1038/s41586-019-1338-5} }
Cemel, I.A., Diernfellner, A.C.R. and Brunner, M.	Antisense Transcription of the lessigreaterNeurosporaless/igreater Frequency Gene Is Rhythmically Regulated by CSP-1 Repressor but Dispensable for Clock Function [BibTeX]	2023	Journal of Biological Rhythms Vol. 38(3), pp. 259-268	article	DOI
BibTeX: @article{Cemel2023, author = {Ibrahim A. Cemel and Axel C. R. Diernfellner and Michael Brunner}, title = {Antisense Transcription of the lessigreaterNeurosporaless/igreater Frequency Gene Is Rhythmically Regulated by CSP-1 Repressor but Dispensable for Clock Function}, journal = {Journal of Biological Rhythms}, publisher = {SAGE Publications}, year = {2023}, volume = {38}, number = {3}, pages = {259--268}, doi = {https://doi.org/10.1177/07487304231153914} }
Cerullo, F., Filbeck, S., Patil, P.R., Hung, H.-C., Xu, H., Vornberger, J., Hofer, F.W., Schmitt, J., Kramer, G., Bukau, B., Hofmann, K., Pfeffer, S. and Joazeiro, C.A.P.	Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue [BibTeX]	2022	Nature Vol. 603(7901), pp. 509-514	article	DOI
BibTeX: @article{Cerullo2022, author = {Federico Cerullo and Sebastian Filbeck and Pratik Rajendra Patil and Hao-Chih Hung and Haifei Xu and Julia Vornberger and Florian W. Hofer and Jaro Schmitt and Guenter Kramer and Bernd Bukau and Kay Hofmann and Stefan Pfeffer and Claudio A. P. Joazeiro}, title = {Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {603}, number = {7901}, pages = {509--514}, doi = {https://doi.org/10.1038/s41586-022-04487-6} }
Ceverino, D., Glover, S.C.O. and Klessen, R.S.	Introducing the FirstLight project: UV luminosity function and scaling relations of primeval galaxies [BibTeX]	2017	Monthly Notices of the Royal Astronomical Society Vol. 470(3), pp. 2791-2798	article	DOI URL
BibTeX: @article{Ceverino2017, author = {Daniel Ceverino, Simon C. O. Glover, Ralf S. Klessen}, title = {Introducing the FirstLight project: UV luminosity function and scaling relations of primeval galaxies}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press}, year = {2017}, volume = {470}, number = {3}, pages = {2791--2798}, url = {http://academic.oup.com/mnras/article-pdf/470/3/2791/18314671/stx1386.pdf}, doi = {https://doi.org/10.1093/mnras/stx1386} }
Ceverino, D., Klessen, R.S. and Glover, S.C.O.	FirstLight II: Star formation rates of primeval galaxies from z=5-15 [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 480(4), pp. 4842-4850	article	DOI
BibTeX: @article{Ceverino2018, author = {Daniel Ceverino and Ralf S Klessen and Simon C O Glover}, title = {FirstLight II: Star formation rates of primeval galaxies from z=5-15}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {480}, number = {4}, pages = {4842--4850}, doi = {https://doi.org/10.1093/mnras/sty2124} }
Ceverino, D., Klessen, R.S. and Glover, S.C.O.	FirstLight III: rest-frame UV-optical spectral energy distributions of simulated galaxies at cosmic dawn [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 484(1), pp. 1366-1377	article	DOI
BibTeX: @article{Ceverino2019, author = {Daniel Ceverino and Ralf S Klessen and Simon C O Glover}, title = {FirstLight III: rest-frame UV-optical spectral energy distributions of simulated galaxies at cosmic dawn}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {484}, number = {1}, pages = {1366--1377}, doi = {https://doi.org/10.1093/mnras/stz079} }
Chen, J., Fleming, T., Katz, S., Dewenter, M., Hofmann, K., Saadatmand, A., Kronlage, M., Werner, M.P., Pokrandt, B., Schreiter, F., Lin, J., Katz, D., Morgenstern, J., Elwakiel, A., Sinn, P., Gröne, H.-J., Hammes, H.-P., Nawroth, P.P., Isermann, B., Sticht, C., Brügger, B., Katus, H.A., Hagenmueller, M. and Backs, J.	CaM Kinase II-updelta Is Required for Diabetic Hyperglycemia and Retinopathy but Not Nephropathy [BibTeX]	2020	Diabetes Vol. 70(2), pp. 616-626	article	DOI
BibTeX: @article{Chen2020, author = {Jessy Chen and Thomas Fleming and Sylvia Katz and Matthias Dewenter and Kai Hofmann and Alireza Saadatmand and Mariya Kronlage and Moritz P. Werner and Bianca Pokrandt and Friederike Schreiter and Jihong Lin and Daniel Katz and Jakob Morgenstern and Ahmed Elwakiel and Peter Sinn and Hermann-Josef Gröne and Hans-Peter Hammes and Peter P. Nawroth and Berend Isermann and Carsten Sticht and Britta Brügger and Hugo A. Katus and Marco Hagenmueller and Johannes Backs}, title = {CaM Kinase II-updelta Is Required for Diabetic Hyperglycemia and Retinopathy but Not Nephropathy}, journal = {Diabetes}, publisher = {American Diabetes Association}, year = {2020}, volume = {70}, number = {2}, pages = {616--626}, doi = {https://doi.org/10.2337/db19-0659} }
Chen, L.-H., Magg, M., Hartwig, T., Glover, S.C.O., Ji, A.P. and Klessen, R.S.	Tracing stars in Milky Way satellites with lessscpgreatera-slothless/scpgreater [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 513, pp. 934-950	article	DOI
BibTeX: @article{Chen2022, author = {Li-Hsin Chen and Mattis Magg and Tilman Hartwig and Simon C O Glover and Alexander P Ji and Ralf S Klessen}, title = {Tracing stars in Milky Way satellites with lessscpgreatera-slothless/scpgreater}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {513}, pages = {934--950}, doi = {https://doi.org/10.1093/mnras/stac933} }
Chen, L.-H., Hartwig, T., Klessen, R.S. and Glover, S.C.O.	Comparing simulated Milky Way satellite galaxies with observations using unsupervised clustering [Abstract] [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 517(4), pp. 6140-6149	article	DOI
Abstract: ABSTRACT We develop a new analysis method that allows us to compare multidimensional observables to a theoretical model. The method is based on unsupervised clustering algorithms which assign the observational and simulated data to clusters in high dimensionality. From the clustering result, a goodness of fit (the p-value) is determined with the Fisher–Freeman–Halton test. We first show that this approach is robust for 2D Gaussian distributions. We then apply the method to the observed MW satellites and simulated satellites from the fiducial model of our semi-analytic code a-sloth . We use the following five observables of the galaxies in the analysis: stellar mass, virial mass, heliocentric distance, mean stellar metallicity [Fe/H], and stellar metallicity dispersion σ[Fe/H]. A low p-value returned from the analysis tells us that our a-sloth fiducial model does not reproduce the mean stellar metallicity of the observed MW satellites well. We implement an ad hoc improvement to the physical model and show that the number of dark matter merger trees which have a p-value &gt; 0.01 increases from 3 to 6. This method can be extended to data with higher dimensionality easily. We plan to further improve the physical model in a-sloth using this method to study elemental abundances of stars in the observed MW satellites.
BibTeX: @article{Chen2022b, author = {Li-Hsin Chen, Tilman Hartwig, Ralf S Klessen, Simon C O Glover}, title = {Comparing simulated Milky Way satellite galaxies with observations using unsupervised clustering}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {517}, number = {4}, pages = {6140--6149}, doi = {https://doi.org/10.1093/mnras/stac2897} }
Cheng, J., Baßler, J., Fischer, P., Lau, B., Kellner, N., Kunze, R., Griesel, S., Kallas, M., Berninghausen, O., Strauss, D., Beckmann, R. and Hurt, E.	Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration [Abstract] [BibTeX]	2019	Molecular Cell Vol. 75(6), pp. 1256-1269.e7	article	DOI URL
Abstract: Summary Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5textasciiacutex > 3textasciiacutex, but this directionality may not be accurate. Here, by analyzing the structure of a series of 90S assembly intermediates from Chaetomium thermophilum, we discover a reverse order of 18S rRNA subdomain incorporation. Large parts of the 18S rRNA 3textasciiacutex and central domains assemble first into the 90S before the 5textasciiacutex domain is integrated. This final incorporation depends on a contact between a heterotrimer Enp2-Bfr2-Lcp5 recruited to the flexible 5textasciiacutex domain and Kre33, which reconstitutes the Kre33-Enp-Brf2-Lcp5 module on the compacted 90S. Keeping the 5textasciiacutex domain temporarily segregated from the 90S scaffold could provide extra time to complete the multifaceted 5textasciiacutex domain folding, which depends on a distinct set of snoRNAs and processing factors.
BibTeX: @article{Cheng2019, author = {Cheng, Jingdong and Baßler, Jochen and Fischer, Paulina and Lau, Benjamin and Kellner, Nikola and Kunze, Ruth and Griesel, Sabine and Kallas, Martina and Berninghausen, Otto and Strauss, Daniela and Beckmann, Roland and Hurt, Ed}, title = {Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration}, journal = {Molecular Cell}, year = {2019}, volume = {75}, number = {6}, pages = {1256--1269.e7}, url = {http://www.sciencedirect.com/science/article/pii/S1097276519304897}, doi = {https://doi.org/10.1016/j.molcel.2019.06.032} }
Cheng, J., Lau, B., Venuta, G.L., Ameismeier, M., Berninghausen, O., Hurt, E. and Beckmann, R.	90S pre-ribosome transformation into the primordial 40S subunit [BibTeX]	2020	Science Vol. 369(6510), pp. 1470-1476	article	DOI
BibTeX: @article{Cheng2020, author = {Jingdong Cheng and Benjamin Lau and Giuseppe La Venuta and Michael Ameismeier and Otto Berninghausen and Ed Hurt and Roland Beckmann}, title = {90S pre-ribosome transformation into the primordial 40S subunit}, journal = {Science}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2020}, volume = {369}, number = {6510}, pages = {1470--1476}, doi = {https://doi.org/10.1126/science.abb4119} }
Cheng, J., La Venuta, G., Lau, B., Berninghausen, O., Beckmann, R. and Hurt, E.	In vitro structural maturation of an early stage pre-40S particle coupled with U3 snoRNA release and central pseudoknot formation [Abstract] [BibTeX]	2022	Nucleic Acids Research Vol. 50(20), pp. 11916-11923	article	DOI URL
Abstract: Abstract The transition of the 90S to the pre-40S pre-ribosome is a decisive step in eukaryotic small subunit biogenesis leading to a first pre-40S intermediate (state Dis-C or primordial pre-40S), where the U3 snoRNA keeps the nascent 18S rRNA locally immature. We in vitro reconstitute the ATP-dependent U3 release from this particle, catalyzed by the helicase Dhr1, and follow this process by cryo-EM revealing two successive pre-40S intermediates, Dis-D and Dis-E. The latter has lost not only U3 but all residual 90S factors including the GTPase Bms1. In vitro remodeling likewise induced the formation of the central pseudoknot, a universally conserved tertiary RNA structure that comprises the core of the small subunit decoding center. Thus, we could structurally reveal a key tertiary RNA folding step that is essential to form the active 40S subunit.
BibTeX: @article{Cheng2022, author = {Jingdong Cheng, Giuseppe La Venuta, Benjamin Lau, Otto Berninghausen, Roland Beckmann, Ed Hurt}, title = {In vitro structural maturation of an early stage pre-40S particle coupled with U3 snoRNA release and central pseudoknot formation}, journal = {Nucleic Acids Research}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {50}, number = {20}, pages = {11916--11923}, url = {https://academic.oup.com/nar/article-pdf/50/20/11916/47609111/gkac910.pdf}, doi = {https://doi.org/10.1093/nar/gkac910} }
Cheng, J., Lau, B., Thoms, M., Ameismeier, M., Berninghausen, O., Hurt, E. and Beckmann, R.	The nucleoplasmic phase of pre-40S formation prior to nuclear export [Abstract] [BibTeX]	2022	Nucleic Acids Research Vol. 50(20), pp. 11924-11937	article	DOI URL
Abstract: Abstract Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23–TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
BibTeX: @article{Cheng2022a, author = {Jingdong Cheng, Benjamin Lau, Matthias Thoms, Michael Ameismeier, Otto Berninghausen, Ed Hurt, Roland Beckmann}, title = {The nucleoplasmic phase of pre-40S formation prior to nuclear export}, journal = {Nucleic Acids Research}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {50}, number = {20}, pages = {11924--11937}, url = {https://academic.oup.com/nar/article-pdf/50/20/11924/47609248/gkac961.pdf}, doi = {https://doi.org/10.1093/nar/gkac961} }
Chiapparino, A., Grbavac, A., Jonker, H.R., Hackmann, Y., Mortensen, S., Zatorska, E., Schott, A., Stier, G., Saxena, K., Wild, K., Schwalbe, H., Strahl, S. and Sinning, I.	Functional implications of MIR domains in protein O-mannosylation [BibTeX]	2020	eLife Vol. 9	article	DOI
BibTeX: @article{Chiapparino2020, author = {Antonella Chiapparino and Antonija Grbavac and Hendrik RA Jonker and Yvonne Hackmann and Sofia Mortensen and Ewa Zatorska and Andrea Schott and Gunter Stier and Krishna Saxena and Klemens Wild and Harald Schwalbe and Sabine Strahl and Irmgard Sinning}, title = {Functional implications of MIR domains in protein O-mannosylation}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2020}, volume = {9}, doi = {https://doi.org/10.7554/elife.61189} }
Chlanda, P., Mekhedov, E., Waters, H., Schwartz, C.L., Fischer, E.R., Ryham, R.J., Cohen, F.S., Blank, P.S. and Zimmerberg, J.	The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes [Abstract] [BibTeX]	2016	Nature Microbiology Vol. 1(6), pp. 16050	article	DOI
Abstract: Influenza A virus haemagglutinin conformational change drives the membrane fusion of viral and endosomal membranes at low pH. Membrane fusion proceeds through an intermediate called hemifusion1,2. For viral fusion, the hemifusion structures are not determined3. Here, influenza virus-like particles4 carrying wild-type haemagglutinin or haemagglutinin hemifusion mutant G1S5 and liposome mixtures were studied at low pH by Volta phase plate cryo-electron tomography, which improves the signal-to-noise ratio close to focus. We determined two distinct hemifusion structures: a hemifusion diaphragm and a novel structure termed a `lipidic junction'. Liposomes with lipidic junctions were ruptured with membrane edges stabilized by haemagglutinin. The rupture frequency and hemifusion diaphragm diameter were not affected by G1S mutation, but decreased when the cholesterol level in the liposomes was close to physiological concentrations. We propose that haemagglutinin induces a merger between the viral and target membranes by one of two independent pathways: a rupture--insertion pathway leading to the lipidic junction and a hemifusion-stalk pathway leading to a fusion pore. The latter is relevant under the conditions of influenza virus infection of cells. Cholesterol concentration functions as a pathway switch because of its negative spontaneous curvature in the target bilayer, as determined by continuum analysis.
BibTeX: @article{Chlanda2016, author = {Chlanda, Petr and Mekhedov, Elena and Waters, Hang and Schwartz, Cindi L. and Fischer, Elizabeth R. and Ryham, Rolf J. and Cohen, Fredric S. and Blank, Paul S. and Zimmerberg, Joshua}, title = {The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes}, journal = {Nature Microbiology}, year = {2016}, volume = {1}, number = {6}, pages = {16050}, doi = {https://doi.org/10.1038/nmicrobiol.2016.50} }
Chlanda, P., Mekhedov, E., Waters, H., Sodt, A., Schwartz, C., Nair, V., Blank, P.S. and Zimmerberg, J.	Palmitoylation Contributes to Membrane Curvature in Influenza A Virus Assembly and Hemagglutinin-Mediated Membrane Fusion [Abstract] [BibTeX]	2017	Journal of Virology Vol. 91(21)	article	DOI URL
Abstract: The highly conserved cytoplasmic tail of influenza virus glycoprotein hemagglutinin (HA) contains three cysteines, posttranslationally modified by covalently bound fatty acids. While viral HA acylation is crucial in virus replication, its physico-chemical role is unknown. We used virus-like particles (VLP) to study the effect of acylation on morphology, protein incorporation, lipid composition, and membrane fusion. Deacylation interrupted HA-M1 interactions since deacylated mutant HA failed to incorporate an M1 layer within spheroidal VLP, and filamentous particles incorporated increased numbers of neuraminidase (NA). While HA acylation did not influence VLP shape, lipid composition, or HA lateral spacing, acylation significantly affected envelope curvature. Compared to wild-type HA, deacylated HA is correlated with released particles with flat envelope curvature in the absence of the matrix (M1) protein layer. The spontaneous curvature of palmitate was calculated by molecular dynamic simulations and was found to be comparable to the curvature values derived from VLP size distributions. Cell-cell fusion assays show a strain-independent failure of fusion pore enlargement among H2 (A/Japan/305/57), H3 (A/Aichi/2/68), and H3 (A/Udorn/72) viruses. In contradistinction, acylation made no difference in the low-pH-dependent fusion of isolated VLPs to liposomes: fusion pores formed and expanded, as demonstrated by the presence of complete fusion products observed using cryo-electron tomography (cryo-ET). We propose that the primary mechanism of action of acylation is to control membrane curvature and to modify HA's interaction with M1 protein, while the stunting of fusion by deacylated HA acting in isolation may be balanced by other viral proteins which help lower the energetic barrier to pore expansion.IMPORTANCE Influenza A virus is an airborne pathogen causing seasonal epidemics and occasional pandemics. Hemagglutinin (HA), a glycoprotein abundant on the virion surface, is important in both influenza A virus assembly and entry. HA is modified by acylation whose removal abrogates viral replication. Here, we used cryo-electron tomography to obtain three-dimensional images to elucidate a role for HA acylation in VLP assembly. Our data indicate that HA acylation contributes to the capability of HA to bend membranes and to HA's interaction with the M1 scaffold protein during virus assembly. Furthermore, our data on VLP and, by hypothesis, virus suggests that HA acylation, while not critical to fusion pore formation, contributes to pore expansion in a target-dependent fashion.
BibTeX: @article{Chlanda2017, author = {Chlanda, Petr and Mekhedov, Elena and Waters, Hang and Sodt, Alexander and Schwartz, Cindi and Nair, Vinod and Blank, Paul S. and Zimmerberg, Joshua}, title = {Palmitoylation Contributes to Membrane Curvature in Influenza A Virus Assembly and Hemagglutinin-Mediated Membrane Fusion}, journal = {Journal of Virology}, publisher = {American Society for Microbiology Journals}, year = {2017}, volume = {91}, number = {21}, url = {https://jvi.asm.org/content/91/21/e00947-17}, doi = {https://doi.org/10.1128/JVI.00947-17} }
Chlanda, P.	Influenza Hemagglutinin and M2 ion channel priming by trypsin: Killing two birds with one stone [Abstract] [BibTeX]	2017	Virology Vol. 509, pp. 131-132	article	DOI URL
Abstract: Influenza A virus membrane fusion and disassembly, prerequisite processes for viral infectivity, depend on acidic pH. In a recent study, Zhirnov et al. reported an important finding---that influenza virions are not permeable to protons unless the hemagglutinin (HA) fusion protein is primed by trypsin cleavage. This raises the question of whether in the viral context the M2 ion channel requires priming prior to its activation by low pH. Here, it is hypothesized that both HA and M2 ion channel direct priming by trypsin is required for their sensitization by low pH.
BibTeX: @article{Chlanda2017a, author = {Chlanda, Petr}, title = {Influenza Hemagglutinin and M2 ion channel priming by trypsin: Killing two birds with one stone}, journal = {Virology}, year = {2017}, volume = {509}, pages = {131--132}, url = {http://www.sciencedirect.com/science/article/pii/S0042682217301885}, doi = {https://doi.org/10.1016/j.virol.2017.06.011} }
Chlanda, P. and Krijnse Locker, J.	The sleeping beauty kissed awake: new methods in electron microscopy to study cellular membranes [Abstract] [BibTeX]	2017	Biochemical Journal Vol. 474(6), pp. 1041-1053	article	DOI URL
Abstract: Electron microscopy (EM) for biological samples, developed in the 1940--1950s, changed our conception about the architecture of eukaryotic cells. It was followed by a period where EM applied to cell biology had seemingly fallen asleep, even though new methods with important implications for modern EM were developed. Among these was the discovery that samples can be preserved by chemical fixation and most importantly by rapid freezing without the formation of crystalline ice, giving birth to the world of cryo-EM. The past 15--20 years are hallmarked by a tremendous interest in EM, driven by important technological advances. Cryo-EM, in particular, is now capable of revealing structures of proteins at a near-atomic resolution owing to improved sample preparation methods, microscopes and cameras. In this review, we focus on the challenges associated with the imaging of membranes by EM and give examples from the field of host--pathogen interactions, in particular of virus-infected cells. Despite the advantages of imaging membranes under native conditions in cryo-EM, conventional EM will remain an important complementary method, in particular if large volumes need to be imaged.
BibTeX: @article{Chlanda2017b, author = {Chlanda, Petr and Krijnse Locker, Jacomine}, title = {The sleeping beauty kissed awake: new methods in electron microscopy to study cellular membranes}, journal = {Biochemical Journal}, year = {2017}, volume = {474}, number = {6}, pages = {1041--1053}, url = {https://portlandpress.com/biochemj/article-pdf/474/6/1041/689221/bcj-2016-0990c.pdf}, doi = {https://doi.org/10.1042/BCJ20160990} }
Christian, W., Barnea, A., Born, R., Keazor, H., Panaite, A. and Talmaţchi, G.	Archäologie und Politik: Die zwei Geschichten des Tropaeum Traiani zwischen Heidelberg und Adamklissi. [BibTeX]	2021		book
BibTeX: @book{Christian2021, author = {Witschel Christian and Alexandru Barnea and Robert Born and Henry Keazor and Adriana Panaite and Gabriel Talmaţchi}, title = {Archäologie und Politik: Die zwei Geschichten des Tropaeum Traiani zwischen Heidelberg und Adamklissi.}, publisher = {Polly Lohmann, Propylaeum}, year = {2021} }
Chuang, H.-P.	Das Steininschriftenprojekt des Wolkenheimklosters während der Liao-Dynastie (907–1125) [BibTeX]	2017		book	DOI
BibTeX: @book{Chuang2017, author = {Hui-Ping Chuang}, title = {Das Steininschriftenprojekt des Wolkenheimklosters während der Liao-Dynastie (907–1125)}, publisher = {De Gruyter}, year = {2017}, doi = {https://doi.org/10.1515/9783110534849} }
Ciuba, K., Hawkes, W., Tojkander, S., Kogan, K., Engel, U., Iskratsch, T. and Lappalainen, P.	Calponin-3 is critical for coordinated contractility of actin stress fibers [Abstract] [BibTeX]	2018	Scientific Reports Vol. 8(1), pp. 17670	article	DOI
Abstract: Contractile actomyosin bundles, stress fibers, contribute to morphogenesis, migration, and mechanosensing of non-muscle cells. In addition to actin and non-muscle myosin II (NMII), stress fibers contain a large array of proteins that control their assembly, turnover, and contractility. Calponin-3 (Cnn3) is an actin-binding protein that associates with stress fibers. However, whether Cnn3 promotes stress fiber assembly, or serves as either a positive or negative regulator of their contractility has remained obscure. Here, we applied U2OS osteosarcoma cells as a model system to study the function of Cnn3. We show that Cnn3 localizes to both NMII-containing contractile ventral stress fibers and transverse arcs, as well as to non-contractile dorsal stress fibers that do not contain NMII. Fluorescence-recovery-after-photobleaching experiments revealed that Cnn3 is a dynamic component of stress fibers. Importantly, CRISPR/Cas9 knockout and RNAi knockdown studies demonstrated that Cnn3 is not essential for stress fiber assembly. However, Cnn3 depletion resulted in increased and uncoordinated contractility of stress fibers that often led to breakage of individual actomyosin bundles within the stress fiber network. Collectively these results provide evidence that Cnn3 is dispensable for the assembly of actomyosin bundles, but that it is required for controlling proper contractility of the stress fiber network.
BibTeX: @article{Ciuba2018, author = {Ciuba, Katarzyna and Hawkes, William and Tojkander, Sari and Kogan, Konstantin and Engel, Ulrike and Iskratsch, Thomas and Lappalainen, Pekka}, title = {Calponin-3 is critical for coordinated contractility of actin stress fibers}, journal = {Scientific Reports}, year = {2018}, volume = {8}, number = {1}, pages = {17670}, doi = {https://doi.org/10.1038/s41598-018-35948-6} }
Clemente, F., Unterländer, M., Dolgova, O., Amorim, C.E.G., Coroado-Santos, F., Neuenschwander, S., Ganiatsou, E., Dávalos, D.I.C., Anchieri, L., Michaud, F., Winkelbach, L., Blöcher, J., Cárdenas, Y.O.A., da Mota, B.S., Kalliga, E., Souleles, A., Kontopoulos, I., Karamitrou-Mentessidi, G., Philaniotou, O., Sampson, A., Theodorou, D., Tsipopoulou, M., Akamatis, I., Halstead, P., Kotsakis, K., Urem-Kotsou, D., Panagiotopoulos, D., Ziota, C., Triantaphyllou, S., Delaneau, O., Jensen, J.D., Moreno-Mayar, J.V., Burger, J., Sousa, V.C., Lao, O., Malaspinas, A.-S. and Papageorgopoulou, C.	The genomic history of the Aegean palatial civilizations [BibTeX]	2021	Cell Vol. 184(10), pp. 2565-2586.e21	article	DOI
BibTeX: @article{Clemente2021, author = {Florian Clemente and Martina Unterländer and Olga Dolgova and Carlos Eduardo G. Amorim and Francisco Coroado-Santos and Samuel Neuenschwander and Elissavet Ganiatsou and Diana I. Cruz Dávalos and Lucas Anchieri and Frédéric Michaud and Laura Winkelbach and Jens Blöcher and Yami Ommar Arizmendi Cárdenas and Bárbara Sousa da Mota and Eleni Kalliga and Angelos Souleles and Ioannis Kontopoulos and Georgia Karamitrou-Mentessidi and Olga Philaniotou and Adamantios Sampson and Dimitra Theodorou and Metaxia Tsipopoulou and Ioannis Akamatis and Paul Halstead and Kostas Kotsakis and Dushka Urem-Kotsou and Diamantis Panagiotopoulos and Christina Ziota and Sevasti Triantaphyllou and Olivier Delaneau and Jeffrey D. Jensen and J. V\ictor Moreno-Mayar and Joachim Burger and Vitor C. Sousa and Oscar Lao and Anna-Sapfo Malaspinas and Christina Papageorgopoulou}, title = {The genomic history of the Aegean palatial civilizations}, journal = {Cell}, publisher = {Elsevier BV}, year = {2021}, volume = {184}, number = {10}, pages = {2565--2586.e21}, doi = {https://doi.org/10.1016/j.cell.2021.03.039} }
Clemm von Hohenberg, C., Weber-Fahr, W., Lebhardt, P., Ravi, N., Braun, U., Gass, N., Becker, R., Sack, M., Cosa Linan, A., Gerchen, M.F., Reinwald, J.R., Oettl, L.-L., Meyer-Lindenberg, A., Vollmayr, B., Kelsch, W. and Sartorius, A.	Lateral habenula perturbation reduces default-mode network connectivity in a rat model of depression [Abstract] [BibTeX]	2018	Translational Psychiatry Vol. 8(1), pp. 68	article	DOI
Abstract: Hyperconnectivity of the default-mode network (DMN) is one of the most widely replicated neuroimaging findings in major depressive disorder (MDD). Further, there is growing evidence for a central role of the lateral habenula (LHb) in the pathophysiology of MDD. There is preliminary neuroimaging evidence linking LHb and the DMN, but no causal relationship has been shown to date. We combined optogenetics and functional magnetic resonance imaging (fMRI), to establish a causal relationship, using an animal model of treatment-resistant depression, namely Negative Cognitive State rats. First, an inhibitory light-sensitive ion channel was introduced into the LHb by viral transduction. Subsequently, laser stimulation was performed during fMRI acquisition on a 9.4 Tesla animal scanner. Neural activity and connectivity were assessed, before, during and after laser stimulation. We observed a connectivity decrease in the DMN following laser-induced LHb perturbation. Our data indicate a causal link between LHb downregulation and reduction in DMN connectivity. These findings may advance our mechanistic understanding of LHb inhibition, which had previously been identified as a promising therapeutic principle, especially for treatment-resistant depression.
BibTeX: @article{ClemmvonHohenberg2018, author = {Clemm von Hohenberg, Christian and Weber-Fahr, Wolfgang and Lebhardt, Philipp and Ravi, Namasivayam and Braun, Urs and Gass, Natalia and Becker, Robert and Sack, Markus and Cosa Linan, Alejandro and Gerchen, Martin Fungisai and Reinwald, Jonathan Rochus and Oettl, Lars-Lennart and Meyer-Lindenberg, Andreas and Vollmayr, Barbara and Kelsch, Wolfgang and Sartorius, Alexander}, title = {Lateral habenula perturbation reduces default-mode network connectivity in a rat model of depression}, journal = {Translational Psychiatry}, year = {2018}, volume = {8}, number = {1}, pages = {68}, doi = {https://doi.org/10.1038/s41398-018-0121-y} }
Cohen, C.M., Wentzensen, N., Lahrmann, B., Tokugawa, D., Poitras, N., Bartels, L., Krauthoff, A., Keil, A., Miranda, F., Castle, P.E., Lorey, T., Hare, B., Darragh, T.M., Grabe, N. and Clarke, M.A.	Automated Evaluation of p16/Ki-67 Dual-Stain Cytology as a Biomarker for Detection of Anal Precancer in Men Who Have Sex With Men and Are Living With Human Immunodeficiency Virus [Abstract] [BibTeX]	2022	Clinical Infectious Diseases Vol. 75(9), pp. 1565-1572	article	DOI
Abstract: Abstract Background Human papillomavirus–related biomarkers such as p16/Ki-67 “dual-stain” (DS) cytology have shown promising clinical performance for anal cancer screening. Here, we assessed the performance of automated evaluation of DS cytology (automated DS) to detect anal precancer in men who have sex with men (MSM) and are living with human immunodeficiency virus (HIV). Methods We conducted a cross-sectional analysis of 320 MSM with HIV undergoing anal cancer screening and high-resolution anoscopy (HRA) in 2009–2010. We evaluated the performance of automated DS based on a deep-learning classifier compared to manual evaluation of DS cytology (manual DS) to detect anal intraepithelial neoplasia grade 2 or 3 (AIN2+) and grade 3 (AIN3). We evaluated different DS-positive cell thresholds quantified by the automated approach and modeled performance compared with other screening strategies in a hypothetical population of MSM with HIV. Results Compared with manual DS, automated DS had significantly higher specificity (50.9% vs 42.2%; P &lt; .001) and similar sensitivity (93.2% vs 92.1%) for detection of AIN2+. Human papillomavirus testing with automated DS triage was significantly more specific than automated DS alone (56.5% vs 50.9%; P &lt; .001), with the same sensitivity (93.2%). In a modeled analysis assuming a 20% AIN2+ prevalence, automated DS detected more precancers than manual DS and anal cytology (186, 184, and 162, respectively) and had the lowest HRA referral rate per AIN2+ case detected (3.1, 3.5, and 3.3, respectively). Conclusions Compared with manual DS, automated DS detects the same number of precancers, with a lower HRA referral rate.
BibTeX: @article{Cohen2022, author = {Camryn M Cohen, Nicolas Wentzensen, Bernd Lahrmann, Diane Tokugawa, Nancy Poitras, Liam Bartels, Alexandra Krauthoff, Andreas Keil, Felipe Miranda, Philip E Castle, Thomas Lorey, Brad Hare, Teresa M Darragh, Niels Grabe, Megan A Clarke}, title = {Automated Evaluation of p16/Ki-67 Dual-Stain Cytology as a Biomarker for Detection of Anal Precancer in Men Who Have Sex With Men and Are Living With Human Immunodeficiency Virus}, journal = {Clinical Infectious Diseases}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {75}, number = {9}, pages = {1565--1572}, doi = {https://doi.org/10.1093/cid/ciac211} }
Colucci, S., Altamura, S., Marques, O., Dropmann, A., Horvat, N.K., Müdder, K., Hammad, S., Dooley, S. and Muckenthaler, M.U.	Liver Sinusoidal Endothelial Cells Suppress Bone Morphogenetic Protein 2 Production in Response to TGFupbeta Pathway Activation [BibTeX]	2021	Hepatology Vol. 74(4), pp. 2186-2200	article	DOI
BibTeX: @article{Colucci2021, author = {Silvia Colucci and Sandro Altamura and Oriana Marques and Anne Dropmann and Natalie K. Horvat and Katja Müdder and Seddik Hammad and Steven Dooley and Martina U. Muckenthaler}, title = {Liver Sinusoidal Endothelial Cells Suppress Bone Morphogenetic Protein 2 Production in Response to TGFupbeta Pathway Activation}, journal = {Hepatology}, publisher = {Wiley}, year = {2021}, volume = {74}, number = {4}, pages = {2186--2200}, doi = {https://doi.org/10.1002/hep.31900} }
Conijn, A., Lange, J., Zube, C., Mächtle, B. and Meier, T.	EARLY FLOODS AND EARLY DIKES: RESEARCH STRATEGY IN COMBINING GEOARCHAEOLOGICAL AND HISTORICAL SOURCES IN THE UPPER RHINE VALLEY [BibTeX]	2020		inproceedings
BibTeX: @inproceedings{Conijn2020, author = {Conijn, Arjan and Lange, Janine and Zube, Carsten and Mächtle, Bertil and Meier, Thomas}, title = {EARLY FLOODS AND EARLY DIKES: RESEARCH STRATEGY IN COMBINING GEOARCHAEOLOGICAL AND HISTORICAL SOURCES IN THE UPPER RHINE VALLEY}, year = {2020} }
Corinna Reinhardt, A.R.	Antike(n) als Andenken und die bürgerliche Reisekultur der zweiten Hälfte des 19. Jahrhunderts: Die Reuter-Villa in Eisenach als Beispiel [BibTeX]	2021	Pegasus 20 - Berliner Beiträge zum Nachleben der Antike, pp. 163–201	incollection
BibTeX: @incollection{CorinnaReinhardt2021, author = {Corinna Reinhardt, Arne Reinhardt}, title = {Antike(n) als Andenken und die bürgerliche Reisekultur der zweiten Hälfte des 19. Jahrhunderts: Die Reuter-Villa in Eisenach als Beispiel}, booktitle = {Pegasus 20 - Berliner Beiträge zum Nachleben der Antike}, publisher = {Lukas Verlag für Kunst- und Geistesgeschichte}, year = {2021}, pages = {163–201} }
Cui, X. and Gutheil, E.	Three-dimensional unsteady large eddy simulation of the vortex structures and the mono-disperse particle dispersion in the idealized human upper respiratory system [Abstract] [BibTeX]	2017	Journal of Aerosol Science Vol. 114, pp. 195-208	article	DOI URL
Abstract: The present study concerns the three-dimensional unsteady large eddy simulation (LES) in an idealized human mouth-throat under the different inspiration flow rates of 15, 30 and 60L/min. Three-dimensional vortices are observed in both the instantaneous and in the mean flow field in the mouth cavity, pharynx, larynx and trachea as well as in the recirculation zone of the pharynx. In the steady flow field it is found that the barrier caused by the tongue may induce hairpin vortices whereas the barrier glottis may cause horseshoe vortices. With the increase of the inspiration flow rate, the distance between the legs of the hairpin vortices in the mouth cavity decreases, and the length scale of the vortex in the trachea decreases with increasing inspiration flow rate. In the unsteady flow field, the counter-rotating vortices in the pharynx and trachea disappear at the highest inspiration flow rate, but the counter-rotating vortices can still be observed at the lowest inspiration flow rate. The vortex in the unsteady flow field is much more complex compared to the steady situation, and more vortices with smaller length scales are observed in the trachea for the increased flow rate. Lagrangian particle tracking is introduced into the model to investigate the process of particle drug delivery for medical treatment of the human airway. It is found that the mono-disperse particles may follow totally different trajectories depending on their initial release positions and the inspiration flow rates as well as on their size. The particles may follow very complex recirculating movements within the recirculation zone, and they may show a swinging, transverse or helical motion due to the vortex of the gas flow. This may also affect the deposition characteristics of the injected particles.
BibTeX: @article{Cui2017, author = {Cui, Xinguang and Gutheil, Eva}, title = {Three-dimensional unsteady large eddy simulation of the vortex structures and the mono-disperse particle dispersion in the idealized human upper respiratory system}, journal = {Journal of Aerosol Science}, publisher = {Elsevier}, year = {2017}, volume = {114}, pages = {195--208}, url = {http://www.sciencedirect.com/science/article/pii/S0021850217300186}, doi = {https://doi.org/10.1016/j.jaerosci.2017.09.005} }
Cui, X.G., Littringer, E.M., Urbanetz, N.A. and Gutheil, E.	LARGE EDDY SIMULATION OF POLYDISPERSE PARTICLE DEPOSITION IN AN IDEALIZED MOUTH-THROAT [BibTeX]	2018	Atomization and Sprays Vol. 28(2), pp. 179-193	article
BibTeX: @article{Cui2018, author = {Cui, X. G. and Littringer, E. M. and Urbanetz, N. A. and Gutheil, Eva}, title = {LARGE EDDY SIMULATION OF POLYDISPERSE PARTICLE DEPOSITION IN AN IDEALIZED MOUTH-THROAT}, journal = {Atomization and Sprays}, year = {2018}, volume = {28}, number = {2}, pages = {179--193} }
Cui, X., Wu, W. and Gutheil, E.	Numerical study of the airflow structures in an idealized mouth-throat under light and heavy breathing intensities using large eddy simulation [Abstract] [BibTeX]	2018	Respiratory Physiology & Neurobiology Vol. 248, pp. 1-9	article	DOI URL
Abstract: An excellent understanding of the airflow structures is critical to enhance the efficiency of drug delivery via the human oral airway. The present paper investigates the characteristics of both steady and unsteady airflow structures in an idealized mouth-throat using large eddy simulation (LES). Representative inhalation flow rates of 15L/min at rest and 60L/min in exercise are considered. The study shows that there are more secondary vortices in the pharynx and the laryngeal jet is much longer and more concave in the steady flow field at 15L/min compared to the higher inspiration rate, which decreases the possibility of drug impinging on the wall. In contrast, the laryngeal jet is much more unsteady at heavy breathing and its strong interaction with the recirculation zone in the trachea leads to a enlarged mixing zone, increasing the possibility for carrying the particles from the laryngeal jet into the recirculation zone, which will lead to a longer residence time of the particles in the trachea and this increases the possibility of drug deposition in this area. In addition, the recirculation zone size is larger, the separation region is far away from glottis, and the reversed flow is slower at light compared to heavy breathing. In conclusion, these airflow structures show distinct properties at light and heavy breathing conditions, particularly in the unsteady flow field. The study provides evidence about the physical processes leading to both enlarged mixing zones and recirculation zones. It is known that stronger secondary vortices, a stronger laryngeal jet and enlarged recirculation zones definitely increase the particle deposition in the upper airway. The present paper aims to uncover the physical properties of the airflow for different breathing conditions, and their detailed effect on particle deposition will be studied in future.
BibTeX: @article{Cui2018a, author = {Cui, Xinguang and Wu, Wenwang and Gutheil, Eva}, title = {Numerical study of the airflow structures in an idealized mouth-throat under light and heavy breathing intensities using large eddy simulation}, journal = {Respiratory Physiology & Neurobiology}, year = {2018}, volume = {248}, pages = {1--9}, url = {http://www.sciencedirect.com/science/article/pii/S1569904817303075}, doi = {https://doi.org/10.1016/j.resp.2017.11.001} }
Cui, X. and Gutheil, E.	Large eddy simulation of the flow pattern in an idealized mouth-throat under unsteady inspiration flow conditions [Abstract] [BibTeX]	2018	Respiratory Physiology & Neurobiology Vol. 252-253, pp. 38-46	article	DOI URL
Abstract: An excellent understanding of the airflow properties is critical to improve the drug delivery efficiency via the extrathoracic airway. The present numerical study focuses on the investigation the characteristics of important airflow structures such as the secondary vortices, the impinging jet and the recirculation zone under unsteady inspiration flow conditions in a circular idealized mouth-throat model using large eddy simulation (LES). Five inhalation cycles are simulated, the last one of which is analyzed in detail at five different times. Two times are chosen during the accelerating branch, one at the peak and two within the decelerating inhalation wave. The flow exhibits an extinct process of the flow transiting from laminar to turbulent during the accelerating phase and transiting back from turbulent to laminar in the decelerating phase. It is found that the flow is much more turbulent during the decelerating phase compared to the accelerating phase of the inspiration wave, which is associated with more smaller secondary vortices, a shorter and more unsteady laryngeal jet, a smaller and more unsteady recirculation zone, as well as an enlarged mixing zone. These differences during the unsteady inspiration require more attention in particular if particle transport and deposition in the upper airway are to be investigated.
BibTeX: @article{Cui2018b, author = {Cui, Xinguang and Gutheil, Eva}, title = {Large eddy simulation of the flow pattern in an idealized mouth-throat under unsteady inspiration flow conditions}, journal = {Respiratory Physiology & Neurobiology}, year = {2018}, volume = {252-253}, pages = {38--46}, url = {http://www.sciencedirect.com/science/article/pii/S1569904817304469}, doi = {https://doi.org/10.1016/j.resp.2018.03.002} }
Cui, C., Liu, Y., Gerloff, D., Rohde, C., Pauli, C., Köhn, M., Misiak, D., Oellerich, T., Schwartz, S., Schmidt, L.-H., Wiewrodt, R., Marra, A., Hillejan, L., Bartel, F., Wickenhauser, C., Hüttelmaier, S., Göllner, S., Zhou, F., Edemir, B. and Müller-Tidow, C.	NOP10 predicts lung cancer prognosis and its associated small nucleolar RNAs drive proliferation and migration [BibTeX]	2020	Oncogene Vol. 40(5), pp. 909-921	article	DOI
BibTeX: @article{Cui2020, author = {Chunhong Cui and Yi Liu and Dennis Gerloff and Christian Rohde and Cornelius Pauli and Marcel Köhn and Danny Misiak and Thomas Oellerich and Schraga Schwartz and Lars-Henning Schmidt and Rainer Wiewrodt and Alessandro Marra and Ludger Hillejan and Frank Bartel and Claudia Wickenhauser and Stefan Hüttelmaier and Stefanie Göllner and Fengbiao Zhou and Bayram Edemir and Carsten Müller-Tidow}, title = {NOP10 predicts lung cancer prognosis and its associated small nucleolar RNAs drive proliferation and migration}, journal = {Oncogene}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {40}, number = {5}, pages = {909--921}, doi = {https://doi.org/10.1038/s41388-020-01570-y} }
D. Panagiotopoulos, V.S.	Η μινωική Κουμάσα και η ευρύτερη περιοχή των Αστερουσίων ως διεπιστημονική πρόκληση [BibTeX]	2022	Τα Αστερούσια του μύθου και της παράδοσης, pp. 19-43	incollection
BibTeX: @incollection{D.Panagiotopoulos2022, author = {D. Panagiotopoulos, V. Savvatianou}, title = {Η μινωική Κουμάσα και η ευρύτερη περιοχή των Αστερουσίων ως διεπιστημονική πρόκληση}, booktitle = {Τα Αστερούσια του μύθου και της παράδοσης}, year = {2022}, pages = {19-43} }
Dame, J., Nüsser, M., Schmidt, S. and Zang, C.	Socio-hydrological dynamics and water conflicts in the upper Huasco valley, Chile [BibTeX]	2023	Frontiers in Water Vol. 5	article	DOI
BibTeX: @article{Dame2023, author = {Juliane Dame and Marcus Nüsser and Susanne Schmidt and Carina Zang}, title = {Socio-hydrological dynamics and water conflicts in the upper Huasco valley, Chile}, journal = {Frontiers in Water}, publisher = {Frontiers Media SA}, year = {2023}, volume = {5}, doi = {https://doi.org/10.3389/frwa.2023.1100977} }
Damo, E., Agarwal, A. and Simonetti, M.	Activation of β2-Adrenergic Receptors in Microglia Alleviates Neuropathic Hypersensitivity in Mice [Abstract] [BibTeX]	2023	Cells Vol. 12(2), pp. 284	article	DOI URL
Abstract: Drugs enhancing the availability of noradrenaline are gaining prominence in the therapy of chronic neuropathic pain. However, underlying mechanisms are not well understood, and research has thus far focused on α2-adrenergic receptors and neuronal excitability. Adrenergic receptors are also expressed on glial cells, but their roles toward antinociception are not well deciphered. This study addresses the contribution of β2-adrenergic receptors (β2-ARs) to the therapeutic modulation of neuropathic pain in mice. We report that selective activation of β2-ARs with Formoterol inhibits pro-inflammatory signaling in microglia ex vivo and nerve injury-induced structural remodeling and functional activation of microglia in vivo. Systemic delivery of Formoterol inhibits behaviors related to neuropathic pain, such as mechanical hypersensitivity, cold allodynia as well as the aversive component of pain, and reverses chronically established neuropathic pain. Using conditional gene targeting for microglia-specific deletion of β2-ARs, we demonstrate that the anti-allodynic effects of Formoterol are primarily mediated by microglia. Although Formoterol also reduces astrogliosis at late stages of neuropathic pain, these functions are unrelated to β2-AR signaling in microglia. Our results underline the value of developing microglial β2-AR agonists for relief from neuropathic pain and clarify mechanistic underpinnings.
BibTeX: @article{Damo2023, author = {Elisa Damo, Amit Agarwal, Manuela Simonetti}, title = {Activation of β2-Adrenergic Receptors in Microglia Alleviates Neuropathic Hypersensitivity in Mice}, journal = {Cells}, publisher = {MDPI AG}, year = {2023}, volume = {12}, number = {2}, pages = {284}, url = {https://www.mdpi.com/2073-4409/12/2/284/pdf}, doi = {https://doi.org/10.3390/cells12020284} }
Das, S., Sharma, M.C., Murari, M.K., Nüsser, M. and Schmidt, S.	Half-a-century (1971–2020) of glacier shrinkage and climatic variability in the Bhaga basin, western Himalaya [BibTeX]	2023	Journal of Mountain Science Vol. 20(2), pp. 299-324	article	DOI
BibTeX: @article{Das2023, author = {Suresh Das and Milap Chand Sharma and Madhav Krishna Murari and Marcus Nüsser and Susanne Schmidt}, title = {Half-a-century (1971–2020) of glacier shrinkage and climatic variability in the Bhaga basin, western Himalaya}, journal = {Journal of Mountain Science}, publisher = {Springer Science and Business Media LLC}, year = {2023}, volume = {20}, number = {2}, pages = {299--324}, doi = {https://doi.org/10.1007/s11629-022-7598-9} }
De Pree, C.G., Galván-Madrid, R., Goss, W.M., Klessen, R.S., Mac Low, M.-M., Peters, T., Wilner, D., Bates, J., Melo, T., Presler-Marshall, B. and Webb-Forgus, R.	Flux Density Variations at 3.6 cm in the Massive Star-forming Region W49A [BibTeX]	2018	The Astrophysical Journal Vol. 863(1), pp. L9	article	DOI
BibTeX: @article{DePree2018, author = {De Pree, C. G. and Galván-Madrid, R. and Goss, W. M. and Klessen, R. S. and Mac Low, M.-M. and Peters, T. and Wilner, D. and Bates, J. and Melo, T. and Presler-Marshall, B. and Webb-Forgus, R.}, title = {Flux Density Variations at 3.6 cm in the Massive Star-forming Region W49A}, journal = {The Astrophysical Journal}, year = {2018}, volume = {863}, number = {1}, pages = {L9}, doi = {https://doi.org/10.3847/2041-8213/aad631} }
Devant, J.M., Hofhaus, G., Bhella, D. and Hansman, G.S.	Heterologous expression of human norovirus GII.4 VP1 leads to assembly of T=4 virus-like particles [Abstract] [BibTeX]	2019	Antiviral Research Vol. 168, pp. 175-182	article	DOI URL
Abstract: Human noroviruses are a leading cause of acute gastroenteritis, yet there are still no vaccines or antivirals available. Expression of the norovirus capsid protein (VP1) in insect cells typically results in the formation of virus-like particles (VLPs) that are morphologically and antigenically comparable to native virions. Indeed, several different norovirus VLP candidates are currently used in clinical trials. So far, structural analysis of norovirus VLPs showed that the capsid has a T = 3 icosahedral symmetry and is composed of 180 copies of VP1 that are folded into three quasi-equivalent subunits (A, B, and C). In this study, the VLP structures of two norovirus GII.4 genetic variants that were identified in 1974 and 2012 were determined using cryo-EM. Surprisingly, we found that greater than 95% of these GII.4 VLPs were larger than virions and 3D reconstruction showed that these VLPs exhibited T = 4 icosahedral symmetry. We also discovered that the T = 4 VLPs presented several novel structural features. The T = 4 particles assembled from 240 copies of VP1 that adopted four quasi-equivalent conformations (A, B, C, and D) and formed two distinct dimers, A/B and C/D. The protruding domains were elevated ∼21 Å off the capsid shell, which was ∼7 Å more than in the previously studied GII.10 T = 3 VLPs. A small cavity and flap-like structure at the icosahedral two-fold axis disrupted the contiguous T = 4 shell. Overall, our findings indicated that GII.4 VP1 sequences assemble into T = 4 VLPs and these larger particles might have important consequences for VLP-based vaccine development.
BibTeX: @article{Devant2019, author = {Jessica M. Devant and Götz Hofhaus and David Bhella and Grant S. Hansman}, title = {Heterologous expression of human norovirus GII.4 VP1 leads to assembly of T=4 virus-like particles}, journal = {Antiviral Research}, publisher = {Elsevier BV}, year = {2019}, volume = {168}, pages = {175--182}, url = {http://www.sciencedirect.com/science/article/pii/S0166354219301998}, doi = {https://doi.org/10.1016/j.antiviral.2019.05.010} }
Devant, J., Hofhaus, G. and Hansman, G.	Novel Structural Features of Human Norovirus Capsid [BibTeX]	2019		article	DOI
BibTeX: @article{Devant2019a, author = {Devant, Jessica and Hofhaus, Götz and Hansman, Grant}, title = {Novel Structural Features of Human Norovirus Capsid}, year = {2019}, doi = {https://doi.org/10.1101/528240} }
Devant, J.M. and Hansman, G.S.	Structural heterogeneity of a human norovirus vaccine candidate [BibTeX]	2021	Virology Vol. 553, pp. 23-34	article	DOI
BibTeX: @article{Devant2021, author = {Jessica M. Devant and Grant S. Hansman}, title = {Structural heterogeneity of a human norovirus vaccine candidate}, journal = {Virology}, publisher = {Elsevier BV}, year = {2021}, volume = {553}, pages = {23--34}, doi = {https://doi.org/10.1016/j.virol.2020.10.005} }
Dewenter, M., Pan, J., Knödler, L., Tzschöckel, N., Henrich, J., Cordero, J., Dobreva, G., Lutz, S., Backs, J., Wieland, T. and Vettel, C.	Chronic isoprenaline/phenylephrine vs. exclusive isoprenaline stimulation in mice: critical contribution of alpha1-adrenoceptors to early cardiac stress responses [BibTeX]	2022	Basic Research in Cardiology Vol. 117(1)	article	DOI
BibTeX: @article{Dewenter2022, author = {Matthias Dewenter and Jianyuan Pan and Laura Knödler and Niklas Tzschöckel and Julian Henrich and Julio Cordero and Gergana Dobreva and Susanne Lutz and Johannes Backs and Thomas Wieland and Christiane Vettel}, title = {Chronic isoprenaline/phenylephrine vs. exclusive isoprenaline stimulation in mice: critical contribution of alpha1-adrenoceptors to early cardiac stress responses}, journal = {Basic Research in Cardiology}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {117}, number = {1}, doi = {https://doi.org/10.1007/s00395-022-00920-z} }
Diernfellner, A.C. and Brunner, M.	Phosphorylation Timers in the Neurospora crassa Circadian Clock [BibTeX]	2020	Journal of Molecular Biology Vol. 432(12), pp. 3449-3465	article	DOI
BibTeX: @article{Diernfellner2020, author = {Axel C.R. Diernfellner and Michael Brunner}, title = {Phosphorylation Timers in the Neurospora crassa Circadian Clock}, journal = {Journal of Molecular Biology}, publisher = {Elsevier BV}, year = {2020}, volume = {432}, number = {12}, pages = {3449--3465}, doi = {https://doi.org/10.1016/j.jmb.2020.04.004} }
Dietrich, S., Oleś, M., Lu, J., Sellner, L., Anders, S., Velten, B., Wu, B., Hüllein, J., da Silva Liberio, M., Walther, T., Wagner, L., Rabe, S., Ghidelli-Disse, S., Bantscheff, M., Oleś, A.K., Słabicki, M., Mock, A., Oakes, C.C., Wang, S., Oppermann, S., Lukas, M., Kim, V., Sill, M., Benner, A., Jauch, A., Sutton, L.A., Young, E., Rosenquist, R., Liu, X., Jethwa, A., Lee, K.S., Lewis, J., Putzker, K., Lutz, C., Rossi, D., Mokhir, A., Oellerich, T., Zirlik, K., Herling, M., Nguyen-Khac, F., Plass, C., Andersson, E., Mustjoki, S., von Kalle, C., Ho, A.D., Hensel, M., Dürig, J., Ringshausen, I., Zapatka, M., Huber, W. and Zenz, T.	Drug-perturbation-based stratification of blood cancer [Abstract] [BibTeX]	2017	The Journal of Clinical Investigation Vol. 128(1), pp. 427-445	article	DOI URL
Abstract: As new generations of targeted therapies emerge and tumor genome sequencing discovers increasingly comprehensive mutation repertoires, the functional relationships of mutations to tumor phenotypes remain largely unknown. Here, we measured ex vivo sensitivity of 246 blood cancers to 63 drugs alongside genome, transcriptome, and DNA methylome analysis to understand determinants of drug response. We assembled a primary blood cancer cell encyclopedia data set that revealed disease-specific sensitivities for each cancer. Within chronic lymphocytic leukemia (CLL), responses to 62% of drugs were associated with 2 or more mutations, and linked the B cell receptor (BCR) pathway to trisomy 12, an important driver of CLL. Based on drug responses, the disease could be organized into phenotypic subgroups characterized by exploitable dependencies on BCR, mTOR, or MEK signaling and associated with mutations, gene expression, and DNA methylation. Fourteen percent of CLLs were driven by mTOR signaling in a non--BCR-dependent manner. Multivariate modeling revealed immunoglobulin heavy chain variable gene (IGHV) mutation status and trisomy 12 as the most important modulators of response to kinase inhibitors in CLL. Ex vivo drug responses were associated with outcome. This study overcomes the perception that most mutations do not influence drug response of cancer, and points to an updated approach to understanding tumor biology, with implications for biomarker discovery and cancer care.
BibTeX: @article{Dietrich2017, author = {Sascha Dietrich and Małgorzata Oleś and Junyan Lu and Leopold Sellner and Simon Anders and Britta Velten and Bian Wu and Jennifer Hüllein and Michelle da Silva Liberio and Tatjana Walther and Lena Wagner and Sophie Rabe and Sonja Ghidelli-Disse and Marcus Bantscheff and Andrzej K. Oleś and Mikołaj Słabicki and Andreas Mock and Christopher C. Oakes and Shihui Wang and Sina Oppermann and Marina Lukas and Vladislav Kim and Martin Sill and Axel Benner and Anna Jauch and Lesley Ann Sutton and Emma Young and Richard Rosenquist and Xiyang Liu and Alexander Jethwa and Kwang Seok Lee and Joe Lewis and Kerstin Putzker and Christoph Lutz and Davide Rossi and Andriy Mokhir and Thomas Oellerich and Katja Zirlik and Marco Herling and Florence Nguyen-Khac and Christoph Plass and Emma Andersson and Satu Mustjoki and Christof von Kalle and Anthony D. Ho and Manfred Hensel and Jan Dürig and Ingo Ringshausen and Marc Zapatka and Wolfgang Huber and Thorsten Zenz}, title = {Drug-perturbation-based stratification of blood cancer}, journal = {The Journal of Clinical Investigation}, publisher = {The American Society for Clinical Investigation}, year = {2017}, volume = {128}, number = {1}, pages = {427--445}, url = {https://www.jci.org/articles/view/93801}, doi = {https://doi.org/10.1172/jci93801} }
	Image, Text, Stone [BibTeX]	2022		book	DOI
BibTeX: @book{Dietrich2022,, title = {Image, Text, Stone}, publisher = {De Gruyter}, year = {2022}, doi = {https://doi.org/10.1515/9783110775761} }
Dittmayer, C., Völcker, E., Wacker, I., Schröder, R. and Bachmann, S.	Scanning electron microscopy of thin sections: A technique to overcome limitations in kidney ultrastructural research [BibTeX]	2017	Ultrastructural Pathology Vol. 41(1), pp. 119-120	article	DOI
BibTeX: @article{Dittmayer2017, author = {Dittmayer, Carsten and Völcker, Eckhard and Wacker, Irene and Schröder, Rasmus and Bachmann, Sebastian}, title = {Scanning electron microscopy of thin sections: A technique to overcome limitations in kidney ultrastructural research}, journal = {Ultrastructural Pathology}, publisher = {Taylor & Francis}, year = {2017}, volume = {41}, number = {1}, pages = {119--120}, note = {PMID: 28230506}, doi = {https://doi.org/10.1080/01913123.2016.1272165} }
Dittmayer, C., Völcker, E., Wacker, I., Schröder, R.R. and Bachmann, S.	Modern field emission scanning electron microscopy provides new perspectives for imaging kidney ultrastructure [Abstract] [BibTeX]	2018	Kidney International Vol. 94(3), pp. 625-631	article	DOI URL
Abstract: Recent progress in electron microscopy (EM) techniques has opened new pathways to study renal tissue in research and pathology. Modern field emission scanning EM may be utilized to scan thin sections of resin-embedded tissue mounted on a conductive support. Here we sought to achieve automated imaging without the typical limitations of transmission EM with equivalent or superior quality. Extended areas of tissue were either imaged in two (nanotomy) or in three dimensions (volume EM) by serial-section-based array tomography. Single-beam and fast-recording multi-beam field emission scanning EM instruments were compared using perfusion-fixed rodent kidneys. High-resolution scans produced excellent images of tissue, cells, and organelles down to macromolecular complexes. Digital stitching of image tiles in both modes allowed seamless Google Earth--like zooming from overview to regions of interest at the nanoscale. Large datasets were created that can be rapidly shared between scientists of different disciplines or pathologists using open source software. Three-dimensional array tomography of thin sections was followed by segmentation to visualize selected features in a large volume. Furthermore, correlative light-EM enabled the identification of functional information in a structural context. Thus, limitations in biomedical transmission EM can be overcome by introducing field emission scanning EM-based technology that permits high-quality, large field-of-view nanotomy, volume EM, and correlative light-EM modes. Advantages of virtual microscopy in clinical and experimental nephrology are illustrated.
BibTeX: @article{Dittmayer2018, author = {Dittmayer, Carsten and Völcker, Eckhard and Wacker, Irene and Schröder, Rasmus R. and Bachmann, Sebastian}, title = {Modern field emission scanning electron microscopy provides new perspectives for imaging kidney ultrastructure}, journal = {Kidney International}, year = {2018}, volume = {94}, number = {3}, pages = {625--631}, url = {http://www.sciencedirect.com/science/article/pii/S0085253818303910}, doi = {https://doi.org/10.1016/j.kint.2018.05.017} }
Dittrich, G.M., Froese, N., Wang, X., Kroeger, H., Wang, H., Szaroszyk, M., Malek-Mohammadi, M., Cordero, J., Keles, M., Korf-Klingebiel, M., Wollert, K.C., Geffers, R., Mayr, M., Conway, S.J., Dobreva, G., Bauersachs, J. and Heineke, J.	Fibroblast GATA-4 and GATA-6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis [BibTeX]	2021	Vol. 116(1)	article	DOI
BibTeX: @article{Dittrich2021, author = {Gesine M. Dittrich and Natali Froese and Xue Wang and Hannah Kroeger and Honghui Wang and Malgorzata Szaroszyk and Mona Malek-Mohammadi and Julio Cordero and Merve Keles and Mortimer Korf-Klingebiel and Kai C. Wollert and Robert Geffers and Manuel Mayr and Simon J. Conway and Gergana Dobreva and Johann Bauersachs and Joerg Heineke}, title = {Fibroblast GATA-4 and GATA-6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {116}, number = {1}, doi = {https://doi.org/10.1007/s00395-021-00862-y} }
Dkhil, S.B., Perkhun, P., Luo, C., Müller, D., Alkarsifi, R., Barulina, E., Quiroz, Y.A.A., Margeat, O., Dubas, S.T., Koganezawa, T., Kuzuhara, D., Yoshimoto, N., Caddeo, C., Mattoni, A., Zimmermann, B., Würfel, U., Pfannmöller, M., Bals, S., Ackermann, J. and Videlot-Ackermann, C.	Direct Correlation of Nanoscale Morphology and Device Performance to Study Photocurrent Generation in Donor-Enriched Phases of Polymer Solar Cells [BibTeX]	2020	ACS Applied Materials & Interfaces Vol. 12(25), pp. 28404-28415	article	DOI
BibTeX: @article{Dkhil2020, author = {Sadok Ben Dkhil and Pavlo Perkhun and Chieh Luo and David Müller and Riva Alkarsifi and Elena Barulina and Yatzil Alejandra Avalos Quiroz and Olivier Margeat and Stephan Thierry Dubas and Tomoyuki Koganezawa and Daiki Kuzuhara and Noriyuki Yoshimoto and Claudia Caddeo and Alessandro Mattoni and Birger Zimmermann and Uli Würfel and Martin Pfannmöller and Sara Bals and Jörg Ackermann and Christine Videlot-Ackermann}, title = {Direct Correlation of Nanoscale Morphology and Device Performance to Study Photocurrent Generation in Donor-Enriched Phases of Polymer Solar Cells}, journal = {ACS Applied Materials & Interfaces}, publisher = {American Chemical Society (ACS)}, year = {2020}, volume = {12}, number = {25}, pages = {28404--28415}, doi = {https://doi.org/10.1021/acsami.0c05884} }
Dobersch, S., Rubio, K., Singh, I., Günther, S., Graumann, J., Cordero, J., Castillo-Negrete, R., Huynh, M.B., Mehta, A., Braubach, P., Cabrera-Fuentes, H., Bernhagen, J., Chao, C.-M., Bellusci, S., Günther, A., Preissner, K.T., Kugel, S., Dobreva, G., Wygrecka, M., Braun, T., Papy-Garcia, D. and Barreto, G.	Positioning of nucleosomes containing upgamma-H2AX precedes active DNA demethylation and transcription initiation [BibTeX]	2021	Vol. 12(1)	article	DOI
BibTeX: @article{Dobersch2021, author = {Stephanie Dobersch and Karla Rubio and Indrabahadur Singh and Stefan Günther and Johannes Graumann and Julio Cordero and Rafael Castillo-Negrete and Minh Bao Huynh and Aditi Mehta and Peter Braubach and Hector Cabrera-Fuentes and Jürgen Bernhagen and Cho-Ming Chao and Saverio Bellusci and Andreas Günther and Klaus T. Preissner and Sita Kugel and Gergana Dobreva and Malgorzata Wygrecka and Thomas Braun and Dulce Papy-Garcia and Guillermo Barreto}, title = {Positioning of nucleosomes containing upgamma-H2AX precedes active DNA demethylation and transcription initiation}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, doi = {https://doi.org/10.1038/s41467-021-21227-y} }
Dodonova, S.O., Aderhold, P., Kopp, J., Ganeva, I., Röhling, S., Hagen, W.J.H., Sinning, I., Wieland, F. and Briggs, J.A.G.	9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments [Abstract] [BibTeX]	2017	eLife Vol. 6, pp. e26691	article	DOI URL
Abstract: COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly.
BibTeX: @article{Dodonova2017, author = {Dodonova, Svetlana O. and Aderhold, Patrick and Kopp, Juergen and Ganeva, Iva and Röhling, Simone and Hagen, Wim J. H. and Sinning, Irmgard and Wieland, Felix and Briggs, John A. G.}, title = {9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2017}, volume = {6}, pages = {e26691}, note = {28621666[pmid]}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28621666}, doi = {https://doi.org/10.7554/eLife.26691} }
Sormani, M.C., Treß, R.G., Ridley, M., Glover, S.C.O., Klessen, R.S., Binney, J., Magorrian, J. and Smith, R.	A theoretical explanation for the Central Molecular Zone asymmetry [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 475(2), pp. 2383-2402	article	DOI
BibTeX: @article{doi:10.1093/mnras/stx3258, author = {Sormani, Mattia C. and Treß, Robin G. and Ridley, Matthew and Glover, Simon C. O. and Klessen, Ralf S. and Binney, James and Magorrian, John and Smith, Rowan}, title = {A theoretical explanation for the Central Molecular Zone asymmetry}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {475}, number = {2}, pages = {2383--2402}, doi = {https://doi.org/10.1093/mnras/stx3258} }
Domínguez, R., Farias, J.P., Fellhauer, M. and Klessen, R.S.	Are hierarchically formed embedded star clusters surviving gas expulsion depending on their initial conditions? [Abstract] [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 508(4), pp. 5410-5424	article	DOI
Abstract: ABSTRACT We investigate the dissolution process of young embedded star clusters with different primordial mass segregation levels using fractal distributions by means of N-body simulations. We combine several star clusters in virial and subvirial global states with Plummer and uniform density profiles to mimic the gas. The star clusters have masses of Mstars = 500 M⊙ that follow an initial mass function where the stars have maximum distance from the centre of r = 1.5 pc. The clusters are placed in clouds that at the same radius have masses of Mcloud = 2000 M⊙, resulting in star formation efficiency of 0.2. We remove the background potential instantaneously at a very early phase, mimicking the most destructive scenario of gas expulsion. The evolution of the fraction of bound stellar mass is followed for a total of 16 Myr for simulations with stellar evolution and without. We compare our results with previous works using equal-mass particles where an analytical physical model was used to estimate the bound mass fraction after gas expulsion. We find that independent of the initial condition, the fraction of bound stellar mass can be well predicted just right after the gas expulsion but tends to be lower at later stages, as these systems evolve due to the stronger two-body interactions resulting from the inclusion of a realistic initial mass function. This discrepancy is independent of the primordial mass segregation level.
BibTeX: @article{Dominguez2021, author = {R Domínguez, J P Farias, M Fellhauer, Ralf S Klessen}, title = {Are hierarchically formed embedded star clusters surviving gas expulsion depending on their initial conditions?}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {508}, number = {4}, pages = {5410--5424}, doi = {https://doi.org/10.1093/mnras/stab2644} }
Dom\inguez, R., Pellegrini, E.W., Klessen, R.S. and Rahner, D.	Modelling the formation of two stellar generations in massive star clusters: the case of 30 Doradus [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 520(4), pp. 5600-5612	article	DOI
BibTeX: @article{Dominguez2023, author = {R Dom\inguez and Eric W Pellegrini and Ralf S Klessen and Daniel Rahner}, title = {Modelling the formation of two stellar generations in massive star clusters: the case of 30 Doradus}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {520}, number = {4}, pages = {5600--5612}, doi = {https://doi.org/10.1093/mnras/stad482} }
Dong, C. and Menzel, L.	Recent snow cover changes over central European low mountain ranges [BibTeX]	2019	Hydrological Processes Vol. 34(2), pp. 321-338	article	DOI
BibTeX: @article{Dong2019, author = {Chunyu Dong and Lucas Menzel}, title = {Recent snow cover changes over central European low mountain ranges}, journal = {Hydrological Processes}, publisher = {Wiley}, year = {2019}, volume = {34}, number = {2}, pages = {321--338}, doi = {https://doi.org/10.1002/hyp.13586} }
Doroudgar, S., Hofmann, C., Boileau, E., Malone, B., Riechert, E., Gorska, A.A., Jakobi, T., Sandmann, C., Jürgensen, L., Kmietczyk, V., Malovrh, E., Burghaus, J., Rettel, M., Stein, F., Younesi, F., Friedrich, U.A., Mauz, V., Backs, J., Kramer, G., Katus, H.A., Dieterich, C. and Völkers, M.	Monitoring Cell-Type–Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress [BibTeX]	2019	Circulation Research Vol. 125(4), pp. 431-448	article	DOI
BibTeX: @article{Doroudgar2019, author = {Shirin Doroudgar and Christoph Hofmann and Etienne Boileau and Brandon Malone and Eva Riechert and Agnieszka A. Gorska and Tobias Jakobi and Clara Sandmann and Lonny Jürgensen and Vivien Kmietczyk and Ellen Malovrh and Jana Burghaus and Mandy Rettel and Frank Stein and Fereshteh Younesi and Ulrike A. Friedrich and Victoria Mauz and Johannes Backs and Günter Kramer and Hugo A. Katus and Christoph Dieterich and Mirko Völkers}, title = {Monitoring Cell-Type–Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress}, journal = {Circulation Research}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, year = {2019}, volume = {125}, number = {4}, pages = {431--448}, doi = {https://doi.org/10.1161/circresaha.119.314817} }
Druschke, M., Schauer, A.T.P., Glover, S.C.O. and Klessen, R.S.	Shape and spin of minihaloes: from large scales to the centres [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 481(3), pp. 3266-3277	article	DOI
BibTeX: @article{Druschke2018, author = {Maik Druschke and Anna T P Schauer and Simon C O Glover and Ralf S Klessen}, title = {Shape and spin of minihaloes: from large scales to the centres}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {481}, number = {3}, pages = {3266--3277}, doi = {https://doi.org/10.1093/mnras/sty2443} }
Druschke, M., Schauer, A.T.P., Glover, S.C.O. and Klessen, R.S.	Shape and spin of minihaloes – II. The effect of streaming velocities [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 498(4), pp. 4839-4852	article	DOI
BibTeX: @article{Druschke2020, author = {Maik Druschke and Anna T P Schauer and Simon C O Glover and Ralf S Klessen}, title = {Shape and spin of minihaloes – II. The effect of streaming velocities}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {498}, number = {4}, pages = {4839--4852}, doi = {https://doi.org/10.1093/mnras/staa2605} }
Durrieu, L., Kirrmaier, D., Schneidt, T., Kats, I., Raghavan, S., Hufnagel, L., Saunders, T.E. and Knop, M.	Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis [Abstract] [BibTeX]	2018	Molecular Systems Biology Vol. 14(9), pp. e8355	article	DOI
Abstract: Abstract Embryogenesis relies on instructions provided by spatially organized signaling molecules known as morphogens. Understanding the principles behind morphogen distribution and how cells interpret locally this information remains a major challenge in developmental biology. Here, we introduce morphogen-age measurements as a novel approach to test models of morphogen gradient formation. Using a tandem fluorescent timer as a protein age sensor, we find a gradient of increasing age of Bicoid along the anterior--posterior axis in the early Drosophila embryo. Quantitative analysis of the protein age distribution across the embryo reveals that the synthesis--diffusion--degradation model is the most likely model underlying Bicoid gradient formation, and rules out other hypotheses for gradient formation. Moreover, we show that the timer can detect transitions in the dynamics associated with syncytial cellularization. Our results provide new insight into Bicoid gradient formation and demonstrate how morphogen-age information can complement knowledge about movement, abundance, and distribution, which should be widely applicable to other systems.
BibTeX: @article{Durrieu2018, author = {Durrieu, Lucia and Kirrmaier, Daniel and Schneidt, Tatjana and Kats, Ilia and Raghavan, Sarada and Hufnagel, Lars and Saunders, Timothy E. and Knop, Michael}, title = {Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis}, journal = {Molecular Systems Biology}, year = {2018}, volume = {14}, number = {9}, pages = {e8355}, doi = {https://doi.org/10.15252/msb.20188355} }
Ebert, M.P., Meindl-Beinker, N.M., Gutting, T., Maenz, M., Betge, J., Schulte, N., Zhan, T., Weidner, P., Burgermeister, E., Hofheinz, R., Vogel, A., Angermeier, S., Bolling, C., de Wit, M., Jakobs, R., Karthaus, M., Stocker, G., Thuss-Patience, P., Leidig, T., Gaiser, T., Kather, J.N. and Haertel, N.	Second-line therapy with nivolumab plus ipilimumab for older patients with oesophageal squamous cell cancer (RAMONA): a multicentre, open-label phase 2 trial [BibTeX]	2022	The Lancet Healthy Longevity Vol. 3(6), pp. e417-e427	article	DOI URL
BibTeX: @article{Ebert2022, author = {Matthias P Ebert, Nadja M Meindl-Beinker, Tobias Gutting, Martin Maenz, Johannes Betge, Nadine Schulte, Tianzuo Zhan, Philip Weidner, Elke Burgermeister, Ralf Hofheinz, Arndt Vogel, Stefan Angermeier, Claus Bolling, Maike de Wit, Ralf Jakobs, Meinolf Karthaus, Gertraud Stocker, Peter Thuss-Patience, Tobias Leidig, Timo Gaiser, Jakob N Kather, Nicolai Haertel}, title = {Second-line therapy with nivolumab plus ipilimumab for older patients with oesophageal squamous cell cancer (RAMONA): a multicentre, open-label phase 2 trial}, journal = {The Lancet Healthy Longevity}, publisher = {Elsevier BV}, year = {2022}, volume = {3}, number = {6}, pages = {e417--e427}, url = {https://api.elsevier.com/content/article/PII:S2666756822001167?httpAccept=text/xml}, doi = {https://doi.org/10.1016/S2666-7568(22)00116-7} }
Effinger, M., Maylein, L. and Šimek, J.	Von der elektronischen Bibliothek zur innovativen Forschungsinfrastruktur [BibTeX]	2019	Bibliothek Forschung und Praxis Vol. 43(2), pp. 311-323	article	DOI
BibTeX: @article{Effinger2019, author = {Maria Effinger and Leonhard Maylein and Jakub Šimek}, title = {Von der elektronischen Bibliothek zur innovativen Forschungsinfrastruktur}, journal = {Bibliothek Forschung und Praxis}, publisher = {Walter de Gruyter GmbH}, year = {2019}, volume = {43}, number = {2}, pages = {311--323}, doi = {https://doi.org/10.1515/bfp-2019-2067} }
Engel, U.	Four-Channel Super-Resolution Imaging by 3-D Structured Illumination [Abstract] [BibTeX]	2017	Super-Resolution Microscopy: Methods and Protocols, pp. 79-94	inbook	DOI
Abstract: Multichannel imaging is used as a readout of relative localization of two or more components and is often the first step in investigating functional ensembles in cells. However, the localization volume of diffraction-limited light microscopy (approx. 200 nm by 500 nm) can accommodate hundred of proteins, calling for increased resolution for these types of analyses. Here, we present a protocol for 4-channel imaging using structured illumination microscopy (SIM), which increases resolution by a factor of two. We use adherent, fixed cells to identify the localization of adhesion proteins using immunofluorescence and fluorescent proteins. We discuss how labeling with the necessary brightness is achieved and how data has to be processed for colocalization analysis.
BibTeX: @inbook{Engel2017, author = {Engel, Ulrike}, title = {Four-Channel Super-Resolution Imaging by 3-D Structured Illumination}, booktitle = {Super-Resolution Microscopy: Methods and Protocols}, publisher = {Springer New York}, year = {2017}, pages = {79--94}, doi = {https://doi.org/10.1007/978-1-4939-7265-4_7} }
Engelmann, L., Thierauf, J., Laureano, N.K., Stark, H.-J., Prigge, E.-S., Horn, D., Freier, K., Grabe, N., Rong, C., Federspil, P., Zaoui, K., Plinkert, P.K., Rotter, N., von Knebel Doeberitz, M., Hess, J. and Affolter, A.	Organotypic Co-Cultures as a Novel 3D Model for Head and Neck Squamous Cell Carcinoma [BibTeX]	2020	Cancers Vol. 12(8), pp. 2330	article	DOI
BibTeX: @article{Engelmann2020, author = {Luca Engelmann and Julia Thierauf and Natalia Koerich Laureano and Hans-Juergen Stark and Elena-Sophie Prigge and Dominik Horn and Kolja Freier and Niels Grabe and Chao Rong and Philippe Federspil and Karim Zaoui and Peter K. Plinkert and Nicole Rotter and Magnus von Knebel Doeberitz and Jochen Hess and Annette Affolter}, title = {Organotypic Co-Cultures as a Novel 3D Model for Head and Neck Squamous Cell Carcinoma}, journal = {Cancers}, publisher = {MDPI AG}, year = {2020}, volume = {12}, number = {8}, pages = {2330}, doi = {https://doi.org/10.3390/cancers12082330} }
Erdmann, P. and Greb, L.	Multidimensional Lewis Acidity: A Consistent Data Set of Chloride, Hydride, Methide, Water and Ammonia Affinities for 183 p-Block Element Lewis Acids [BibTeX]	2021	ChemPhysChem Vol. 22(10), pp. 935-943	article	DOI
BibTeX: @article{Erdmann2021, author = {Philipp Erdmann and Lutz Greb}, title = {Multidimensional Lewis Acidity: A Consistent Data Set of Chloride, Hydride, Methide, Water and Ammonia Affinities for 183 p-Block Element Lewis Acids}, journal = {ChemPhysChem}, publisher = {Wiley}, year = {2021}, volume = {22}, number = {10}, pages = {935--943}, doi = {https://doi.org/10.1002/cphc.202100150} }
Erdmann, P. and Greb, L.	What Distinguishes the Strength and the Effect of a Lewis Acid: Analysis of the Gutmann–Beckett Method [BibTeX]	2021	Angewandte Chemie International Edition	article	DOI
BibTeX: @article{Erdmann2021a, author = {Philipp Erdmann and Lutz Greb}, title = {What Distinguishes the Strength and the Effect of a Lewis Acid: Analysis of the Gutmann–Beckett Method}, journal = {Angewandte Chemie International Edition}, publisher = {Wiley}, year = {2021}, doi = {https://doi.org/10.1002/anie.202114550} }
Fan, Y., Wang, H., Gemmeke, H., Hopp, T. and Hesser, J.	Model-data-driven image reconstruction with neural networks for ultrasound computed tomography breast imaging [BibTeX]	2022	Neurocomputing Vol. 467, pp. 10-21	article	DOI URL
BibTeX: @article{Fan2022, author = {Yuling Fan, Hongjian Wang, Hartmut Gemmeke, Torsten Hopp, Juergen Hesser}, title = {Model-data-driven image reconstruction with neural networks for ultrasound computed tomography breast imaging}, journal = {Neurocomputing}, publisher = {Elsevier BV}, year = {2022}, volume = {467}, pages = {10--21}, url = {https://api.elsevier.com/content/article/PII:S092523122101393X?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.neucom.2021.09.035} }
Farnoud, A., Cui, X., Baumann, I. and Gutheil, E.	Numerical Simulation of the Dispersion and Deposition of a Spray Carried by a Pulsating Airflow in a Patient-Specific Human Nasal Cavity [BibTeX]	2017	Atomization and Sprays Vol. 27	article	DOI
BibTeX: @article{Farnoud2017, author = {Farnoud, Ali and Cui, Xinguang and Baumann, Ingo and Gutheil, Eva}, title = {Numerical Simulation of the Dispersion and Deposition of a Spray Carried by a Pulsating Airflow in a Patient-Specific Human Nasal Cavity}, journal = {Atomization and Sprays}, year = {2017}, volume = {27}, doi = {https://doi.org/10.1615/AtomizSpr.2017020782} }
Feilen, L.P., Haubrich, K., Strecker, P., Probst, S., Eggert, S., Stier, G., Sinning, I., Konietzko, U., Kins, S., Simon, B. and Wild, K.	Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction [Abstract] [BibTeX]	2017	Frontiers in Molecular Neuroscience Vol. 10, pp. 140	article	DOI
Abstract: Physiological function and pathology of the Alzheimer's disease causing amyloid precursor protein (APP) are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs). The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD) including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR) techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.
BibTeX: @article{Feilen2017, author = {Feilen, Lukas P. and Haubrich, Kevin and Strecker, Paul and Probst, Sabine and Eggert, Simone and Stier, Gunter and Sinning, Irmgard and Konietzko, Uwe and Kins, Stefan and Simon, Bernd and Wild, Klemens}, title = {Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction}, journal = {Frontiers in Molecular Neuroscience}, year = {2017}, volume = {10}, pages = {140}, doi = {https://doi.org/10.3389/fnmol.2017.00140} }
Fetner, R. and Trębicka, J.	Human remains from Bakr Awa, Iraqi Kurdistan, 2017 [BibTeX]	2017	Bioarchaeology of the Near East Vol. 11, pp. 63-69	article
BibTeX: @article{Fetner2017, author = {Fetner, Rafal and Trębicka, Joanna}, title = {Human remains from Bakr Awa, Iraqi Kurdistan, 2017}, journal = {Bioarchaeology of the Near East}, year = {2017}, volume = {11}, pages = {63--69} }
Filbeck, S., Cerullo, F., Paternoga, H., Tsaprailis, G., Joazeiro, C.A. and Pfeffer, S.	Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC [BibTeX]	2021	Molecular Cell Vol. 81(1), pp. 104-114.e6	article	DOI URL
BibTeX: @article{Filbeck2021, author = {Sebastian Filbeck and Federico Cerullo and Helge Paternoga and George Tsaprailis and Claudio A.P. Joazeiro and Stefan Pfeffer}, title = {Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2021}, volume = {81}, number = {1}, pages = {104--114.e6}, url = {https://www.sciencedirect.com/science/article/pii/S1097276520307796}, doi = {https://doi.org/10.1016/j.molcel.2020.11.001} }
Filbeck, S., Cerullo, F., Pfeffer, S. and Joazeiro, C.A.	Ribosome-associated quality-control mechanisms from bacteria to humans [BibTeX]	2022	Molecular Cell Vol. 82(8), pp. 1451-1466	article	DOI URL
BibTeX: @article{Filbeck2022, author = {Sebastian Filbeck, Federico Cerullo, Stefan Pfeffer, Claudio A.P. Joazeiro}, title = {Ribosome-associated quality-control mechanisms from bacteria to humans}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2022}, volume = {82}, number = {8}, pages = {1451--1466}, url = {https://api.elsevier.com/content/article/PII:S1097276522002945?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.molcel.2022.03.038} }
Finlayson, S., Bogacz, B., Mara, H. and Panagiotopoulos, D.	Searching for ancient Aegean administrators: Computational experiments on identical seal impressions [BibTeX]	2021	Journal of Archaeological Science Vol. 136, pp. 105490	article	DOI
BibTeX: @article{Finlayson2021, author = {Sarah Finlayson and Bartosz Bogacz and Hubert Mara and Diamantis Panagiotopoulos}, title = {Searching for ancient Aegean administrators: Computational experiments on identical seal impressions}, journal = {Journal of Archaeological Science}, publisher = {Elsevier BV}, year = {2021}, volume = {136}, pages = {105490}, doi = {https://doi.org/10.1016/j.jas.2021.105490} }
Fiore, F., Dereddi, R.R., Alhalaseh, K., Coban, I., Harb, A. and Agarwal, A.	Norepinephrine regulates Ca²⁺ signals and fate of oligodendrocyte progenitor cells in the cortex [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: AbstractOligodendrocyte precursor cells (OPCs) represent the most abundant group of proliferating cells in the adult central nervous system. OPCs serve as progenitors for oligodendrocyte (OLs) throughout the life, and contribute to developmental and adaptive myelination, and myelin repair during diseased state. OPCs make synaptic and extra-synaptic contacts with axons, and detect and respond to neuronal activity. How OPCs translate the information relayed by the neuronal activity into Ca2+ signals, which in turn influence their fate and survival, is less understood. We developed novel transgenic mouse lines expressing a cytosolic and membrane anchored variants of genetically encoded Ca2+ sensors (GCaMP6f or mGCaMP6s) in OPCs, performed 2-photon microscopy in the somatosensory cortex of the awake behaving mice, and simultaneously monitored intracellular Ca2+ signals and their cell-fate progression. We found Ca2+ signals in OPCs mainly occur within processes and confine to micrometer-size segments called Ca2+ microdomains. Microdomain Ca2+ signals enhanced in OPCs when mice engage in exploratory behavior. OPCs exhibit distinct Ca2+ signals while they proliferate to maintain their precursor pool or differentiate to generate new OL. When mice engaged in exploratory behavior, the cortical projections of noradrenergic neurons in locus coeruleus showed increased firing rate and norepinephrine release. Norepinephrine activated all three subtypes of alpha1 adrenergic receptor expressed by OPCs and evoked intracellular Ca2+ increase in OPCs. A chemogenetic activation of noradrenergic neurons, promoted differentiation of cortical OPCs into OL, and at the same time suppressed OPC proliferation rate. Hence, we uncovered that various cell types of oligodendrocyte lineage exhibits unique signatures of Ca2+ activity, which these cells might integrate for making their fate decisions, and norepinephrine signaling can be a potent regulator of OPC fate.
BibTeX: @article{Fiore2022, author = {Frederic Fiore, Ram R. Dereddi, Khaleel Alhalaseh, Ilknur Coban, Ali Harb, Amit Agarwal}, title = {Norepinephrine regulates Ca²⁺ signals and fate of oligodendrocyte progenitor cells in the cortex}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.08.31.505555} }
Fotiadou, E., Konopczyŉski, T., Hesser, J. and Vullings, R.	End-to-end trained encoder–decoder convolutional neural network for fetal electrocardiogram signal denoising [BibTeX]	2020	Physiological Measurement Vol. 41(1), pp. 015005	article	DOI
BibTeX: @article{Fotiadou2020, author = {Eleni Fotiadou and Tomasz Konopczyŉski and Jürgen Hesser and Rik Vullings}, title = {End-to-end trained encoder–decoder convolutional neural network for fetal electrocardiogram signal denoising}, journal = {Physiological Measurement}, publisher = {IOP Publishing}, year = {2020}, volume = {41}, number = {1}, pages = {015005}, doi = {https://doi.org/10.1088/1361-6579/ab69b9} }
François, P., Caffau, E., Bonifacio, P., Spite, M., Spite, F., Cayrel, R., Christlieb, N., Gallagher, A.J., Klessen, R., Koch, A., Ludwig, H.-G., Monaco, L., Plez, B., Steffen, M. and Zaggia, S.	TOPoS. V. Abundance ratios in a sample of very metal-poor turn-off stars [BibTeX]	2018	Astronomy & Astrophysics Vol. 620, pp. A187	article	DOI
BibTeX: @article{Francois2018, author = {François, P. and Caffau, E. and Bonifacio, P. and Spite, M. and Spite, F. and Cayrel, R. and Christlieb, N. and Gallagher, A. J. and Klessen, R. and Koch, A. and Ludwig, H.-G. and Monaco, L. and Plez, B. and Steffen, M. and Zaggia, S.}, title = {TOPoS. V. Abundance ratios in a sample of very metal-poor turn-off stars}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2018}, volume = {620}, pages = {A187}, doi = {https://doi.org/10.1051/0004-6361/201834375} }
Franeck, A., Walch, S., Seifried, D., Clarke, S.D., Ossenkopf-Okada, V., Glover, S.C.O., Klessen, R.S., Girichidis, P., Naab, T., Wünsch, R., Clark, P.C., Pellegrini, E. and Peters, T.	Synthetic [C II] emission maps of a simulated molecular cloud in formation [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 481(4), pp. 4277-4299	article	DOI
BibTeX: @article{Franeck2018, author = {Franeck, A. and Walch, S. and Seifried, D. and Clarke, S. D. and Ossenkopf-Okada, V. and Glover, S. C. O. and Klessen, R. S. and Girichidis, P. and Naab, T. and Wünsch, R. and Clark, P. C. and Pellegrini, E. and Peters, T.}, title = {Synthetic [C II] emission maps of a simulated molecular cloud in formation}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {481}, number = {4}, pages = {4277--4299}, doi = {https://doi.org/10.1093/mnras/sty2507} }
Frank, L., Weinmann, R., Erdel, F., Trojanowski, J. and Rippe, K.	Transcriptional Activation of Heterochromatin by Recruitment of dCas9 Activators [BibTeX]	2021	Methods in Molecular Biology, pp. 307-320	incollection	DOI
BibTeX: @incollection{Frank2021, author = {Lukas Frank and Robin Weinmann and Fabian Erdel and Jorge Trojanowski and Karsten Rippe}, title = {Transcriptional Activation of Heterochromatin by Recruitment of dCas9 Activators}, booktitle = {Methods in Molecular Biology}, publisher = {Springer US}, year = {2021}, pages = {307--320}, doi = {https://doi.org/10.1007/978-1-0716-1597-3_17} }
Frank, L., Rademacher, A., Mücke, N., Tirier, S.M., Koeleman, E., Knotz, C., Schumacher, S., Stainczyk, S., Westermann, F., Fröhling, S., Chudasama, P. and Rippe, K.	ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats [BibTeX]	2022	Nucleic Acids Research	article	DOI
BibTeX: @article{Frank2022, author = {Lukas Frank and Anne Rademacher and Norbert Mücke and Stephan M Tirier and Emma Koeleman and Caroline Knotz and Sabrina Schumacher and Sabine A Stainczyk and Frank Westermann and Stefan Fröhling and Priya Chudasama and Karsten Rippe}, title = {ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats}, journal = {Nucleic Acids Research}, publisher = {Oxford University Press (OUP)}, year = {2022}, doi = {https://doi.org/10.1093/nar/gkac113} }
	Sacred Scripture / Sacred Space [BibTeX]	2019		book	DOI
BibTeX: @book{Frese2019,, title = {Sacred Scripture / Sacred Space}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110629156} }
Friedrich, M., Sankowski, R., Bunse, L., Kilian, M., Green, E., Guevara, C.R., Pusch, S., Poschet, G., Sanghvi, K., Hahn, M., Bunse, T., Münch, P., Gegner, H.M., Sonner, J.K., von Landenberg, A., Cichon, F., Aslan, K., Trobisch, T., Schirmer, L., Abu-Sammour, D., Kessler, T., Ratliff, M., Schrimpf, D., Sahm, F., Hopf, C., Heiland, D.H., Schnell, O., Beck, J., Böttcher, C., Fernandez-Zapata, C., Priller, J., Heiland, S., Gutcher, I., Quintana, F.J., von Deimling, A., Wick, W., Prinz, M. and Platten, M.	Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas [BibTeX]	2021	Nature Cancer Vol. 2(7), pp. 723-740	article	DOI
BibTeX: @article{Friedrich2021, author = {Mirco Friedrich and Roman Sankowski and Lukas Bunse and Michael Kilian and Edward Green and Carina Ramallo Guevara and Stefan Pusch and Gernot Poschet and Khwab Sanghvi and Markus Hahn and Theresa Bunse and Philipp Münch and Hagen M. Gegner and Jana K. Sonner and Anna von Landenberg and Frederik Cichon and Katrin Aslan and Tim Trobisch and Lucas Schirmer and Denis Abu-Sammour and Tobias Kessler and Miriam Ratliff and Daniel Schrimpf and Felix Sahm and Carsten Hopf and Dieter H. Heiland and Oliver Schnell and Jürgen Beck and Chotima Böttcher and Camila Fernandez-Zapata and Josef Priller and Sabine Heiland and Ilona Gutcher and Francisco J. Quintana and Andreas von Deimling and Wolfgang Wick and Marco Prinz and Michael Platten}, title = {Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas}, journal = {Nature Cancer}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {2}, number = {7}, pages = {723--740}, doi = {https://doi.org/10.1038/s43018-021-00201-z} }
Froese, N., Cordero, J., Abouissa, A., Trogisch, F.A., Grein, S., Szaroszyk, M., Wang, Y., Gigina, A., Korf-Klingebiel, M., Bosnjak, B., Davenport, C.F., Wiehlmann, L., Geffers, R., Riechert, E., Jürgensen, L., Boileau, E., Lin, Y., Dieterich, C., Förster, R., Bauersachs, J., Ola, R., Dobreva, G., Völkers, M. and Heineke, J.	Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication [BibTeX]	2022	iScience Vol. 25(3), pp. 103965	article	DOI URL
BibTeX: @article{Froese2022, author = {Natali Froese, Julio Cordero, Aya Abouissa, Felix A. Trogisch, Steve Grein, Malgorzata Szaroszyk, Yong Wang, Anna Gigina, Mortimer Korf-Klingebiel, Berislav Bosnjak, Colin F. Davenport, Lutz Wiehlmann, Robert Geffers, Eva Riechert, Lonny Jürgensen, Etienne Boileau, Yanzhu Lin, Christoph Dieterich, Reinhold Förster, Johann Bauersachs, Roxana Ola, Gergana Dobreva, Mirko Völkers, Joerg Heineke}, title = {Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication}, journal = {iScience}, publisher = {Elsevier BV}, year = {2022}, volume = {25}, number = {3}, pages = {103965}, url = {https://api.elsevier.com/content/article/PII:S2589004222002358?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.isci.2022.103965} }
Fromm, L., Falk, S., Flemming, D., Schuller, J.M., Thoms, M., Conti, E. and Hurt, E.	Reconstitution of the complete pathway of ITS2 processing at the pre-ribosome [Abstract] [BibTeX]	2017	Nature Communications Vol. 8(1), pp. 1787	article	DOI
Abstract: Removal of internal transcribed spacer 2 (ITS2) from pre-ribosomal RNA is essential to make functional ribosomes. This complicated processing reaction begins with a single endonucleolytic cleavage followed by exonucleolytic trimming at both new cleavage sites to generate mature 5.8S and 25S rRNA. We reconstituted the 7Stextrightarrow5.8S processing branch within ITS2 using purified exosome and its nuclear cofactors. We find that both Rrp44's ribonuclease activities are required for initial RNA shortening followed by hand over to the exonuclease Rrp6. During the in vitro reaction, ITS2-associated factors dissociate and the underlying `foot' structure of the pre-60S particle is dismantled. 7S pre-rRNA processing is independent of 5S RNP rotation, but 26Stextrightarrow25S trimming is a precondition for subsequent 7Stextrightarrow5.8S processing. To complete the in vitro assay, we reconstituted the entire cycle of ITS2 removal with a total of 18 purified factors, catalysed by the integrated activities of the two participating RNA-processing machines, the Las1 complex and nuclear exosome.
BibTeX: @article{Fromm2017, author = {Fromm, Lisa and Falk, Sebastian and Flemming, Dirk and Schuller, Jan Michael and Thoms, Matthias and Conti, Elena and Hurt, Ed}, title = {Reconstitution of the complete pathway of ITS2 processing at the pre-ribosome}, journal = {Nature Communications}, year = {2017}, volume = {8}, number = {1}, pages = {1787}, doi = {https://doi.org/10.1038/s41467-017-01786-9} }
Fronza, R., Lusic, M., Schmidt, M. and Lucic, B.	Spatial–Temporal Variations in Atmospheric Factors Contribute to SARS-CoV-2 Outbreak [BibTeX]	2020	Viruses Vol. 12(6), pp. 588	article	DOI
BibTeX: @article{Fronza2020, author = {Raffaele Fronza and Marina Lusic and Manfred Schmidt and Bojana Lucic}, title = {Spatial–Temporal Variations in Atmospheric Factors Contribute to SARS-CoV-2 Outbreak}, journal = {Viruses}, publisher = {MDPI AG}, year = {2020}, volume = {12}, number = {6}, pages = {588}, doi = {https://doi.org/10.3390/v12060588} }
de Frutos, F., Ochoa, J.P., Navarro-Peñalver, M., Baas, A., Bjerre, J.V., Zorio, E., Méndez, I., Lorca, R., Verdonschot, J.A., Garc\ia-Granja, P.E., Bilinska, Z., Fatkin, D., Fuentes-Cañamero, M.E., Garc\ia-Pinilla, J.M., Garc\ia-Álvarez, M.I., Girolami, F., Barriales-Villa, R., D\iez-López, C., Lopes, L.R., Wahbi, K., Garc\ia-Álvarez, A., Rodr\iguez-Sánchez, I., Rekondo-Olaetxea, J., Rodr\iguez-Palomares, J.F., Gallego-Delgado, M., Meder, B., Kubanek, M., Hansen, F.G., Restrepo-Córdoba, M.A., Palomino-Doza, J., Ruiz-Guerrero, L., Sarquella-Brugada, G., Perez-Perez, A.J., Bermúdez-Jiménez, F.J., Ripoll-Vera, T., Rasmussen, T.B., Jansen, M., Sabater-Molina, M., Elliot, P.M., Garcia-Pavia, P., Cabrera-Romero, E., Cobo-Marcos, M., Escobar-Lopez, L., Dom\inguez, F., González-López, E., Gimeno-Blanes, J.R., Dooijes, D., Ledesma, B.L., Fortea, I.R., Bermejo, J., Espinosa, M.A., Fernández, A.I., Vilches, S., Gómez, C., Gómez, J., Coto, E., Reguero, J.J.R., Heymans, S., Brunner, H., López-D\iaz, J., Truszkowska, G., Ploski, R., Chmielewski, P., Johnson, R., Robles-Mezcua, A., D\iaz-Expósito, A., Pérez-Cabeza, A.I., Jiménez-Rubio, C., Payá, V.C., Favilli, S., Syrris, P., Cannie, D., Billon, C., Lopez-Sainz, A., Calvo, M., de Bobadilla, Á.C.F., Onaindia-Gandarias, J.J., Gaztañaga-Arantzamendi, L., Zamarreño-Golvano, E., Limeres, J., Gutiérrez-Garc\ia, L., Villacorta, E., Haas, J., Krebsova, A., Mogensen, J., Cesar, S., Campuzano, O., Gutiérrez, R.F., Alvarez-Rubio, J., Cremer-Luengos, D., Antoniutti, G., Caimi-Martinez, F., Mac\ias, R., Jiménez-Jáimez, J., Peña-Peña, M.L., López, S.L.D.-A., Acereda, T.P., Corada, B.A., Piqueras-Flores, J., Negreira-Caamaño, M., R\io, J.M.-d., Jiménez, M.V.M., Villanueva, E., Gonzáles, J.L., Fernández, A., Toscanini, U., Favaloro, L.E. and D\iez, C.H.	Natural History of MYH7-Related Dilated Cardiomyopathy [BibTeX]	2022	Journal of the American College of Cardiology Vol. 80(15), pp. 1447-1461	article	DOI
BibTeX: @article{Frutos2022, author = {Fernando de Frutos and Juan Pablo Ochoa and Marina Navarro-Peñalver and Annette Baas and Jesper Vandborg Bjerre and Esther Zorio and Irene Méndez and Rebeca Lorca and Job A.J. Verdonschot and Pablo Elpidio Garc\ia-Granja and Zofia Bilinska and Diane Fatkin and M. Eugenia Fuentes-Cañamero and José M. Garc\ia-Pinilla and Mar\ia I. Garc\ia-Álvarez and Francesca Girolami and Roberto Barriales-Villa and Carles D\iez-López and Luis R. Lopes and Karim Wahbi and Ana Garc\ia-Álvarez and Ibon Rodr\iguez-Sánchez and Javier Rekondo-Olaetxea and José F. Rodr\iguez-Palomares and Mar\ia Gallego-Delgado and Benjamin Meder and Milos Kubanek and Frederikke G. Hansen and Mar\ia Alejandra Restrepo-Córdoba and Julián Palomino-Doza and Luis Ruiz-Guerrero and Georgia Sarquella-Brugada and Alberto José Perez-Perez and Francisco José Bermúdez-Jiménez and Tomas Ripoll-Vera and Torsten Bloch Rasmussen and Mark Jansen and Maria Sabater-Molina and Perry M. Elliot and Pablo Garcia-Pavia and Eva Cabrera-Romero and Marta Cobo-Marcos and Luis Escobar-Lopez and Fernando Dom\inguez and Esther González-López and Juan Ramón Gimeno-Blanes and Dennis Dooijes and Bernabé López Ledesma and Inés Roche Fortea and Javier Bermejo and Maria Angeles Espinosa and Ana Isabel Fernández and Silvia Vilches and Cristina Gómez and Juan Gómez and Eliecer Coto and José Julián Rodr\iguez Reguero and S.R.B. Heymans and H.G. Brunner and Javier López-D\iaz and Grażyna Truszkowska and Rafal Ploski and Przemysław Chmielewski and Renee Johnson and Ainhoa Robles-Mezcua and Arancha D\iaz-Expósito and Alejandro I. Pérez-Cabeza and Clara Jiménez-Rubio and Vicente Climent Payá and Silvia Favilli and Petros Syrris and Douglas Cannie and Clarisse Billon and Angela Lopez-Sainz and Margarita Calvo and Ángela Cacicedo Fernández de Bobadilla and Jose Juan Onaindia-Gandarias and Larraitz Gaztañaga-Arantzamendi and Estibaliz Zamarreño-Golvano and Javier Limeres and Laura Gutiérrez-Garc\ia and Eduardo Villacorta and Jan Haas and Alice Krebsova and Jens Mogensen and Sergi Cesar and Oscar Campuzano and Raúl Franco Gutiérrez and Jorge Alvarez-Rubio and David Cremer-Luengos and Guido Antoniutti and Fiama Caimi-Martinez and Rosa Mac\ias and Juan Jiménez-Jáimez and Mar\ia Luisa Peña-Peña and Salvador Lucas D\iez-Aja López and Tania Pino Acereda and Blanca Arnáez Corada and Jesús Piqueras-Flores and Martin Negreira-Caamaño and Jorge Martinez-del R\io and Mar\ia Victoria Mogollón Jiménez and Elena Villanueva and José Luis Gonzáles and Adrián Fernández and Ulises Toscanini and Lilian E. Favaloro and Carlota Hernández D\iez}, title = {Natural History of MYH7-Related Dilated Cardiomyopathy}, journal = {Journal of the American College of Cardiology}, publisher = {Elsevier BV}, year = {2022}, volume = {80}, number = {15}, pages = {1447--1461}, doi = {https://doi.org/10.1016/j.jacc.2022.07.023} }
Fueller, J., Herbst, K., Meurer, M., Gubicza, K., Kurtulmus, B., Knopf, J.D., Kirrmaier, D., Buchmuller, B.C., Pereira, G., Lemberg, M.K. and Knop, M.	CRISPR-Cas12a-assisted PCR tagging of mammalian genes [Abstract] [BibTeX]	2019	bioRxiv	article	DOI URL
Abstract: Here we describe a simple and time-efficient strategy for endogenous gene tagging in mammalian tissue culture cells. We take advantage of CRISPR-Cas12a-induced double strand breaks and their repair by homologous recombination using heterologous templates with short homology arms. Assembly of these templates and the Cas12a endonuclease is restricted to a single PCR step followed by DNA transfection, which avoids handling of RNAs, recombinant proteins or cloning of plasmids. The method is robust and works in all cell lines tested with tagging efficiency of up to 20% without selection, and up to 60% when selection markers are used. We show application in different cell lines and make a comprehensive set of C-terminal tagging constructs available to the research community.
BibTeX: @article{Fueller2019, author = {Fueller, Julia and Herbst, Konrad and Meurer, Matthias and Gubicza, Krisztina and Kurtulmus, Bahtiyar and Knopf, Julia D. and Kirrmaier, Daniel and Buchmuller, Benjamin C. and Pereira, Gislene and Lemberg, Marius K. and Knop, Michael}, title = {CRISPR-Cas12a-assisted PCR tagging of mammalian genes}, journal = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, year = {2019}, url = {https://www.biorxiv.org/content/early/2019/10/30/473876}, doi = {https://doi.org/10.1101/473876} }
Gan, Z., Li, H., Naser, P.V., Oswald, M.J. and Kuner, R.	Suppression of neuropathic pain and comorbidities by recurrent cycles of repetitive transcranial direct current motor cortex stimulation in mice [BibTeX]	2021	Vol. 11(1)	article	DOI
BibTeX: @article{Gan2021, author = {Zheng Gan and Han Li and Paul Vincent Naser and Manfred Josef Oswald and Rohini Kuner}, title = {Suppression of neuropathic pain and comorbidities by recurrent cycles of repetitive transcranial direct current motor cortex stimulation in mice}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41598-021-89122-6} }
Gan, Z., Li, H., Naser, P.V., Han, Y., Tan, L.L., Oswald, M.J. and Kuner, R.	Repetitive non-invasive prefrontal stimulation reverses neuropathic pain via neural remodelling in mice [BibTeX]	2021	Vol. 201, pp. 102009	article	DOI
BibTeX: @article{Gan2021a, author = {Zheng Gan and Han Li and Paul V. Naser and Yechao Han and Linette Liqi Tan and Manfred J. Oswald and Rohini Kuner}, title = {Repetitive non-invasive prefrontal stimulation reverses neuropathic pain via neural remodelling in mice}, publisher = {Elsevier BV}, year = {2021}, volume = {201}, pages = {102009}, doi = {https://doi.org/10.1016/j.pneurobio.2021.102009} }
Gan, Z., Gangadharan, V., Liu, S., Körber, C., Tan, L.L., Li, H., Oswald, M.J., Kang, J., Martin-Cortecero, J., Männich, D., Groh, A., Kuner, T., Wieland, S. and Kuner, R.	Layer-specific pain relief pathways originating from primary motor cortex [BibTeX]	2022	Science Vol. 378(6626), pp. 1336-1343	article	DOI
BibTeX: @article{Gan2022, author = {Zheng Gan and Vijayan Gangadharan and Sheng Liu and Christoph Körber and Linette Liqi Tan and Han Li and Manfred Josef Oswald and Juhyun Kang and Jesus Martin-Cortecero and Deepitha Männich and Alexander Groh and Thomas Kuner and Sebastian Wieland and Rohini Kuner}, title = {Layer-specific pain relief pathways originating from primary motor cortex}, journal = {Science}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2022}, volume = {378}, number = {6626}, pages = {1336--1343}, doi = {https://doi.org/10.1126/science.add4391} }
Gangadharan, V., Zheng, H., Taberner, F.J., Landry, J., Nees, T.A., Pistolic, J., Agarwal, N., Männich, D., Benes, V., Helmstaedter, M., Ommer, B., Lechner, S.G., Kuner, T. and Kuner, R.	Neuropathic pain caused by miswiring and abnormal end organ targeting [BibTeX]	2022	Nature Vol. 606(7912), pp. 137-145	article	DOI URL
BibTeX: @article{Gangadharan2022, author = {Vijayan Gangadharan, Hongwei Zheng, Francisco J. Taberner, Jonathan Landry, Timo A. Nees, Jelena Pistolic, Nitin Agarwal, Deepitha Männich, Vladimir Benes, Moritz Helmstaedter, Björn Ommer, Stefan G. Lechner, Thomas Kuner, Rohini Kuner}, title = {Neuropathic pain caused by miswiring and abnormal end organ targeting}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {606}, number = {7912}, pages = {137--145}, url = {https://www.nature.com/articles/s41586-022-04777-z.pdf}, doi = {https://doi.org/10.1038/s41586-022-04777-z} }
Gao, R., Liang, X., Cheedipudi, S., Cordero, J., Jiang, X., Zhang, Q., Caputo, L., Günther, S., Kuenne, C., Ren, Y., Bhattacharya, S., Yuan, X., Barreto, G., Chen, Y., Braun, T., Evans, S.M., Sun, Y. and Dobreva, G.	Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [BibTeX]	2019	Cell Research Vol. 29(6), pp. 486-501	article	DOI
BibTeX: @article{Gao2019, author = {Rui Gao and Xingqun Liang and Sirisha Cheedipudi and Julio Cordero and Xue Jiang and Qingquan Zhang and Luca Caputo and Stefan Günther and Carsten Kuenne and Yonggang Ren and Shoumo Bhattacharya and Xuejun Yuan and Guillermo Barreto and Yihan Chen and Thomas Braun and Sylvia M. Evans and Yunfu Sun and Gergana Dobreva}, title = {Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate}, journal = {Cell Research}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {29}, number = {6}, pages = {486--501}, doi = {https://doi.org/10.1038/s41422-019-0168-1} }
Garg, S., Reyes-Palomares, A., He, L., Bergeron, A., Lavallée, V.-P., Lemieux, S., Gendron, P., Rohde, C., Xia, J., Jagdhane, P., Müller-Tidow, C., Lipka, D.B., Imren, S., Humphries, R.K., Waskow, C., Vick, B., Jeremias, I., Richard-Carpentier, G., Hébert, J., Sauvageau, G., Zaugg, J.B., Barabé, F. and Pabst, C.	Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML [BibTeX]	2019	Blood Vol. 134(3), pp. 263-276	article	DOI
BibTeX: @article{Garg2019, author = {Swati Garg and Armando Reyes-Palomares and Lixiazi He and Anne Bergeron and Vincent-Philippe Lavallée and Sébastien Lemieux and Patrick Gendron and Christian Rohde and Jianglong Xia and Prarabdha Jagdhane and Carsten Müller-Tidow and Daniel B. Lipka and Suzan Imren and R. Keith Humphries and Claudia Waskow and Binje Vick and Irmela Jeremias and Guillaume Richard-Carpentier and Josée Hébert and Guy Sauvageau and Judith B. Zaugg and Frédéric Barabé and Caroline Pabst}, title = {Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML}, journal = {Blood}, publisher = {American Society of Hematology}, year = {2019}, volume = {134}, number = {3}, pages = {263--276}, doi = {https://doi.org/10.1182/blood.2018862383} }
Geen, S., Watson, S.K., Rosdahl, J., Bieri, R., Klessen, R.S. and Hennebelle, P.	On the indeterministic nature of star formation on the cloud scale [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 481(2), pp. 2548-2569	article	DOI
BibTeX: @article{Geen2018, author = {Sam Geen and Stuart K Watson and Joakim Rosdahl and Rebekka Bieri and Ralf S Klessen and Patrick Hennebelle}, title = {On the indeterministic nature of star formation on the cloud scale}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {481}, number = {2}, pages = {2548--2569}, doi = {https://doi.org/10.1093/mnras/sty2439} }
	Black Boxes - Versiegelungskontexte und Öffnungsversuche [BibTeX]	2020		book	DOI
BibTeX: @book{Geitz2020,, title = {Black Boxes - Versiegelungskontexte und Öffnungsversuche}, publisher = {De Gruyter}, year = {2020}, doi = {https://doi.org/10.1515/9783110701319} }
Gerber, J.L., Guzmán, S.I.M., Worf, L., Hubbe, P., Kopp, J. and Peschek, J.	Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease [BibTeX]	2023		article	DOI
BibTeX: @article{Gerber2023, author = {Janina Lara Gerber and Suria Itzel Morales Guzmán and Lorenz Worf and Petra Hubbe and Jürgen Kopp and Jirka Peschek}, title = {Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease}, publisher = {Cold Spring Harbor Laboratory}, year = {2023}, doi = {https://doi.org/10.1101/2023.03.30.534986} }
Gesine M. Dittrich, J.H.	TNF-α signaling: TACE inhibition to put out the burning heart [Abstract] [BibTeX]	2020	PLOS Biology Vol. 18(12), pp. e3001037	article	DOI
Abstract: More than 20 years ago, Seta and colleagues hypothesized that cytokines, which are activated by myocardial injury, significantly drive heart failure progression and would therefore be effective targets to treat cardiac dysfunction. Unfortunately, several clinical trials inhibiting key cytokines like tumor necrosis factor alpha (TNF-α) and interleukin 1 beta (Il-1β) turned out negative or even revealed adverse clinical effects. Providing a potential mechanistic explanation for the ineffectiveness of TNF-α blockade in heart failure, novel findings demonstrate that the membrane-bound precursor form of TNF-α, transmembrane TNF-α (tmTNF-α), mediates cardioprotective effects during pressure overload-induced cardiac remodeling. This study suggests that preventing tmTNF-α cleavage by targeting the TNF-α converting enzyme (TACE) rather than inhibiting TNF-α signaling altogether might be a valuable therapeutic approach.
BibTeX: @article{GesineM.Dittrich2020, author = {Gesine M. Dittrich, Joerg Heineke}, title = {TNF-α signaling: TACE inhibition to put out the burning heart}, journal = {PLOS Biology}, publisher = {Public Library of Science (PLoS)}, year = {2020}, volume = {18}, number = {12}, pages = {e3001037}, doi = {https://doi.org/10.1371/journal.pbio.3001037} }
Gi, W.-T., Haas, J., Sedaghat-Hamedani, F., Kayvanpour, E., Tappu, R., Lehmann, D.H., Samani, O.S., Wisdom, M., Keller, A., Katus, H.A. and Meder, B.	Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy [Abstract] [BibTeX]	2020	Journal of Clinical Medicine Vol. 9(5), pp. 1499	article	DOI URL
Abstract: In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (p < 2 × 10−16). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to TTN substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome–environment interaction in DCM besides simple gene expression regulation.
BibTeX: @article{Gi2020, author = {Weng-Tein Gi, Jan Haas, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Rewati Tappu, David Hermann Lehmann, Omid Shirvani Samani, Michael Wisdom, Andreas Keller, Hugo A. Katus, Benjamin Meder}, title = {Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy}, journal = {Journal of Clinical Medicine}, publisher = {MDPI AG}, year = {2020}, volume = {9}, number = {5}, pages = {1499}, url = {https://www.mdpi.com/2077-0383/9/5/1499/pdf}, doi = {https://doi.org/10.3390/jcm9051499} }
Giebel, N., Jaime-Soguero, A., del Arco, A.G., Landry, J.J.M., Tietje, M., Villacorta, L., Benes, V., Fernández-Sáiz, V. and Acebrón, S.P.	USP42 protects ZNRF3/RNF43 from R-spondin-dependent clearance and inhibits Wnt signalling [BibTeX]	2021	EMBO reports Vol. 22(5)	article	DOI
BibTeX: @article{Giebel2021, author = {Nicole Giebel and Anchel Jaime-Soguero and Ana Garc\ia del Arco and Jonathan J M Landry and Marlene Tietje and Laura Villacorta and Vladimir Benes and Vanesa Fernández-Sáiz and Sergio P Acebrón}, title = {USP42 protects ZNRF3/RNF43 from R-spondin-dependent clearance and inhibits Wnt signalling}, journal = {EMBO reports}, publisher = {EMBO}, year = {2021}, volume = {22}, number = {5}, doi = {https://doi.org/10.15252/embr.202051415} }
Girichidis, P., Seifried, D., Naab, T., Peters, T., Walch, S., Wünsch, R., Glover, S.C.O. and Klessen, R.S.	The SILCC project - V. The impact of magnetic fields on the chemistry and the formation of molecular clouds [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 480(3), pp. 3511-3540	article	DOI
BibTeX: @article{Girichidis2018, author = {Girichidis, Philipp and Seifried, Daniel and Naab, Thorsten and Peters, Thomas and Walch, Stefanie and Wünsch, Richard and Glover, Simon C. O. and Klessen, Ralf S.}, title = {The SILCC project - V. The impact of magnetic fields on the chemistry and the formation of molecular clouds}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {480}, number = {3}, pages = {3511--3540}, doi = {https://doi.org/10.1093/mnras/sty2016} }
Grimm, L.M., Sinn, S., Krstić, M., D'Este, E., Sonntag, I., Prasetyanto, E.A., Kuner, T., Wenzel, W., Cola, L.D. and Biedermann, F.	Fluorescent Nanozeolite Receptors for the Highly Selective and Sensitive Detection of Neurotransmitters in Water and Biofluids (Adv. Mater. 49/2021) [BibTeX]	2021	Advanced Materials Vol. 33(49), pp. 2170383	article	DOI
BibTeX: @article{Grimm2021, author = {Laura M. Grimm, Stephan Sinn, Marjan Krstić, Elisa D'Este, Ivo Sonntag, Eko Adi Prasetyanto, Thomas Kuner, Wolfgang Wenzel, Luisa De Cola, Frank Biedermann}, title = {Fluorescent Nanozeolite Receptors for the Highly Selective and Sensitive Detection of Neurotransmitters in Water and Biofluids (Adv. Mater. 49/2021)}, journal = {Advanced Materials}, publisher = {Wiley}, year = {2021}, volume = {33}, number = {49}, pages = {2170383}, doi = {https://doi.org/10.1002/adma.202170383} }
Grinberger, A.	Identifying the Effects of Mobility Domains on VGI: Towards an Analytical Approach [BibTeX]	2018		inproceedings
BibTeX: @inproceedings{Grinberger2018, author = {Grinberger, A.}, title = {Identifying the Effects of Mobility Domains on VGI: Towards an Analytical Approach}, year = {2018} }
Grinberger, A.Y., Schott, M., Raifer, M. and Zipf, A.	An analysis of the spatial and temporal distribution of large-scale data production events in OpenStreetMap [BibTeX]	2021	Transactions in GIS Vol. 25(2), pp. 622-641	article	DOI
BibTeX: @article{Grinberger2021, author = {A. Yair Grinberger and Moritz Schott and Martin Raifer and Alexander Zipf}, title = {An analysis of the spatial and temporal distribution of large-scale data production events in OpenStreetMap}, journal = {Transactions in GIS}, publisher = {Wiley}, year = {2021}, volume = {25}, number = {2}, pages = {622--641}, doi = {https://doi.org/10.1111/tgis.12746} }
Grund, A., Szaroszyk, M., Korf-Klingebiel, M., Mohammadi, M.M., Trogisch, F.A., Schrameck, U., Gigina, A., Tiedje, C., Gaestel, M., Kraft, T., Hegermann, J., Batkai, S., Thum, T., Perrot, A., dos Remedios, C., Riechert, E., Völkers, M., Doroudgar, S., Jungmann, A., Bauer, R., Yin, X., Mayr, M., Wollert, K.C., Pich, A., Xiao, H., Katus, H.A., Bauersachs, J., Müller, O.J. and Heineke, J.	TIP 30 counteracts cardiac hypertrophy and failure by inhibiting translational elongation [BibTeX]	2019	EMBO Molecular Medicine Vol. 11(10)	article	DOI
BibTeX: @article{Grund2019, author = {Andrea Grund and Malgorzata Szaroszyk and Mortimer Korf-Klingebiel and Mona Malek Mohammadi and Felix A Trogisch and Ulrike Schrameck and Anna Gigina and Christopher Tiedje and Matthias Gaestel and Theresia Kraft and Jan Hegermann and Sandor Batkai and Thomas Thum and Andreas Perrot and Cris dos Remedios and Eva Riechert and Mirko Völkers and Shirin Doroudgar and Andreas Jungmann and Ralf Bauer and Xiaoke Yin and Manuel Mayr and Kai C Wollert and Andreas Pich and Hua Xiao and Hugo A Katus and Johann Bauersachs and Oliver J Müller and Joerg Heineke}, title = {TIP 30 counteracts cardiac hypertrophy and failure by inhibiting translational elongation}, journal = {EMBO Molecular Medicine}, publisher = {EMBO}, year = {2019}, volume = {11}, number = {10}, doi = {https://doi.org/10.15252/emmm.201810018} }
Gutting, T., Hauber, V., Pahl, J., Klapproth, K., Wu, W., Dobrota, I., Herweck, F., Reichling, J., Helm, L., Schroeder, T., Li, B., Weidner, P., Zhan, T., Eckardt, M., Betge, J., Belle, S., Sticht, C., Gaiser, T., Boutros, M., Ebert, M.P., Cerwenka, A. and Burgermeister, E.	PPARupgamma induces PD-L1 expression in MSSmathplus colorectal cancer cells [BibTeX]	2021	Vol. 10(1), pp. 1906500	article	DOI
BibTeX: @article{Gutting2021, author = {Tobias Gutting and Veronika Hauber and Jens Pahl and Kay Klapproth and Wenyue Wu and Ioana Dobrota and Frank Herweck and Juliane Reichling and Laura Helm and Torsten Schroeder and Beifang Li and Philip Weidner and Tianzuo Zhan and Maximilian Eckardt and Johannes Betge and Sebastian Belle and Carsten Sticht and Timo Gaiser and Michael Boutros and Matthias P.A. Ebert and Adelheid Cerwenka and Elke Burgermeister}, title = {PPARupgamma induces PD-L1 expression in MSSmathplus colorectal cancer cells}, publisher = {Informa UK Limited}, year = {2021}, volume = {10}, number = {1}, pages = {1906500}, doi = {https://doi.org/10.1080/2162402x.2021.1906500} }
Gutting, T., Merkel, A., Fink, D.J., Hetjens, S., Weidner, P., Yu, Y., Kähler, G., Ebert, M.P., Gaiser, T., Burgermeister, E. and Belle, S.	Expression of the EGFR-RAS Inhibitory Proteins DOK1 and MTMR7 and its Significance in Colorectal Adenoma and Adenoma Recurrence [Abstract] [BibTeX]	2021	Journal of Gastrointestinal and Liver Diseases Vol. 30(4), pp. 446-455	article	DOI URL
Abstract: Background and Aims: Colorectal adenomas are precursor lesions for colorectal cancer (CRC), a major cause of cancer-related death. Despite all molecular insights, there are still unknown variables in the development of CRC as well as uncertainties regarding adenoma recurrence after resection. We aimed to characterize the expression of docking protein 1 (DOK1) and myotubularin-related protein 7 (MTMR7), which share inhibiting functions on EGFR-RAS-signalling, a major oncogenic driver in CRC, and their association with clinical variables and adenoma recurrence. Methods: This observational study is based on clinical data obtained from patients who underwent routine endoscopy and consecutive follow-up examinations. Immunohistochemistry was conducted both in dysplastic tissue and adjacent non-dysplastic mucosa followed by microscopical assessment. Recurrence was differentiated between local, segmental and distant relapse. Results: A total of 56 patients (23 females) gathering 96 adenomas/polyps were included. 36 patients experienced a metachronous lesion, 23 patients had simultaneous lesions in their index endoscopy. Female patients showed lower levels of MTMR7 in adenomas (p=0.0318). Adenomas of young patients showed lower DOK1 than those of older patients (p=0.0469). Big adenomas showed a higher expression of DOK1 than small lesions (p=0.0044). In serrated lesions, DOK1 was reduced (p=0.0026) and correlated with the quantity of lesions (p < 0.001). MTMR7 was significantly reduced in distant (p=0.05) and local segmental recurrence (p=0.0362), while DOK1 showed higher expression in recurrence (p=0.0291). Conclusions: We found ambivalent results regarding the role of the markers as potential tumor suppressors, implying a context-dependent function of these molecules which might change in the course of time. DOK1 may play an inhibiting role in the serrated pathway. Remarkably, molecular markers have the potential to predict recurrence, since a combined expression analysis of high DOK1 and low MTMR7 correlated with the likelihood of segmental adenoma recurrence.
BibTeX: @article{Gutting2021a, author = {Tobias Gutting, Andreas Merkel, David J Fink, Svetlana Hetjens, Philip Weidner, Yanxiong Yu, Georg Kähler, Matthias P. Ebert, Timo Gaiser, Elke Burgermeister, Sebastian Belle}, title = {Expression of the EGFR-RAS Inhibitory Proteins DOK1 and MTMR7 and its Significance in Colorectal Adenoma and Adenoma Recurrence}, journal = {Journal of Gastrointestinal and Liver Diseases}, publisher = {Romanian Society of Gastroenterology and Hepatology}, year = {2021}, volume = {30}, number = {4}, pages = {446--455}, url = {https://jgld.ro/jgld/index.php/jgld/article/download/3681/1781}, doi = {https://doi.org/10.15403/jgld-3681} }
Haas, J., Frese, K.S., Sedaghat-Hamedani, F., Kayvanpour, E., Tappu, R., Nietsch, R., Tugrul, O.F., Wisdom, M., Dietrich, C., Amr, A., Weis, T., Niederdränk, T., Murphy, M.P., Krieg, T., Dörr, M., Völker, U., Fielitz, J., Frey, N., Felix, S.B., Keller, A., Katus, H.A. and Meder, B.	Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy [Abstract] [BibTeX]	2021	International Journal of Molecular Sciences Vol. 22(4), pp. 1999	article	DOI URL
Abstract: With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and non-ischemic HF by using a multi-OMICS approach. Serum metabolites and mRNAseq and epigenetic DNA methylation profiles were analyzed from blood and left ventricular heart biopsy specimens of the same individuals. In total we collected serum from n = 82 patients with Dilated Cardiomyopathy (DCM) and n = 51 controls in the screening stage. We identified several metabolites involved in glycolysis and citric acid cycle to be elevated up to 5.7-fold in DCM (p = 1.7 × 10−6). Interestingly, cardiac mRNA and epigenetic changes of genes encoding rate-limiting enzymes of these pathways could also be found and validated in our second stage of metabolite assessment in n = 52 DCM, n = 39 ischemic HF and n = 57 controls. In conclusion, we identified a new set of metabolomic biomarkers for HF. We were able to identify underlying biological cascades that potentially represent suitable intervention targets.
BibTeX: @article{Haas2021, author = {Jan Haas, Karen S. Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Rewati Tappu, Rouven Nietsch, Oguz Firat Tugrul, Michael Wisdom, Carsten Dietrich, Ali Amr, Tanja Weis, Torsten Niederdränk, Michael P. Murphy, Thomas Krieg, Marcus Dörr, Uwe Völker, Jens Fielitz, Norbert Frey, Stephan B. Felix, Andreas Keller, Hugo A. Katus, Benjamin Meder}, title = {Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2021}, volume = {22}, number = {4}, pages = {1999}, url = {https://www.mdpi.com/1422-0067/22/4/1999/pdf}, doi = {https://doi.org/10.3390/ijms22041999} }
Haemmerlé, L., Woods, T.E., Klessen, R.S., Heger, A. and Whalen, D.J.	The evolution of supermassive Population III stars [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 474(2), pp. 2757-2773	article	DOI
BibTeX: @article{Haemmerle2018, author = {Haemmerlé, Lionel and Woods, T. E. and Klessen, Ralf S. and Heger, Alexander and Whalen, Daniel J.}, title = {The evolution of supermassive Population III stars}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {474}, number = {2}, pages = {2757--2773}, doi = {https://doi.org/10.1093/mnras/stx2919} }
Haemmerlé, L., Woods, T.E., Klessen, R.S., Heger, A. and Whalen, D.J.	On the Rotation of Supermassive Stars [BibTeX]	2018	The Astrophysical Journal Vol. 853(1), pp. L3	article	DOI
BibTeX: @article{Haemmerle2018a, author = {Haemmerlé, Lionel and Woods, Tyrone E. and Klessen, Ralf S. and Heger, Alexander and Whalen, Daniel J.}, title = {On the Rotation of Supermassive Stars}, journal = {The Astrophysical Journal}, year = {2018}, volume = {853}, number = {1}, pages = {L3}, doi = {https://doi.org/10.3847/2041-8213/aaa462} }
Hahn, A., Bode, J., Schuhegger, S., Krüwel, T., Sturm, V.J., Zhang, K., Jende, J.M., Tews, B., Heiland, S., Bendszus, M., Breckwoldt, M.O., Ziener, C.H. and Kurz, F.T.	Brain tumor classification of virtual NMR voxels based on realistic blood vessel-induced spin dephasing using support vector machines [BibTeX]	2020	NMR in Biomedicine	article	DOI
BibTeX: @article{Hahn2020a, author = {Artur Hahn and Julia Bode and Sarah Schuhegger and Thomas Krüwel and Volker J.F. Sturm and Ke Zhang and Johann M.E. Jende and Björn Tews and Sabine Heiland and Martin Bendszus and Michael O. Breckwoldt and Christian H. Ziener and Felix T. Kurz}, title = {Brain tumor classification of virtual NMR voxels based on realistic blood vessel-induced spin dephasing using support vector machines}, journal = {NMR in Biomedicine}, publisher = {Wiley}, year = {2020}, doi = {https://doi.org/10.1002/nbm.4307} }
Hahn, A., Bode, J., Alexander, A., Karimian-Jazi, K., Schregel, K., Schwarz, D., Sommerkamp, A.C., Krüwel, T., Abdollahi, A., Wick, W., Platten, M., Bendszus, M., Tews, B., Kurz, F.T. and Breckwoldt, M.O.	Large-scale characterization of the microvascular geometry in development and disease by tissue clearing and quantitative ultramicroscopy [BibTeX]	2020	Journal of Cerebral Blood Flow & Metabolism, pp. 0271678X2096185	article	DOI
BibTeX: @article{Hahn2020b, author = {Artur Hahn and Julia Bode and Allen Alexander and Kianush Karimian-Jazi and Katharina Schregel and Daniel Schwarz and Alexander C Sommerkamp and Thomas Krüwel and Amir Abdollahi and Wolfgang Wick and Michael Platten and Martin Bendszus and Björn Tews and Felix T Kurz and Michael O Breckwoldt}, title = {Large-scale characterization of the microvascular geometry in development and disease by tissue clearing and quantitative ultramicroscopy}, journal = {Journal of Cerebral Blood Flow & Metabolism}, publisher = {SAGE Publications}, year = {2020}, pages = {0271678X2096185}, doi = {https://doi.org/10.1177/0271678x20961854} }
Haldemann, J., Ksoll, V., Walter, D., Alibert, Y., Klessen, R.S., Benz, W., Koethe, U., Ardizzone, L. and Rother, C.	Exoplanet characterization using conditional invertible neural networks [BibTeX]	2023	Astronomy &ampmathsemicolon Astrophysics Vol. 672, pp. A180	article	DOI
BibTeX: @article{Haldemann2023, author = {Jonas Haldemann and Victor Ksoll and Daniel Walter and Yann Alibert and Ralf S. Klessen and Willy Benz and Ullrich Koethe and Lynton Ardizzone and Carsten Rother}, title = {Exoplanet characterization using conditional invertible neural networks}, journal = {Astronomy &ampmathsemicolon Astrophysics}, publisher = {EDP Sciences}, year = {2023}, volume = {672}, pages = {A180}, doi = {https://doi.org/10.1051/0004-6361/202243230} }
Hansen, C.J., Koch, A., Mashonkina, L., Magg, M., Bergemann, M., Sitnova, T., Gallagher, A.J., Ilyin, I., Caffau, E., Zhang, H., Strassmeier, K.G. and Klessen, R.S.	Mono-enriched stars and Galactic chemical evolution [BibTeX]	2020	Astronomy & Astrophysics Vol. 643	article	DOI
BibTeX: @article{Hansen2020, author = {C. J. Hansen and A. Koch and L. Mashonkina and M. Magg and M. Bergemann and T. Sitnova and A. J. Gallagher and I. Ilyin and E. Caffau and H.W. Zhang and K. G. Strassmeier and R. S. Klessen}, title = {Mono-enriched stars and Galactic chemical evolution}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2020}, volume = {643}, doi = {https://doi.org/10.1051/0004-6361/202038805} }
Hartwig, T., Ishigaki, M.N., Klessen, R.S. and Yoshida, N.	Fingerprint of the first stars: multi-enriched extremely metal-poor stars in the TOPoS survey [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 482(1), pp. 1204-1210	article	DOI
BibTeX: @article{Hartwig2018, author = {Tilman Hartwig and Miho N Ishigaki and Ralf S Klessen and Naoki Yoshida}, title = {Fingerprint of the first stars: multi-enriched extremely metal-poor stars in the TOPoS survey}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {482}, number = {1}, pages = {1204--1210}, doi = {https://doi.org/10.1093/mnras/sty2783} }
Hartwig, T., Yoshida, N., Magg, M., Frebel, A., Glover, S.C.O., Gómez, F.A., Griffen, B., Ishigaki, M.N., Ji, A.P., Klessen, R.S., O'Shea, B.W. and Tominaga, N.	Descendants of the first stars: the distinct chemical signature of second-generation stars [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 478(2), pp. 1795-1810	article	DOI
BibTeX: @article{Hartwig2018a, author = {Tilman Hartwig and Naoki Yoshida and Mattis Magg and Anna Frebel and Simon C O Glover and Facundo A Gómez and Brendan Griffen and Miho N Ishigaki and Alexander P Ji and Ralf S Klessen and Brian W O'Shea and Nozomu Tominaga}, title = {Descendants of the first stars: the distinct chemical signature of second-generation stars}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {478}, number = {2}, pages = {1795--1810}, doi = {https://doi.org/10.1093/mnras/sty1176} }
Hartwig, T., Magg, M., Chen, L.-H., Tarumi, Y., Bromm, V., Glover, S.C.O., Ji, A.P., Klessen, R.S., Latif, M.A., Volonteri, M. and Yoshida, N.	Public Release of A-SLOTH: Ancient Stars and Local Observables by Tracing Halos [BibTeX]	2022	The Astrophysical Journal Vol. 936(1), pp. 45	article	DOI
BibTeX: @article{Hartwig2022, author = {Tilman Hartwig, Mattis Magg, Li-Hsin Chen, Yuta Tarumi, Volker Bromm, Simon C. O. Glover, Alexander P. Ji, Ralf S. Klessen, Muhammad A. Latif, Marta Volonteri, Naoki Yoshida}, title = {Public Release of A-SLOTH: Ancient Stars and Local Observables by Tracing Halos}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2022}, volume = {936}, number = {1}, pages = {45}, doi = {https://doi.org/10.3847/1538-4357/ac7150} }
Hassan, W., Jeelani, G., Dimri, A.P. and Nüsser, M.	Assessment of the spatial extent of permafrost in the Upper Indus Basin (UIB) [BibTeX]	2023	Journal of Mountain Science Vol. 20(6), pp. 1508-1525	article	DOI
BibTeX: @article{Hassan2023, author = {Wasim Hassan and G. Jeelani and A. P. Dimri and Marcus Nüsser}, title = {Assessment of the spatial extent of permafrost in the Upper Indus Basin (UIB)}, journal = {Journal of Mountain Science}, publisher = {Springer Science and Business Media LLC}, year = {2023}, volume = {20}, number = {6}, pages = {1508--1525}, doi = {https://doi.org/10.1007/s11629-023-7985-x} }
	Bilddaten in den Digitalen Geisteswissenschaften [BibTeX]	2020		book	DOI
BibTeX: @book{Hastik2020,, title = {Bilddaten in den Digitalen Geisteswissenschaften}, publisher = {Harrassowitz Verlag}, year = {2020}, doi = {https://doi.org/10.13173/9783447114608} }
Hatchfield, H.P., Sormani, M.C., Tress, R.G., Battersby, C., Smith, R.J., Glover, S.C.O. and Klessen, R.S.	Dynamically Driven Inflow onto the Galactic Center and its Effect upon Molecular Clouds [BibTeX]	2021	The Astrophysical Journal Vol. 922(1), pp. 79	article	DOI
BibTeX: @article{Hatchfield2021, author = {H Perry Hatchfield and Mattia C. Sormani and Robin G. Tress and Cara Battersby and Rowan J. Smith and Simon C. O. Glover and Ralf S. Klessen}, title = {Dynamically Driven Inflow onto the Galactic Center and its Effect upon Molecular Clouds}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2021}, volume = {922}, number = {1}, pages = {79}, doi = {https://doi.org/10.3847/1538-4357/ac1e89} }
Hausmann, D., Hoffmann, D.C., Venkataramani, V., Jung, E., Horschitz, S., Tetzlaff, S.K., Jabali, A., Hai, L., Kessler, T., Azoŕin, D.D., Weil, S., Kourtesakis, A., Sievers, P., Habel, A., Breckwoldt, M.O., Karreman, M.A., Ratliff, M., Messmer, J.M., Yang, Y., Reyhan, E., Wendler, S., Löb, C., Mayer, C., Figarella, K., Osswald, M., Solecki, G., Sahm, F., Garaschuk, O., Kuner, T., Koch, P., Schlesner, M., Wick, W. and Winkler, F.	Autonomous rhythmic activity in glioma networks drives brain tumour growth [BibTeX]	2022	Nature Vol. 613(7942), pp. 179-186	article	DOI
BibTeX: @article{Hausmann2022, author = {David Hausmann and Dirk C. Hoffmann and Varun Venkataramani and Erik Jung and Sandra Horschitz and Svenja K. Tetzlaff and Ammar Jabali and Ling Hai and Tobias Kessler and Daniel D. Azoŕin and Sophie Weil and Alexandros Kourtesakis and Philipp Sievers and Antje Habel and Michael O. Breckwoldt and Matthia A. Karreman and Miriam Ratliff and Julia M. Messmer and Yvonne Yang and Ekin Reyhan and Susann Wendler and Cathrin Löb and Chanté Mayer and Katherine Figarella and Matthias Osswald and Gergely Solecki and Felix Sahm and Olga Garaschuk and Thomas Kuner and Philipp Koch and Matthias Schlesner and Wolfgang Wick and Frank Winkler}, title = {Autonomous rhythmic activity in glioma networks drives brain tumour growth}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {613}, number = {7942}, pages = {179--186}, doi = {https://doi.org/10.1038/s41586-022-05520-4} }
He, L., Arnold, C., Thoma, J., Rohde, C., Kholmatov, M., Garg, S., Hsiao, C.-C., Viol, L., Zhang, K., Sun, R., Schmidt, C., Janssen, M., MacRae, T., Huber, K., Thiede, C., Hébert, J., Sauvageau, G., Spratte, J., Fluhr, H., Aust, G., Müller-Tidow, C., Niehrs, C., Pereira, G., Hamann, J., Tanaka, M., Zaugg, J.B. and Pabst, C.	CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia [BibTeX]	2022	EMBO Molecular Medicine Vol. 14(4)	article	DOI
BibTeX: @article{He2022, author = {Lixiazi He and Christian Arnold and Judith Thoma and Christian Rohde and Maksim Kholmatov and Swati Garg and Cheng-Chih Hsiao and Linda Viol and Kaiqing Zhang and Rui Sun and Christina Schmidt and Maike Janssen and Tara MacRae and Karin Huber and Christian Thiede and Josée Hébert and Guy Sauvageau and Julia Spratte and Herbert Fluhr and Gabriela Aust and Carsten Müller-Tidow and Christof Niehrs and Gislene Pereira and Jörg Hamann and Motomu Tanaka and Judith B Zaugg and Caroline Pabst}, title = {CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia}, journal = {EMBO Molecular Medicine}, publisher = {EMBO}, year = {2022}, volume = {14}, number = {4}, doi = {https://doi.org/10.15252/emmm.202114990} }
Hecht, S., Bubenzer, O., Mächtle, B. and Tafelmaier, Y.	Blick in den Untergrund – Geophysikalische Untersuchungen in der Höhle Haus am Rosenstein [BibTeX]	2022	Arch. Ausgr. Baden-Württemberg 2021, pp. 85-88	incollection
BibTeX: @incollection{Hecht2022, author = {Stefan Hecht, Olaf Bubenzer, Bertil Mächtle, Yvonne Tafelmaier}, title = {Blick in den Untergrund – Geophysikalische Untersuchungen in der Höhle Haus am Rosenstein}, booktitle = {Arch. Ausgr. Baden-Württemberg 2021}, publisher = {wbg Theiss}, year = {2022}, pages = {85--88} }
Heckmann, D., Frank, A., Arnold, M., Gietz, P. and Roth, C.	Citation segmentation from sparse &ampmathsemicolon noisy data: A joint inference approach with Markov logic networks [BibTeX]	2014	Digital Scholarship in the Humanities Vol. 31(2), pp. 333-356	article	DOI
BibTeX: @article{Heckmann2014, author = {Dustin Heckmann and Anette Frank and Matthias Arnold and Peter Gietz and Christian Roth}, title = {Citation segmentation from sparse &ampmathsemicolon noisy data: A joint inference approach with Markov logic networks}, journal = {Digital Scholarship in the Humanities}, publisher = {Oxford University Press (OUP)}, year = {2014}, volume = {31}, number = {2}, pages = {333--356}, doi = {https://doi.org/10.1093/llc/fqu061} }
Heckmann, D., Frank, A., Arnold, M., Gietz, P. and Roth, C.	Citation Segmentation from Sparse & Noisy Data: An Unsupervised Joint Inference Approach with Markov Logic Networks [BibTeX]	2015		article	DOI
BibTeX: @article{Heckmann2015, author = {Heckmann, Dustin and Frank, Anette and Arnold, Matthias and Gietz, Peter and Roth, Christian}, title = {Citation Segmentation from Sparse & Noisy Data: An Unsupervised Joint Inference Approach with Markov Logic Networks}, publisher = {Zenodo}, year = {2015}, doi = {https://doi.org/10.5281/ZENODO.4623281} }
Heidenreich, E., Pfeffer, T., Kracke, T., Mechtel, N., Nawroth, P., Hoffmann, G.F., Schmitt, C.P., Hell, R., Poschet, G. and Peters, V.	A Novel UPLC-MS/MS Method Identifies Organ-Specific Dipeptide Profiles [BibTeX]	2021	Vol. 22(18), pp. 9979	article	DOI
BibTeX: @article{Heidenreich2021, author = {Elena Heidenreich and Tilman Pfeffer and Tamara Kracke and Nils Mechtel and Peter Nawroth and Georg F Hoffmann and Claus Peter Schmitt and Rüdiger Hell and Gernot Poschet and Verena Peters}, title = {A Novel UPLC-MS/MS Method Identifies Organ-Specific Dipeptide Profiles}, publisher = {MDPI AG}, year = {2021}, volume = {22}, number = {18}, pages = {9979}, doi = {https://doi.org/10.3390/ijms22189979} }
Heil, J., Olsavszky, V., Busch, K., Klapproth, K., de la Torre, C., Sticht, C., Sandorski, K., Hoffmann, J., Schönhaber, H., Zierow, J., Winkler, M., Schmid, C.D., Staniczek, T., Daniels, D.E., Frayne, J., Metzgeroth, G., Nowak, D., Schneider, S., Neumaier, M., Weyer, V., Groden, C., Gröne, H.-J., Richter, K., Mogler, C., Taketo, M.M., Schledzewski, K., Géraud, C., Goerdt, S. and Koch, P.-S.	Bone marrow sinusoidal endothelium controls terminal erythroid differentiation and reticulocyte maturation [BibTeX]	2021	Nature Communications Vol. 12(1)	article	DOI
BibTeX: @article{Heil2021, author = {Joschka Heil and Victor Olsavszky and Katrin Busch and Kay Klapproth and Carolina de la Torre and Carsten Sticht and Kajetan Sandorski and Johannes Hoffmann and Hiltrud Schönhaber and Johanna Zierow and Manuel Winkler and Christian David Schmid and Theresa Staniczek and Deborah E. Daniels and Jan Frayne and Georgia Metzgeroth and Daniel Nowak and Sven Schneider and Michael Neumaier and Vanessa Weyer and Christoph Groden and Hermann-Josef Gröne and Karsten Richter and Carolin Mogler and Makoto Mark Taketo and Kai Schledzewski and Cyrill Géraud and Sergij Goerdt and Philipp-Sebastian Koch}, title = {Bone marrow sinusoidal endothelium controls terminal erythroid differentiation and reticulocyte maturation}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, doi = {https://doi.org/10.1038/s41467-021-27161-3} }
Heinen, P. and Gasenzer, T.	Complex Langevin approach to interacting Bose gases [BibTeX]	2022		article	DOI
BibTeX: @article{Heinen2022, author = {Heinen, Philipp and Gasenzer, Thomas}, title = {Complex Langevin approach to interacting Bose gases}, publisher = {arXiv}, year = {2022}, doi = {https://doi.org/10.48550/ARXIV.2204.10661} }
Heinen, P. and Gasenzer, T.	Simulating the Berezinskii-Kosterlitz-Thouless Transition with Complex Langevin [BibTeX]	2023		misc	DOI
BibTeX: @misc{Heinen2023a, author = {Heinen, Philipp and Gasenzer, Thomas}, title = {Simulating the Berezinskii-Kosterlitz-Thouless Transition with Complex Langevin}, publisher = {arXiv}, year = {2023}, doi = {https://doi.org/10.48550/ARXIV.2304.05699} }
Hemstedt, T.J., Bengtson, C.P., Ramírez, O., Oliveira, A.M. and Bading, H.	Reciprocal Interaction of Dendrite Geometry and Nuclear Calcium--VEGFD Signaling Gates Memory Consolidation and Extinction [Abstract] [BibTeX]	2017	Journal of Neuroscience Vol. 37(29), pp. 6946-6955	article	DOI URL
Abstract: Nuclear calcium is an important signaling end point in synaptic excitation--transcription coupling that is critical for long-term neuroadaptations. Here, we show that nuclear calcium acting via a target gene, VEGFD, is required for hippocampus-dependent fear memory consolidation and extinction in mice. Nuclear calcium--VEGFD signaling upholds the structural integrity and complexity of the dendritic arbor of CA1 neurons that renders those cells permissive for the efficient generation of synaptic input-evoked nuclear calcium transients driving the expression of plasticity-related genes. Therefore, the gating of memory functions rests on the reciprocally reinforcing maintenance of an intact dendrite geometry and a functional synapse-to-nucleus communication axis. In psychiatric and neurodegenerative disorders, therapeutic application of VEGFD may help to stabilize dendritic structures and network connectivity, which may prevent cognitive decline and could boost the efficacy of extinction-based exposure therapies.SIGNIFICANCE STATEMENT This study uncovers a reciprocal relationship between dendrite geometry, the ability to generate nuclear calcium transients in response to synaptic inputs, and the subsequent induction of expression of plasticity-related and dendritic structure-preserving genes. Insufficient nuclear calcium signaling in CA1 hippocampal neurons and, consequently, reduced expression of the nuclear calcium target gene VEGFD, a dendrite maintenance factor, leads to reduced-complexity basal dendrites of CA1 neurons, which severely compromises the animals' consolidation of both memory and extinction memory. The structure-protective function of VEGFD may prove beneficial in psychiatric disorders as well as neurodegenerative and aging-related conditions that are associated with loss of neuronal structures, dysfunctional excitation--transcription coupling, and cognitive decline.
BibTeX: @article{Hemstedt2017, author = {Hemstedt, Thekla J. and Bengtson, C. Peter and Ramírez, Omar and Oliveira, Ana M.M. and Bading, Hilmar}, title = {Reciprocal Interaction of Dendrite Geometry and Nuclear Calcium--VEGFD Signaling Gates Memory Consolidation and Extinction}, journal = {Journal of Neuroscience}, publisher = {Society for Neuroscience}, year = {2017}, volume = {37}, number = {29}, pages = {6946--6955}, url = {https://www.jneurosci.org/content/37/29/6946}, doi = {https://doi.org/10.1523/JNEUROSCI.2345-16.2017} }
Henke, K.	Building and Improving an OCR Classifier for Republican Chinese Newspaper Text [BibTeX]	2021		article	DOI
BibTeX: @article{Henke2021, author = {Henke, Konstantin}, title = {Building and Improving an OCR Classifier for Republican Chinese Newspaper Text}, publisher = {Heidelberg University Library}, year = {2021}, doi = {https://doi.org/10.11588/HEIDOK.00030845} }
Henke, K. and Arnold, M.	An OCR Classifier for Republican Chinese Newspaper Text – Creation and Post-processing [BibTeX]	2021		article	DOI
BibTeX: @article{Henke2021a, author = {Henke, Konstantin and Arnold, Matthias}, title = {An OCR Classifier for Republican Chinese Newspaper Text – Creation and Post-processing}, publisher = {Zenodo}, year = {2021}, doi = {https://doi.org/10.5281/ZENODO.5772127} }
Henkel, C., Mühle, S., Bendo, G., Józsa, G.I.G., Gong, Y., Viti, S., Aalto, S., Combes, F., García-Burillo, S., Hunt, L.K., Mangum, J., Martín, S., Muller, S., Ott, J., van der Werf, P., Malawi, A.A., Ismail, H., Alkhuja, E., Asiri, H.M., Aladro, R., Alves, F., Ao, Y., Baan, W.A., Costagliola, F., Fuller, G., Greene, J., Impellizzeri, C.M.V., Kamali, F., Klessen, R.S., Mauersberger, R., Tang, X.D., Tristram, K., Wang, M. and Zhang, J.S.	Molecular line emission in NGC 4945, imaged with ALMA [BibTeX]	2018	Astronomy & Astrophysics Vol. 615, pp. A155	article	DOI
BibTeX: @article{Henkel2018, author = {Henkel, C. and Mühle, S. and Bendo, G. and Józsa, G. I. G. and Gong, Y. and Viti, S. and Aalto, S. and Combes, F. and García-Burillo, S. and Hunt, L. K. and Mangum, J. and Martín, S. and Muller, S. and Ott, J. and van der Werf, P. and Malawi, A. A. and Ismail, H. and Alkhuja, E. and Asiri, H. M. and Aladro, R. and Alves, F. and Ao, Y. and Baan, W. A. and Costagliola, F. and Fuller, G. and Greene, J. and Impellizzeri, C. M. V. and Kamali, F. and Klessen, R. S. and Mauersberger, R. and Tang, X. D. and Tristram, K. and Wang, M. and Zhang, J. S.}, title = {Molecular line emission in NGC 4945, imaged with ALMA}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {615}, pages = {A155}, doi = {https://doi.org/10.1051/0004-6361/201732174} }
Herbst, S.A., Vesterlund, M., Helmboldt, A.J., Jafari, R., Siavelis, I., Stahl, M., Schitter, E.C., Liebers, N., Brinkmann, B.J., Czernilofsky, F., Roider, T., Bruch, P.-M., Iskar, M., Kittai, A., Huang, Y., Lu, J., Richter, S., Mermelekas, G., Umer, H.M., Knoll, M., Kolb, C., Lenze, A., Cao, X., Österholm, C., Wahnschaffe, L., Herling, C., Scheinost, S., Ganzinger, M., Mansouri, L., Kriegsmann, K., Kriegsmann, M., Anders, S., Zapatka, M., Poeta, G.D., Zucchetto, A., Bomben, R., Gattei, V., Dreger, P., Woyach, J., Herling, M., Müller-Tidow, C., Rosenquist, R., Stilgenbauer, S., Zenz, T., Huber, W., Tausch, E., Lehtiö, J. and Dietrich, S.	Proteogenomics refines the molecular classification of chronic lymphocytic leukemia [BibTeX]	2022	Nature Communications Vol. 13(1)	article	DOI
BibTeX: @article{Herbst2022, author = {Sophie A. Herbst and Mattias Vesterlund and Alexander J. Helmboldt and Rozbeh Jafari and Ioannis Siavelis and Matthias Stahl and Eva C. Schitter and Nora Liebers and Berit J. Brinkmann and Felix Czernilofsky and Tobias Roider and Peter-Martin Bruch and Murat Iskar and Adam Kittai and Ying Huang and Junyan Lu and Sarah Richter and Georgios Mermelekas and Husen Muhammad Umer and Mareike Knoll and Carolin Kolb and Angela Lenze and Xiaofang Cao and Cecilia Österholm and Linus Wahnschaffe and Carmen Herling and Sebastian Scheinost and Matthias Ganzinger and Larry Mansouri and Katharina Kriegsmann and Mark Kriegsmann and Simon Anders and Marc Zapatka and Giovanni Del Poeta and Antonella Zucchetto and Riccardo Bomben and Valter Gattei and Peter Dreger and Jennifer Woyach and Marco Herling and Carsten Müller-Tidow and Richard Rosenquist and Stephan Stilgenbauer and Thorsten Zenz and Wolfgang Huber and Eugen Tausch and Janne Lehtiö and Sascha Dietrich}, title = {Proteogenomics refines the molecular classification of chronic lymphocytic leukemia}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {13}, number = {1}, doi = {https://doi.org/10.1038/s41467-022-33385-8} }
Hesse, A., Köster, K., Steiner, J., Michl, J., Vorobyov, V., Dasari, D., Wrachtrup, J. and Jendrzejewski, F.	Direct control of high magnetic fields for cold atom experiments based on NV centers [Abstract] [BibTeX]	2021	New Journal of Physics Vol. 23(2), pp. 023037	article	DOI
Abstract: In cold atomic gases the interactions between the atoms are directly controllable through external magnetic fields. The magnetic field control is typically performed indirectly by stabilizing the current through a pair of Helmholtz coils, which produce this large bias field. Here, we overcome the limitations of such an indirect control through a direct feedback scheme, which is based on nitrogen-vacancy centers acting as a magnetic field sensor. This allows us to measure and stabilize fields of 4.66 mT down to 12 nT RMS noise over the course of 24 h, measured on a 1 Hz bandwidth. We achieve a control of better than 1 ppm after 20 minutes of integration time, ensuring high long-term stability for experiments. This approach extends direct magnetic field control to strong magnetic fields, which could enable new precise quantum simulations in this regime.
BibTeX: @article{Hesse2021, author = {Alexander Hesse and Kerim Köster and Jakob Steiner and Julia Michl and Vadim Vorobyov and Durga Dasari and Jörg Wrachtrup and Fred Jendrzejewski}, title = {Direct control of high magnetic fields for cold atom experiments based on NV centers}, journal = {New Journal of Physics}, publisher = {IOP Publishing}, year = {2021}, volume = {23}, number = {2}, pages = {023037}, doi = {https://doi.org/10.1088/1367-2630/abe1e5} }
Hesser, J. and Brivio, D.	X-ray based nanoparticle imaging [BibTeX]	2020		incollection	DOI
BibTeX: @incollection{Hesser2020, author = {Juergen Hesser and Davide Brivio}, title = {X-ray based nanoparticle imaging}, publisher = {IOP Publishing}, year = {2020}, doi = {https://doi.org/10.1088/978-0-7503-2396-3ch12} }
Hilf, N., Kuttruff-Coqui, S., Frenzel, K., Bukur, V., Stevanović, S., Gouttefangeas, C., Platten, M., Tabatabai, G., Dutoit, V., van der Burg, S.H., thor Straten, P., Martínez-Ricarte, F., Ponsati, B., Okada, H., Lassen, U., Admon, A., Ottensmeier, C.H., Ulges, A., Kreiter, S., von Deimling, A., Skardelly, M., Migliorini, D., Kroep, J.R., Idorn, M., Rodon, J., Piró, J., Poulsen, H.S., Shraibman, B., McCann, K., Mendrzyk, R., Löwer, M., Stieglbauer, M., Britten, C.M., Capper, D., Welters, M.J.P., Sahuquillo, J., Kiesel, K., Derhovanessian, E., Rusch, E., Bunse, L., Song, C., Heesch, S., Wagner, C., Kemmer-Brück, A., Ludwig, J., Castle, J.C., Schoor, O., Tadmor, A.D., Green, E., Fritsche, J., Meyer, M., Pawlowski, N., Dorner, S., Hoffgaard, F., Rössler, B., Maurer, D., Weinschenk, T., Reinhardt, C., Huber, C., Rammensee, H.-G., Singh-Jasuja, H., Sahin, U., Dietrich, P.-Y. and Wick, W.	Actively personalized vaccination trial for newly diagnosed glioblastoma [Abstract] [BibTeX]	2019	Nature Vol. 565(7738), pp. 240-245	article	DOI
Abstract: Patients with glioblastoma currently do not sufficiently benefit from recent breakthroughs in cancer treatment that use checkpoint inhibitors1,2. For treatments using checkpoint inhibitors to be successful, a high mutational load and responses to neoepitopes are thought to be essential3. There is limited intratumoural infiltration of immune cells4 in glioblastoma and these tumours contain only 30--50 non-synonymous mutations5. Exploitation of the full repertoire of tumour antigens---that is, both unmutated antigens and neoepitopes---may offer more effective immunotherapies, especially for tumours with a low mutational load. Here, in the phase I trial GAPVAC-101 of the Glioma Actively Personalized Vaccine Consortium (GAPVAC), we integrated highly individualized vaccinations with both types of tumour antigens into standard care to optimally exploit the limited target space for patients with newly diagnosed glioblastoma. Fifteen patients with glioblastomas positive for human leukocyte antigen (HLA)-A02:01 or HLA-A24:02 were treated with a vaccine (APVAC1) derived from a premanufactured library of unmutated antigens followed by treatment with APVAC2, which preferentially targeted neoepitopes. Personalization was based on mutations and analyses of the transcriptomes and immunopeptidomes of the individual tumours. The GAPVAC approach was feasible and vaccines that had poly-ICLC (polyriboinosinic-polyribocytidylic acid-poly-l-lysine carboxymethylcellulose) and granulocyte--macrophage colony-stimulating factor as adjuvants displayed favourable safety and strong immunogenicity. Unmutated APVAC1 antigens elicited sustained responses of central memory CD8+ T cells. APVAC2 induced predominantly CD4+ T cell responses of T helper 1 type against predicted neoepitopes.
BibTeX: @article{Hilf2019, author = {Hilf, Norbert and Kuttruff-Coqui, Sabrina and Frenzel, Katrin and Bukur, Valesca and Stevanović, Stefan and Gouttefangeas, Cécile and Platten, Michael and Tabatabai, Ghazaleh and Dutoit, Valerie and van der Burg, Sjoerd H. and thor Straten, Per and Martínez-Ricarte, Francisco and Ponsati, Berta and Okada, Hideho and Lassen, Ulrik and Admon, Arie and Ottensmeier, Christian H. and Ulges, Alexander and Kreiter, Sebastian and von Deimling, Andreas and Skardelly, Marco and Migliorini, Denis and Kroep, Judith R. and Idorn, Manja and Rodon, Jordi and Piró, Jordi and Poulsen, Hans S. and Shraibman, Bracha and McCann, Katy and Mendrzyk, Regina and Löwer, Martin and Stieglbauer, Monika and Britten, Cedrik M. and Capper, David and Welters, Marij J. P. and Sahuquillo, Juan and Kiesel, Katharina and Derhovanessian, Evelyna and Rusch, Elisa and Bunse, Lukas and Song, Colette and Heesch, Sandra and Wagner, Claudia and Kemmer-Brück, Alexandra and Ludwig, Jörg and Castle, John C. and Schoor, Oliver and Tadmor, Arbel D. and Green, Edward and Fritsche, Jens and Meyer, Miriam and Pawlowski, Nina and Dorner, Sonja and Hoffgaard, Franziska and Rössler, Bernhard and Maurer, Dominik and Weinschenk, Toni and Reinhardt, Carsten and Huber, Christoph and Rammensee, Hans-Georg and Singh-Jasuja, Harpreet and Sahin, Ugur and Dietrich, Pierre-Yves and Wick, Wolfgang}, title = {Actively personalized vaccination trial for newly diagnosed glioblastoma}, journal = {Nature}, year = {2019}, volume = {565}, number = {7738}, pages = {240--245}, doi = {https://doi.org/10.1038/s41586-018-0810-y} }
Himmels, P., Paredes, I., Adler, H., Karakatsani, A., Luck, R., Marti, H.H., Ermakova, O., Rempel, E., Stoeckli, E.T. and Ruiz de Almodóvar, C.	Motor neurons control blood vessel patterning in the developing spinal cord [Abstract] [BibTeX]	2017	Nature Communications Vol. 8(1), pp. 14583	article	DOI
Abstract: Formation of a precise vascular network within the central nervous system is of critical importance to assure delivery of oxygen and nutrients and for accurate functionality of neuronal networks. Vascularization of the spinal cord is a highly stereotypical process. However, the guidance cues controlling blood vessel patterning in this organ remain largely unknown. Here we describe a new neuro-vascular communication mechanism that controls vessel guidance in the developing spinal cord. We show that motor neuron columns remain avascular during a developmental time window, despite expressing high levels of the pro-angiogenic vascular endothelial growth factor (VEGF). We describe that motor neurons express the VEGF trapping receptor sFlt1 via a Neuropilin-1-dependent mechanism. Using a VEGF gain-of-function approach in mice and a motor neuron-specific sFlt1 loss-of-function approach in chicken, we show that motor neurons control blood vessel patterning by an autocrine mechanism that titrates motor neuron-derived VEGF via their own expression of sFlt1.
BibTeX: @article{Himmels2017, author = {Himmels, Patricia and Paredes, Isidora and Adler, Heike and Karakatsani, Andromachi and Luck, Robert and Marti, Hugo H. and Ermakova, Olga and Rempel, Eugen and Stoeckli, Esther T. and Ruiz de Almodóvar, Carmen}, title = {Motor neurons control blood vessel patterning in the developing spinal cord}, journal = {Nature Communications}, year = {2017}, volume = {8}, number = {1}, pages = {14583}, doi = {https://doi.org/10.1038/ncomms14583} }
Hinsenkamp, I., Köhler, J.P., Flächsenhaar, C., Hitkova, I., Meessen, S.E., Gaiser, T., Wieland, T., Weiss, C., Röcken, C., Mowat, M., Quante, M., Taxauer, K., Mejias-Luque, R., Gerhard, M., Vogelmann, R., Meindl-Beinker, N., Ebert, M. and Burgermeister, E.	Functional antagonism between CagA and DLC1 in gastric cancer [Abstract] [BibTeX]	2022	Cell Death Discovery Vol. 8(1)	article	DOI URL
Abstract: AbstractHelicobacter (H.) pylori-induced gastritis is a risk factor for gastric cancer (GC). Deleted-in-liver-cancer-1 (DLC1/ARHGAP7) inhibits RHOA, a downstream mediator of virulence factor cytotoxin-A (CagA) signalling and driver of consensus-molecular-subtype-2 diffuse GC. DLC1 located to enterochromaffin-like and MIST1+ stem/chief cells in the stomach. DLC1+ cells were reduced in H. pylori gastritis and GC, and in mice infected with H. pylori. DLC1 positivity inversely correlated with tumour progression in patients. GC cells retained an N-terminal truncation variant DLC1v4 in contrast to full-length DLC1v1 in non-neoplastic tissues. H. pylori and CagA downregulated DLC1v1/4 promoter activities. DLC1v1/4 inhibited cell migration and counteracted CagA-driven stress phenotypes enforcing focal adhesion. CagA and DLC1 interacted via their N- and C-terminal domains, proposing that DLC1 protects against H. pylori by neutralising CagA. H. pylori-induced DLC1 loss is an early molecular event, which makes it a potential marker or target for subtype-aware cancer prevention or therapy.
BibTeX: @article{Hinsenkamp2022, author = {Isabel Hinsenkamp, Jan P. Köhler, Christoph Flächsenhaar, Ivana Hitkova, Sabine Eberhart Meessen, Timo Gaiser, Thomas Wieland, Christel Weiss, Christoph Röcken, Michael Mowat, Michael Quante, Karin Taxauer, Raquel Mejias-Luque, Markus Gerhard, Roger Vogelmann, Nadja Meindl-Beinker, Matthias Ebert, Elke Burgermeister}, title = {Functional antagonism between CagA and DLC1 in gastric cancer}, journal = {Cell Death Discovery}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {8}, number = {1}, url = {https://www.nature.com/articles/s41420-022-01134-x.pdf}, doi = {https://doi.org/10.1038/s41420-022-01134-x} }
Hoefflin, R., Harlander, S., Schäfer, S., Metzger, P., Kuo, F., Schönenberger, D., Adlesic, M., Peighambari, A., Seidel, P., Chen, C.-y., Consenza-Contreras, M., Jud, A., Lahrmann, B., Grabe, N., Heide, D., Uhl, F.M., Chan, T.A., Duyster, J., Zeiser, R., Schell, C., Heikenwalder, M., Schilling, O., Hakimi, A.A., Boerries, M. and Frew, I.J.	HIF-1upalpha and HIF-2upalpha differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Hoefflin2020, author = {Rouven Hoefflin and Sabine Harlander and Silvia Schäfer and Patrick Metzger and Fengshen Kuo and Désirée Schönenberger and Mojca Adlesic and Asin Peighambari and Philipp Seidel and Chia-yi Chen and Miguel Consenza-Contreras and Andreas Jud and Bernd Lahrmann and Niels Grabe and Danijela Heide and Franziska M. Uhl and Timothy A. Chan and Justus Duyster and Robert Zeiser and Christoph Schell and Mathias Heikenwalder and Oliver Schilling and A. Ari Hakimi and Melanie Boerries and Ian J. Frew}, title = {HIF-1upalpha and HIF-2upalpha differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-17873-3} }
Hoefflin, R., Harlander, S., Abhari, B.A., Peighambari, A., Adlesic, M., Seidel, P., Zodel, K., Haug, S., Göcmen, B., Li, Y., Lahrmann, B., Grabe, N., Heide, D., Boerries, M., Köttgen, A., Heikenwalder, M. and Frew, I.J.	Therapeutic Effects of Inhibition of Sphingosine-1-Phosphate Signaling in HIF-2upalpha Inhibitor-Resistant Clear Cell Renal Cell Carcinoma [BibTeX]	2021	Cancers Vol. 13(19), pp. 4801	article	DOI
BibTeX: @article{Hoefflin2021, author = {Rouven Hoefflin and Sabine Harlander and Behnaz A. Abhari and Asin Peighambari and Mojca Adlesic and Philipp Seidel and Kyra Zodel and Stefan Haug and Burulca Göcmen and Yong Li and Bernd Lahrmann and Niels Grabe and Danijela Heide and Melanie Boerries and Anna Köttgen and Mathias Heikenwalder and Ian J. Frew}, title = {Therapeutic Effects of Inhibition of Sphingosine-1-Phosphate Signaling in HIF-2upalpha Inhibitor-Resistant Clear Cell Renal Cell Carcinoma}, journal = {Cancers}, publisher = {MDPI AG}, year = {2021}, volume = {13}, number = {19}, pages = {4801}, doi = {https://doi.org/10.3390/cancers13194801} }
Hoffmann, J., Gamboa, S.M., Hofmann, A., Gliemann, H., Welle, A., Wacker, I., Schröder, R.R., Ness, L., Hagenmeyer, V. and Gengenbach, U.	Siloxane-functionalised surface patterns as templates for the ordered deposition of thin lamellar objects [Abstract] [BibTeX]	2019	Scientific Reports Vol. 9(1), pp. 17952	article	DOI
Abstract: A novel method is demonstrated for ordered deposition of thin lamellar objects from a liquid environment onto solid substrates by solid/fluid/solid-driven organisation. Surface functionalisation forms a template pattern that accumulates the lamellar objects by site-selective wetting of the target area without the need for a physical fluid containment. Contrary to conventional handling methods, no mechanical contact occurs, which facilitates the ordered deposition without wrinkles or ruptures. An additive and a subtractive process for the creation of such templates are presented. The subtractive process starts with the complete silanisation of the substrate in the vapour phase followed by site-selective oxygen plasma treatment of the siloxane film. The additive process uses microcontact printing to transfer the target pattern. Both processes are characterised by optical inspection of the wetting contours and it is found that site-selective plasma treatment shows a better pattern fidelity. The patterns obtained by site-selective plasma treatment are also subject to ToF-SIMS analysis and show good chemical contrast between hydrophilic and hydrophobic areas. The ordered deposition of lamellar objects by this new method is demonstrated for 60thinspacenm thick ultramicrotome sections of epoxide resin on pre-patterned glass substrates.
BibTeX: @article{Hoffmann2019, author = {Hoffmann, Julian and Gamboa, Sofia Madrigal and Hofmann, Andreas and Gliemann, Hartmut and Welle, Alexander and Wacker, Irene and Schröder, Rasmus R. and Ness, Len and Hagenmeyer, Veit and Gengenbach, Ulrich}, title = {Siloxane-functionalised surface patterns as templates for the ordered deposition of thin lamellar objects}, journal = {Scientific Reports}, year = {2019}, volume = {9}, number = {1}, pages = {17952}, doi = {https://doi.org/10.1038/s41598-019-54507-1} }
	The Roll in England and France in the Late Middle Ages [BibTeX]	2019		book	DOI
BibTeX: @book{Holz2019,, title = {The Roll in England and France in the Late Middle Ages}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110645125} }
Holzer, K., Ori, A., Cooke, A., Dauch, D., Drucker, E., Riemenschneider, P., Andres-Pons, A., DiGuilio, A.L., Mackmull, M.-T., Baßler, J., Roessler, S., Breuhahn, K., Zender, L., Glavy, J.S., Dombrowski, F., Hurt, E., Schirmacher, P., Beck, M. and Singer, S.	Nucleoporin Nup155 is part of the p53 network in liver cancer [BibTeX]	2019	Nature Communications Vol. 10(1)	article	DOI
BibTeX: @article{Holzer2019, author = {Kerstin Holzer and Alessandro Ori and Amy Cooke and Daniel Dauch and Elisabeth Drucker and Philip Riemenschneider and Amparo Andres-Pons and Amanda L. DiGuilio and Marie-Therese Mackmull and Jochen Baßler and Stephanie Roessler and Kai Breuhahn and Lars Zender and Joseph S. Glavy and Frank Dombrowski and Ed Hurt and Peter Schirmacher and Martin Beck and Stephan Singer}, title = {Nucleoporin Nup155 is part of the p53 network in liver cancer}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {10}, number = {1}, doi = {https://doi.org/10.1038/s41467-019-10133-z} }
Howard, C.S., Pudritz, R.E., Harris, W.E. and Klessen, R.S.	Simulating the UV escape fractions from molecular cloud populations in star-forming dwarf and spiral galaxies [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 475(3), pp. 3121-3134	article	DOI
BibTeX: @article{Howard2018, author = {Howard, Corey S. and Pudritz, Ralph E. and Harris, William E. and Klessen, Ralf S.}, title = {Simulating the UV escape fractions from molecular cloud populations in star-forming dwarf and spiral galaxies}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {475}, number = {3}, pages = {3121--3134}, doi = {https://doi.org/10.1093/mnras/stx3276} }
Huang, J., Brenna, C., ul Maula Khan, A., Daniele, C., Rudolf, R., Heuveline, V. and Gretz, N.	A cationic near infrared fluorescent agent and ethyl-cinnamate tissue clearing protocol for vascular staining and imaging [Abstract] [BibTeX]	2019	Scientific Reports Vol. 9(1), pp. 521	article	DOI
Abstract: Understanding vascular structures and dysfunction is a fundamental challenge. This task has been approached by using traditional methodologies such as microscopic computed tomography and magnetic resonance imaging. Both techniques are not only expensive but also time-consuming. Here, we present a new method for visualizing vascular structures in different organs in an efficient manner. A cationic near infrared (NIR) fluorescent dye was developed with attractive features to specifically stain blood vessels. Furthermore, we refined the process of organ staining and harvesting by retrograde perfusion and optimized the subsequent dehydration and clearing process by the use of an automatic tissue processor and a non-toxic substance, ethyl-cinnamate. Using this approach, the time interval between organ harvesting and microscopic analysis can be reduced from day(s) or weeks to 4thinspacehours. Finally, we have demonstrated that the new NIR fluorescent agent in combination with confocal or light-sheet microscopy can be efficiently used for visualization of vascular structures, such as the blood vessels in different organs e.g. glomeruli in kidneys, with an extremely high resolution. Our approach facilitates the development of automatic image processing and the quantitative analysis to study vascular and kidney diseases.
BibTeX: @article{Huang2019, author = {Jiaguo Huang and Cinzia Brenna and Arif ul Maula Khan and Cristina Daniele and Rüdiger Rudolf and Vincent Heuveline and Norbert Gretz}, title = {A cationic near infrared fluorescent agent and ethyl-cinnamate tissue clearing protocol for vascular staining and imaging}, journal = {Scientific Reports}, publisher = {Springer Nature}, year = {2019}, volume = {9}, number = {1}, pages = {521}, doi = {https://doi.org/10.1038/s41598-018-36741-1} }
	Paper Stories – Paper and Book History in Early Modern Europe [BibTeX]	2023		book	DOI
BibTeX: @book{Hufnagel2023,, title = {Paper Stories – Paper and Book History in Early Modern Europe}, publisher = {De Gruyter}, year = {2023}, doi = {https://doi.org/10.1515/9783111162768} }
Hussain, A., Schmidt, S. and Nüsser, M.	Dynamics of Mountain Urbanisation: Evidence from the Trans-Himalayan Town of Kargil, Ladakh, India [BibTeX]	2023	Land Vol. 12(4), pp. 920	article	DOI
BibTeX: @article{Hussain2023, author = {Altaf Hussain and Susanne Schmidt and Marcus Nüsser}, title = {Dynamics of Mountain Urbanisation: Evidence from the Trans-Himalayan Town of Kargil, Ladakh, India}, journal = {Land}, publisher = {MDPI AG}, year = {2023}, volume = {12}, number = {4}, pages = {920}, doi = {https://doi.org/10.3390/land12040920} }
Ibáñez-Mejía, J.C., Low, M.-M.M. and Klessen, R.S.	Gravity versus Magnetic Fields in Forming Molecular Clouds [Abstract] [BibTeX]	2022	The Astrophysical Journal Vol. 925(2), pp. 196	article	DOI
Abstract: Abstract Magnetic fields are dynamically important in the diffuse interstellar medium. Understanding how gravitationally bound, star-forming clouds form requires modeling of the fields in a self-consistent, supernova-driven, turbulent, magnetized, stratified disk. We employ the FLASH magnetohydrodynamics code to follow the formation and early evolution of clouds with final masses of 3–8 × 103 M ⊙ within such a simulation. We use the code’s adaptive mesh refinement capabilities to concentrate numerical resolution in zoom-in regions covering single clouds, allowing us to investigate the detailed dynamics and field structure of individual self-gravitating clouds in a consistent background medium. Our goal is to test the hypothesis that dense clouds are dynamically evolving objects far from magnetohydrostatic equilibrium. We find that the cloud envelopes are magnetically supported with field lines parallel to density gradients and flow velocity, as indicated by the histogram of relative orientations and other statistical measures. In contrast, the dense cores of the clouds are gravitationally dominated, with gravitational energy exceeding internal, kinetic, or magnetic energy and accelerations due to gravity exceeding those due to magnetic or thermal pressure gradients. In these regions, field directions vary strongly, with a slight preference toward being perpendicular to density gradients, as shown by three-dimensional histograms of relative orientation.
BibTeX: @article{IbanezMejia2022, author = {Juan C. Ibáñez-Mejía, Mordecai-Mark Mac Low, Ralf S. Klessen}, title = {Gravity versus Magnetic Fields in Forming Molecular Clouds}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2022}, volume = {925}, number = {2}, pages = {196}, doi = {https://doi.org/10.3847/1538-4357/ac3b58} }
Heidelberg, T.	iGEM 2022 Wiki [BibTeX]	2022		misc
BibTeX: @misc{IGEMWiki2022, author = {Team Heidelberg}, title = {iGEM 2022 Wiki}, year = {2022} }
Ilgenfritz, E.-M., Pawlowski, J.M., Rothkopf, A. and Trunin, A.	Finite-temperature gluon spectral functions from $$N_f=2+1+1$$Nf=2+1+1lattice QCD [Abstract] [BibTeX]	2018	The European Physical Journal C Vol. 78(2), pp. 127	article	DOI
Abstract: We investigate gluon correlation functions and spectral functions at finite temperature in Landau gauge on lattice QCD ensembles with $$N_f=2+1+1$$Nf=2+1+1dynamical twisted-mass quarks flavors, generated by the tmfT collaboration. They cover a temperature range from $$0.8backslashle T/T_Cbackslashle 4$$0.8≤T/TC≤4using the fixed-scale approach. Our study of spectral properties is based on a novel Bayesian approach for the extraction of non-positive-definite spectral functions. For each binned spatial momentum we take into account the gluon correlation functions at all available discrete imaginary frequencies. Clear indications for the existence of a well defined quasi-particle peak are obtained. Due to a relatively small number of imaginary frequencies available, we focus on the momentum and temperature dependence of the position of this spectral feature. The corresponding dispersion relation reveals different in-medium masses for longitudinal and transversal gluons at high temperatures, qualitatively consistent with weak coupling expectations.
BibTeX: @article{Ilgenfritz2018, author = {Ilgenfritz, Ernst-Michael and Pawlowski, Jan M. and Rothkopf, Alexander and Trunin, Anton}, title = {Finite-temperature gluon spectral functions from $$N_f=2+1+1$$Nf=2+1+1lattice QCD}, journal = {The European Physical Journal C}, year = {2018}, volume = {78}, number = {2}, pages = {127}, doi = {https://doi.org/10.1140/epjc/s10052-018-5593-7} }
Irmgard Sinning, M.A.M.	Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes [BibTeX]	2022	Current Opinion in Structural Biology Vol. 75, pp. 102428	article	DOI URL
BibTeX: @article{IrmgardSinning2022, author = {Irmgard Sinning, Melanie A. McDowell}, title = {Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes}, journal = {Current Opinion in Structural Biology}, publisher = {Elsevier BV}, year = {2022}, volume = {75}, pages = {102428}, url = {https://api.elsevier.com/content/article/PII:S0959440X22001075?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.sbi.2022.102428} }
Ismail, S., Flemming, D., Thoms, M., Gomes-Filho, J.V., Randau, L., Beckmann, R. and Hurt, E.	Emergence of the primordial pre-60S from the 90S pre-ribosome [BibTeX]	2022	Cell Reports Vol. 39(1), pp. 110640	article	DOI URL
BibTeX: @article{Ismail2022, author = {Sherif Ismail, Dirk Flemming, Matthias Thoms, José Vicente Gomes-Filho, Lennart Randau, Roland Beckmann, Ed Hurt}, title = {Emergence of the primordial pre-60S from the 90S pre-ribosome}, journal = {Cell Reports}, publisher = {Elsevier BV}, year = {2022}, volume = {39}, number = {1}, pages = {110640}, url = {https://api.elsevier.com/content/article/PII:S2211124722003928?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.celrep.2022.110640} }
Izquierdo, A.F., Smith, R.J., Glover, S.C.O., Klessen, R.S., Treß, R.G., Sormani, M.C., Clark, P.C., Duarte-Cabral, A. and Zucker, C.	The Cloud Factory II: gravoturbulent kinematics of resolved molecular clouds in a galactic potential [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 500(4), pp. 5268-5296	article	DOI
BibTeX: @article{Izquierdo2020, author = {Andrés F Izquierdo and Rowan J Smith and Simon C O Glover and Ralf S Klessen and Robin G Treß and Mattia C Sormani and Paul C Clark and Ana Duarte-Cabral and Catherine Zucker}, title = {The Cloud Factory II: gravoturbulent kinematics of resolved molecular clouds in a galactic potential}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {500}, number = {4}, pages = {5268--5296}, doi = {https://doi.org/10.1093/mnras/staa3470} }
J. Kellerer, F.S.	Monte Carlo simulations of the electron — gas interactions in the KATRIN experiment [Abstract] [BibTeX]	2022	Journal of Instrumentation Vol. 17(06), pp. P06029	article	DOI
Abstract: Abstract At the KATRIN experiment, the electron antineutrino mass is inferred from the shape of the β-decay spectrum of tritium. Important systematic effects in the Windowless Gaseous Tritium Source (WGTS) of the experiment include the energy loss by electron scattering, and the extended starting potential. In the WGTS, primary high-energy electrons from β-decay produce an extended secondary spectrum of electrons through various atomic and molecular processes including ionization, recombination, cluster formation and scattering. In addition to providing data essential to the simulation of energy loss processes, the electron spectrum also provides information important in the simulation of plasma processes. These simulations will then provide an insight on the starting potential. Here, a Monte Carlo approach is used to model the electron spectrum in the source for a given magnetic and electric field configuration. The spectrum is evaluated at different positions within the WGTS, which allows for a direct analysis of the spectrum close to the rear wall and detector end of the experiment. Alongside electrons, also ions are tracked by the simulation, resulting in a full description of the currents in the source.
BibTeX: @article{J.Kellerer2022, author = {J. Kellerer, F. Spanier}, title = {Monte Carlo simulations of the electron — gas interactions in the KATRIN experiment}, journal = {Journal of Instrumentation}, publisher = {IOP Publishing}, year = {2022}, volume = {17}, number = {06}, pages = {P06029}, doi = {https://doi.org/10.1088/1748-0221/17/06/P06029} }
Jahnke, K., Ritzmann, N., Fichtler, J., Nitschke, A., Dreher, Y., Abele, T., Hofhaus, G., Platzman, I., Schröder, R.R., Müller, D.J., Spatz, J.P. and Göpfrich, K.	Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells [Abstract] [BibTeX]	2021	Nature Communications Vol. 12(1)	article	DOI URL
Abstract: AbstractBottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Here, we realize a strategic merger of both approaches to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. When DNA origami plates are modified with the pH-sensitive triplex motif, the proton-pumping E. coli can trigger their attachment to giant unilamellar lipid vesicles (GUVs) upon illumination. A DNA cortex is formed upon DNA origami polymerization, which sculpts and deforms the GUVs. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells.
BibTeX: @article{Jahnke2021, author = {Kevin Jahnke and Noah Ritzmann and Julius Fichtler and Anna Nitschke and Yannik Dreher and Tobias Abele and Götz Hofhaus and Ilia Platzman and Rasmus R. Schröder and Daniel J. Müller and Joachim P. Spatz and Kerstin Göpfrich}, title = {Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, url = {https://www.nature.com/articles/s41467-021-24103-x.pdf}, doi = {https://doi.org/10.1038/s41467-021-24103-x} }
Janssen, M., Schmidt, C., Bruch, P.-M., Blank, M.F., Rohde, C., Waclawiczek, A., Heid, D., Renders, S., Göllner, S., Vierbaum, L., Besenbeck, B., Herbst, S.A., Knoll, M., Kolb, C., Przybylla, A., Weidenauer, K., Ludwig, A.K., Fabre, M., Gu, M., Schlenk, R.F., Stölzel, F., Bornhäuser, M., Röllig, C., Platzbecker, U., Baldus, C., Serve, H., Sauer, T., Raffel, S., Pabst, C., Vassiliou, G., Vick, B., Jeremias, I., Trumpp, A., Krijgsveld, J., Müller-Tidow, C. and Dietrich, S.	Venetoclax synergizes with gilteritinib in FLT3 wild-type high-risk acute myeloid leukemia by suppressing MCL-1 [Abstract] [BibTeX]	2022	Blood Vol. 140(24), pp. 2594-2610	article	DOI URL
Abstract: Abstract BCL-2 inhibition has been shown to be effective in acute myeloid leukemia (AML) in combination with hypomethylating agents or low-dose cytarabine. However, resistance and relapse represent major clinical challenges. Therefore, there is an unmet need to overcome resistance to current venetoclax-based strategies. We performed high-throughput drug screening to identify effective combination partners for venetoclax in AML. Overall, 64 antileukemic drugs were screened in 31 primary high-risk AML samples with or without venetoclax. Gilteritinib exhibited the highest synergy with venetoclax in FLT3 wild-type AML. The combination of gilteritinib and venetoclax increased apoptosis, reduced viability, and was active in venetoclax-azacitidine–resistant cell lines and primary patient samples. Proteomics revealed increased FLT3 wild-type signaling in specimens with low in vitro response to the currently used venetoclax-azacitidine combination. Mechanistically, venetoclax with gilteritinib decreased phosphorylation of ERK and GSK3B via combined AXL and FLT3 inhibition with subsequent suppression of the antiapoptotic protein MCL-1. MCL-1 downregulation was associated with increased MCL-1 phosphorylation of serine 159, decreased phosphorylation of threonine 161, and proteasomal degradation. Gilteritinib and venetoclax were active in an FLT3 wild-type AML patient-derived xenograft model with TP53 mutation and reduced leukemic burden in 4 patients with FLT3 wild-type AML receiving venetoclax-gilteritinib off label after developing refractory disease under venetoclax-azacitidine. In summary, our results suggest that combined inhibition of FLT3/AXL potentiates venetoclax response in FLT3 wild-type AML by inducing MCL-1 degradation. Therefore, the venetoclax-gilteritinib combination merits testing as a potentially active regimen in patients with high-risk FLT3 wild-type AML.
BibTeX: @article{Janssen2022, author = {Maike Janssen, Christina Schmidt, Peter-Martin Bruch, Maximilian F. Blank, Christian Rohde, Alexander Waclawiczek, Daniel Heid, Simon Renders, Stefanie Göllner, Lisa Vierbaum, Birgit Besenbeck, Sophie A. Herbst, Mareike Knoll, Carolin Kolb, Adriana Przybylla, Katharina Weidenauer, Anne Kathrin Ludwig, Margarete Fabre, Muxin Gu, Richard F. Schlenk, Friedrich Stölzel, Martin Bornhäuser, Christoph Röllig, Uwe Platzbecker, Claudia Baldus, Hubert Serve, Tim Sauer, Simon Raffel, Caroline Pabst, George Vassiliou, Binje Vick, Irmela Jeremias, Andreas Trumpp, Jeroen Krijgsveld, Carsten Müller-Tidow, Sascha Dietrich}, title = {Venetoclax synergizes with gilteritinib in FLT3 wild-type high-risk acute myeloid leukemia by suppressing MCL-1}, journal = {Blood}, publisher = {American Society of Hematology}, year = {2022}, volume = {140}, number = {24}, pages = {2594--2610}, url = {https://ashpublications.org/blood/article-pdf/140/24/2594/2023999/blood_bld-2021-014241-main.pdf}, doi = {https://doi.org/10.1182/blood.2021014241} }
Jauch, A.S., Wohlfeil, S.A., Weller, C., Dietsch, B., Häfele, V., Stojanovic, A., Kittel, M., Nolte, H., Cerwenka, A., Neumaier, M., Schledzewski, K., Sticht, C., Reiners-Koch, P.-S., Goerdt, S. and Géraud, C.	Lyve-1 deficiency enhances the hepatic immune microenvironment entailing altered susceptibility to melanoma liver metastasis [Abstract] [BibTeX]	2022	Cancer Cell International Vol. 22(1)	article	DOI
Abstract: Abstract Background Hyaluronan receptor LYVE-1 is expressed by liver sinusoidal endothelial cells (LSEC), lymphatic endothelial cells and specialized macrophages. Besides binding to hyaluronan, LYVE-1 can mediate adhesion of leukocytes and cancer cells to endothelial cells. Here, we assessed the impact of LYVE-1 on physiological liver functions and metastasis. Methods Mice with deficiency of Lyve-1 (Lyve-1-KO) were analyzed using histology, immunofluorescence, microarray analysis, plasma proteomics and flow cytometry. Liver metastasis was studied by intrasplenic/intravenous injection of melanoma (B16F10 luc2, WT31) or colorectal carcinoma (MC38). Results Hepatic architecture, liver size, endothelial differentiation and angiocrine functions were unaltered in Lyve-1-KO. Hyaluronan plasma levels were significantly increased in Lyve-1-KO. Besides, plasma proteomics revealed increased carbonic anhydrase-2 and decreased FXIIIA. Furthermore, gene expression analysis of LSEC indicated regulation of immunological pathways. Therefore, liver metastasis of highly and weakly immunogenic tumors, i.e. melanoma and colorectal carcinoma (CRC), was analyzed. Hepatic metastasis of B16F10 luc2 and WT31 melanoma cells, but not MC38 CRC cells, was significantly reduced in Lyve-1-KO mice. In vivo retention assays with B16F10 luc2 cells were unaltered between Lyve-1-KO and control mice. However, in tumor-free Lyve-1-KO livers numbers of hepatic CD4+, CD8+ and regulatory T cells were increased. In addition, iron deposition was found in F4/80+ liver macrophages known to exert pro-inflammatory effects. Conclusion Lyve-1 deficiency controlled hepatic metastasis in a tumor cell-specific manner leading to reduced growth of hepatic metastases of melanoma, but not CRC. Anti-tumorigenic effects are likely due to enhancement of the premetastatic hepatic immune microenvironment influencing early liver metastasis formation.
BibTeX: @article{Jauch2022, author = {Anna Sophia Jauch, Sebastian A. Wohlfeil, Céline Weller, Bianca Dietsch, Verena Häfele, Ana Stojanovic, Maximilian Kittel, Hendrik Nolte, Adelheid Cerwenka, Michael Neumaier, Kai Schledzewski, Carsten Sticht, Philipp-Sebastian Reiners-Koch, Sergij Goerdt, Cyrill Géraud}, title = {Lyve-1 deficiency enhances the hepatic immune microenvironment entailing altered susceptibility to melanoma liver metastasis}, journal = {Cancer Cell International}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {22}, number = {1}, doi = {https://doi.org/10.1186/s12935-022-02800-x} }
Jauch, I., Kamm, J., Benn, L., Rettig, L., Friederich, H.-C., Tesarz, J., Kuner, T. and Wieland, S.	2MDR, a Microcomputer-Controlled Visual Stimulation Device for Psychotherapy-Like Treatments of Mice [BibTeX]	2023	eneuro Vol. 10(6), pp. ENEURO.0394-22.2023	article	DOI
BibTeX: @article{Jauch2023, author = {Isa Jauch and Jan Kamm and Luca Benn and Lukas Rettig and Hans-Christoph Friederich and Jonas Tesarz and Thomas Kuner and Sebastian Wieland}, title = {2MDR, a Microcomputer-Controlled Visual Stimulation Device for Psychotherapy-Like Treatments of Mice}, journal = {eneuro}, publisher = {Society for Neuroscience}, year = {2023}, volume = {10}, number = {6}, pages = {ENEURO.0394--22.2023}, doi = {https://doi.org/10.1523/eneuro.0394-22.2023} }
Jaura, O., Glover, S.C.O., Klessen, R.S. and Paardekooper, J.-P.	SPRAI: coupling of radiative feedback and primordial chemistry in moving mesh hydrodynamics [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 475, pp. 2822-2834	article	DOI
BibTeX: @article{Jaura2018, author = {Jaura, O and Glover, S C O and Klessen, R S and Paardekooper, J-P}, title = {SPRAI: coupling of radiative feedback and primordial chemistry in moving mesh hydrodynamics}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {475}, pages = {2822--2834}, doi = {https://doi.org/10.1093/mnras/stx3356} }
Jaura, O., Magg, M., Glover, S.C.O. and Klessen, R.S.	SPRAI-II: multifrequency radiative transfer for variable gas densities [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 499(3), pp. 3594-3609	article	DOI
BibTeX: @article{Jaura2020, author = {Ondrej Jaura and Mattis Magg and Simon C O Glover and Ralf S Klessen}, title = {SPRAI-II: multifrequency radiative transfer for variable gas densities}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {499}, number = {3}, pages = {3594--3609}, doi = {https://doi.org/10.1093/mnras/staa3054} }
Jaura, O., Glover, S.C.O., Wollenberg, K.M.J., Klessen, R.S., Geen, S. and Haemmerlé, L.	Trapping of H lessscpgreateriiless/scpgreater regions in Population III star formation [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 512(1), pp. 116-136	article	DOI
BibTeX: @article{Jaura2022, author = {Ondrej Jaura and Simon C O Glover and Katharina M J Wollenberg and Ralf S Klessen and Sam Geen and Lionel Haemmerlé}, title = {Trapping of H lessscpgreateriiless/scpgreater regions in Population III star formation}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {512}, number = {1}, pages = {116--136}, doi = {https://doi.org/10.1093/mnras/stac487} }
Jiménez-Donaire, M.J., Usero, A., Bešlić, I., Tafalla, M., Chacón-Tanarro, A., Salomé, Q., Eibensteiner, C., Garc\ia-Rodr\iguez, A., Hacar, A., Barnes, A.T., Bigiel, F., Chevance, M., Colombo, D., Dale, D.A., Davis, T.A., Glover, S.C.O., Kauffmann, J., Klessen, R.S., Leroy, A.K., Neumann, L., Pan, H., Pety, J., Querejeta, M., Saito, T., Schinnerer, E., Stuber, S. and Williams, T.G.	A constant Nlesssubgreater2less/subgreaterHlesssupgreatermathplusless/supgreater (1-0)-to-HCN (1-0) ratio on kiloparsec scales [BibTeX]	2023	Astronomy &ampmathsemicolon Astrophysics Vol. 676, pp. L11	article	DOI
BibTeX: @article{JimenezDonaire2023, author = {M. J. Jiménez-Donaire and A. Usero and I. Bešlić and M. Tafalla and A. Chacón-Tanarro and Q. Salomé and C. Eibensteiner and A. Garc\ia-Rodr\iguez and A. Hacar and A. T. Barnes and F. Bigiel and M. Chevance and D. Colombo and D. A. Dale and T. A. Davis and S. C. O. Glover and J. Kauffmann and R. S. Klessen and A. K. Leroy and L. Neumann and H. Pan and J. Pety and M. Querejeta and T. Saito and E. Schinnerer and S. Stuber and T. G. Williams}, title = {A constant Nlesssubgreater2less/subgreaterHlesssupgreatermathplusless/supgreater (1-0)-to-HCN (1-0) ratio on kiloparsec scales}, journal = {Astronomy &ampmathsemicolon Astrophysics}, publisher = {EDP Sciences}, year = {2023}, volume = {676}, pages = {L11}, doi = {https://doi.org/10.1051/0004-6361/202347050} }
Jing, Y., Ren, Y., Witzel, H.R. and Dobreva, G.	A BMP4-p38 MAPK signaling axis controls ISL1 protein stability and activity during cardiogenesis [BibTeX]	2021	Stem Cell Reports Vol. 16(8), pp. 1894-1905	article	DOI
BibTeX: @article{Jing2021, author = {Yanyan Jing and Yonggang Ren and Hagen Roland Witzel and Gergana Dobreva}, title = {A BMP4-p38 MAPK signaling axis controls ISL1 protein stability and activity during cardiogenesis}, journal = {Stem Cell Reports}, publisher = {Elsevier BV}, year = {2021}, volume = {16}, number = {8}, pages = {1894--1905}, doi = {https://doi.org/10.1016/j.stemcr.2021.06.017} }
Juaire, K.D., Lapouge, K., Becker, M.M., Kotova, I., Michelhans, M., Carapito, R., Wild, K., Bahram, S. and Sinning, I.	Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia [BibTeX]	2021	Structure Vol. 29(1), pp. 15-28.e7	article	DOI
BibTeX: @article{Juaire2021, author = {Keven D. Juaire and Karine Lapouge and Matthias M.M. Becker and Irina Kotova and Michelle Michelhans and Raphael Carapito and Klemens Wild and Seiamak Bahram and Irmgard Sinning}, title = {Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia}, journal = {Structure}, publisher = {Elsevier BV}, year = {2021}, volume = {29}, number = {1}, pages = {15--28.e7}, doi = {https://doi.org/10.1016/j.str.2020.09.008} }
Juan Aguilar, P.A.M.	Das dritte und vierte Relief von Gundük [BibTeX]	2019	Zeitschrift für Assyriologie 109, pp. 238-246	incollection
BibTeX: @incollection{JuanAguilar2019, author = {Juan Aguilar, Peter A. Miglus}, title = {Das dritte und vierte Relief von Gundük}, booktitle = {Zeitschrift für Assyriologie 109}, publisher = {DeGruyter}, year = {2019}, pages = {238-246} }
Juneja, M.	Can Art History be Made Global? Meditations from the Periphery [BibTeX]	2023		book	DOI
BibTeX: @book{Juneja2023, author = {Monica Juneja}, title = {Can Art History be Made Global? Meditations from the Periphery}, publisher = {De Gruyter}, year = {2023}, doi = {https://doi.org/10.1515/9783111217062/html} }
Jungmann, M., Vardag, S.N., Kutzner, F., Keppler, F., Schmidt, M., Aeschbach, N., Gerhard, U., Zipf, A., Lautenbach, S., Siegmund, A., Goeschl, T. and Butz, A.	Zooming-in for climate action—hyperlocal greenhouse gas data for mitigation action? [BibTeX]	2022	Climate Action Vol. 1(1)	article	DOI
BibTeX: @article{Jungmann2022, author = {M Jungmann and S N Vardag and F Kutzner and F Keppler and M Schmidt and N Aeschbach and U Gerhard and A Zipf and S Lautenbach and A Siegmund and T Goeschl and A Butz}, title = {Zooming-in for climate action—hyperlocal greenhouse gas data for mitigation action?}, journal = {Climate Action}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {1}, number = {1}, doi = {https://doi.org/10.1007/s44168-022-00007-4} }
Kamm, G.B., Boffi, J.C., Zuza, K., Nencini, S., Campos, J., Schrenk-Siemens, K., Sonntag, I., Kabaoğlu, B., Hay, M.Y.A.E., Schwarz, Y., Tappe-Theodor, A., Bruns, D., Acuna, C., Kuner, T. and Siemens, J.	A synaptic temperature sensor for body cooling [BibTeX]	2021	Neuron Vol. 109(20), pp. 3283-3297.e11	article	DOI
BibTeX: @article{Kamm2021, author = {Gretel B. Kamm and Juan C. Boffi and Kristina Zuza and Sara Nencini and Joaquin Campos and Katrin Schrenk-Siemens and Ivo Sonntag and Burçe Kabaoğlu and Muad Y. Abd El Hay and Yvonne Schwarz and Anke Tappe-Theodor and Dieter Bruns and Claudio Acuna and Thomas Kuner and Jan Siemens}, title = {A synaptic temperature sensor for body cooling}, journal = {Neuron}, publisher = {Elsevier BV}, year = {2021}, volume = {109}, number = {20}, pages = {3283--3297.e11}, doi = {https://doi.org/10.1016/j.neuron.2021.10.001} }
Kammerer, J., Schröder, R., Perkhun, P., Margeat, O., Köntges, W., Videlot-Ackermann, C., Ackermann, J., Wacker, I. and Pfannmöller, M.	Morphology of NFA Organic Photovoltaic Blends by Automated Segmentation of Spatially Resolved Electron Spectra [BibTeX]	2019		inproceedings	DOI
BibTeX: @inproceedings{Kammerer2019, author = {Kammerer, Jochen and Schröder, Rasum and Perkhun, Pavlo and Margeat, Olivier and Köntges, Wolfgang and Videlot-Ackermann, Christine and Ackermann, Jörg and Wacker, Irene and Pfannmöller, Martin}, title = {Morphology of NFA Organic Photovoltaic Blends by Automated Segmentation of Spatially Resolved Electron Spectra}, year = {2019}, doi = {https://doi.org/10.29363/nanoge.ngfm.2019.167} }
Kammerer, J.A., Duan, X., Neubrech, F., Schröder, R.R., Liu, N. and Pfannmöller, M.	Stabilizing upgamma-MgH 2 at Nanotwins in Mechanically Constrained Nanoparticles [BibTeX]	2021	Advanced Materials Vol. 33(11), pp. 2008259	article	DOI
BibTeX: @article{Kammerer2021, author = {Jochen A. Kammerer and Xiaoyang Duan and Frank Neubrech and Rasmus R. Schröder and Na Liu and Martin Pfannmöller}, title = {Stabilizing upgamma-MgH 2 at Nanotwins in Mechanically Constrained Nanoparticles}, journal = {Advanced Materials}, publisher = {Wiley}, year = {2021}, volume = {33}, number = {11}, pages = {2008259}, doi = {https://doi.org/10.1002/adma.202008259} }
van de Kamp, T., Schwermann, A.H., dos Santos Rolo, T., Lösel, P.D., Engler, T., Etter, W., Faragó, T., Göttlicher, J., Heuveline, V., Kopmann, A., Mähler, B., Mörs, T., Odar, J., Rust, J., Jerome, N.T., Vogelgesang, M., Baumbach, T. and Krogmann, L.	Parasitoid biology preserved in mineralized fossils [BibTeX]	2018	Nature Communications Vol. 9(1), pp. 3325	article	DOI
BibTeX: @article{Kamp2018, author = {Thomas van de Kamp and Achim H. Schwermann and Tomy dos Santos Rolo and Philipp D. Lösel and Thomas Engler and Walter Etter and Tomáš Faragó and Jörg Göttlicher and Vincent Heuveline and Andreas Kopmann and Bastian Mähler and Thomas Mörs and Janes Odar and Jes Rust and Nicholas Tan Jerome and Matthias Vogelgesang and Tilo Baumbach and Lars Krogmann}, title = {Parasitoid biology preserved in mineralized fossils}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2018}, volume = {9}, number = {1}, pages = {3325}, doi = {https://doi.org/10.1038/s41467-018-05654-y} }
van de Kamp, T., Mikó, I., Staniczek, A.H., Eggs, B., Bajerlein, D., Faragó, T., Hagelstein, L., Hamann, E., Spiecker, R., Baumbach, T., Janšta, P. and Krogmann, L.	Evolution of flexible biting in hyperdiverse parasitoid wasps [BibTeX]	2022	Proceedings of the Royal Society B: Biological Sciences Vol. 289(1967)	article	DOI
BibTeX: @article{Kamp2022, author = {Thomas van de Kamp and István Mikó and Arnold H. Staniczek and Benjamin Eggs and Daria Bajerlein and Tomáš Faragó and Lea Hagelstein and Elias Hamann and Rebecca Spiecker and Tilo Baumbach and Petr Janšta and Lars Krogmann}, title = {Evolution of flexible biting in hyperdiverse parasitoid wasps}, journal = {Proceedings of the Royal Society B: Biological Sciences}, publisher = {The Royal Society}, year = {2022}, volume = {289}, number = {1967}, doi = {https://doi.org/10.1098/rspb.2021.2086} }
Kang, D.E., Pellegrini, E.W., Ardizzone, L., Klessen, R.S., Koethe, U., Glover, S.C.O. and Ksoll, V.F.	Emission-line diagnostics of H ii regions using conditional invertible neural networks [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 512(1), pp. 617-647	article	DOI
BibTeX: @article{Kang2022, author = {Da Eun Kang, Eric W Pellegrini, Lynton Ardizzone, Ralf S Klessen, Ullrich Koethe, Simon C O Glover, Victor F Ksoll}, title = {Emission-line diagnostics of H ii regions using conditional invertible neural networks}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {512}, number = {1}, pages = {617--647}, doi = {https://doi.org/10.1093/mnras/stac222} }
Kang, D.E., Ksoll, V.F., Itrich, D., Testi, L., Klessen, R.S., Hennebelle, P. and Molinari, S.	Spectral classification of young stars using conditional invertible neural networks [BibTeX]	2023	Astronomy &ampmathsemicolon Astrophysics Vol. 674, pp. A175	article	DOI
BibTeX: @article{Kang2023a, author = {Da Eun Kang and Victor F. Ksoll and Dominika Itrich and Leonardo Testi and Ralf S. Klessen and Patrick Hennebelle and Sergio Molinari}, title = {Spectral classification of young stars using conditional invertible neural networks}, journal = {Astronomy &ampmathsemicolon Astrophysics}, publisher = {EDP Sciences}, year = {2023}, volume = {674}, pages = {A175}, doi = {https://doi.org/10.1051/0004-6361/202346345} }
Karaca, K.G., Brito, D.V., Kupke, J., Zeuch, B. and Oliveira, A.M.	Engram reactivation during memory retrieval predicts long-term memory performance in aged mice [BibTeX]	2021	Neurobiology of Aging Vol. 101, pp. 256-261	article	DOI
BibTeX: @article{Karaca2021, author = {Kubra Gulmez Karaca and David V.C. Brito and Janina Kupke and Benjamin Zeuch and Ana M.M. Oliveira}, title = {Engram reactivation during memory retrieval predicts long-term memory performance in aged mice}, journal = {Neurobiology of Aging}, publisher = {Elsevier BV}, year = {2021}, volume = {101}, pages = {256--261}, doi = {https://doi.org/10.1016/j.neurobiolaging.2021.01.019} }
Karoii, D.H., Azizi, H. and Skutella, T.	Microarray and in silico analysis of DNA repair genes between human testis of patients with nonobstructive azoospermia and normal cells [BibTeX]	2022	Cell Biochemistry and Function Vol. 40(8), pp. 865-879	article	DOI
BibTeX: @article{Karoii2022, author = {Danial Hashemi Karoii, Hossein Azizi, Thomas Skutella}, title = {Microarray and in silico analysis of DNA repair genes between human testis of patients with nonobstructive azoospermia and normal cells}, journal = {Cell Biochemistry and Function}, publisher = {Wiley}, year = {2022}, volume = {40}, number = {8}, pages = {865--879}, doi = {https://doi.org/10.1002/cbf.3747} }
Kater, L., Thoms, M., Barrio-Garcia, C., Cheng, J., Ismail, S., Ahmed, Y.L., Bange, G., Kressler, D., Berninghausen, O., Sinning, I., Hurt, E. and Beckmann, R.	Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes [Abstract] [BibTeX]	2017	Cell Vol. 171(7), pp. 1599-1610.e14	article	DOI URL
Abstract: Summary Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
BibTeX: @article{Kater2017, author = {Kater, Lukas and Thoms, Matthias and Barrio-Garcia, Clara and Cheng, Jingdong and Ismail, Sherif and Ahmed, Yasar Luqman and Bange, Gert and Kressler, Dieter and Berninghausen, Otto and Sinning, Irmgard and Hurt, Ed and Beckmann, Roland}, title = {Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes}, journal = {Cell}, year = {2017}, volume = {171}, number = {7}, pages = {1599--1610.e14}, url = {http://www.sciencedirect.com/science/article/pii/S0092867417314290}, doi = {https://doi.org/10.1016/j.cell.2017.11.039} }
Kater, L., Mitterer, V., Thoms, M., Cheng, J., Berninghausen, O., Beckmann, R. and Hurt, E.	Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis [BibTeX]	2020	Molecular Cell Vol. 79(4), pp. 615-628.e5	article	DOI
BibTeX: @article{Kater2020, author = {Lukas Kater and Valentin Mitterer and Matthias Thoms and Jingdong Cheng and Otto Berninghausen and Roland Beckmann and Ed Hurt}, title = {Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2020}, volume = {79}, number = {4}, pages = {615--628.e5}, doi = {https://doi.org/10.1016/j.molcel.2020.06.032} }
Kats, I., Khmelinskii, A., Kschonsak, M., Huber, F., Knieß, R.A., Bartosik, A. and Knop, M.	Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome [Abstract] [BibTeX]	2018	Molecular Cell Vol. 70(3)	article	DOI URL
Abstract: Summary Most eukaryotic proteins are N-terminally acetylated. This modification can be recognized as a signal for selective protein degradation (degron) by the N-end rule pathways. However, the prevalence and specificity of such degrons in the proteome are unclear. Here, by systematically examining how protein turnover is affected by N-terminal sequences, we perform a comprehensive survey of degrons in the yeast N-terminome. We find that approximately 26% of nascent protein N termini encode cryptic degrons. These degrons exhibit high hydrophobicity and are frequently recognized by the E3 ubiquitin ligase Doa10, suggesting a role in protein quality control. In contrast, N-terminal acetylation rarely functions as a degron. Surprisingly, we identify two pathways where N-terminal acetylation has the opposite function and blocks protein degradation through the E3 ubiquitin ligase Ubr1. Our analysis highlights the complexity of N-terminal degrons and argues that hydrophobicity, not N-terminal acetylation, is the predominant feature of N-terminal degrons in nascent proteins.
BibTeX: @article{KATS2018488, author = {Ilia Kats and Anton Khmelinskii and Marc Kschonsak and Florian Huber and Robert A. Knieß and Anna Bartosik and Michael Knop}, title = {Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome}, journal = {Molecular Cell}, year = {2018}, volume = {70}, number = {3}, url = {http://www.sciencedirect.com/science/article/pii/S1097276518302363}, doi = {https://doi.org/10.1016/j.molcel.2018.03.033} }
Kellner, N., Griesel, S. and Hurt, E.	A Homologous Recombination System to Generate Epitope-Tagged Target Genes in Chaetomium thermophilum: A Genetic Approach to Investigate Native Thermostable Proteins [BibTeX]	2022	International Journal of Molecular Sciences Vol. 23(6), pp. 3198	article	DOI
BibTeX: @article{Kellner2022, author = {Nikola Kellner and Sabine Griesel and Ed Hurt}, title = {A Homologous Recombination System to Generate Epitope-Tagged Target Genes in Chaetomium thermophilum: A Genetic Approach to Investigate Native Thermostable Proteins}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2022}, volume = {23}, number = {6}, pages = {3198}, doi = {https://doi.org/10.3390/ijms23063198} }
Kempf, G., Stjepanovic, G., Sloan, J., Hendricks, A., Lapouge, K. and Sinning, I.	The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane [Abstract] [BibTeX]	2018	Structure Vol. 26(11), pp. 1440-1450.e5	article	DOI URL
Abstract: Summary The Escherichia coli signal recognition particle (SRP) receptor, FtsY, plays a fundamental role in co-translational targeting of membrane proteins via the SRP pathway. Efficient targeting relies on membrane interaction of FtsY and heterodimerization with the SRP protein Ffh, which is driven by detachment of α helix (αN1) in FtsY. Here we show that apart from the heterodimer, FtsY forms a nucleotide-dependent homodimer on the membrane, and upon αN1 removal also in solution. Homodimerization triggers reciprocal stimulation of GTP hydrolysis and occurs in vivo. Biochemical characterization together with integrative modeling suggests that the homodimer employs the same interface as the heterodimer. Structure determination of FtsY NG+1 with GMPPNP shows that a dimerization-induced conformational switch of the γ-phosphate is conserved in Escherichia coli, filling an important gap in SRP GTPase activation. Our findings add to the current understanding of SRP GTPases and may challenge previous studies that did not consider homodimerization of FtsY.
BibTeX: @article{Kempf2018, author = {Kempf, Georg and Stjepanovic, Goran and Sloan, Jeremy and Hendricks, Astrid and Lapouge, Karine and Sinning, Irmgard}, title = {The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane}, journal = {Structure}, year = {2018}, volume = {26}, number = {11}, pages = {1440--1450.e5}, url = {http://www.sciencedirect.com/science/article/pii/S0969212618302545}, doi = {https://doi.org/10.1016/j.str.2018.07.008} }
Kern, O.A., Koutsodendris, A., Süfke, F., Gutjahr, M., Mächtle, B. and Pross, J.	Persistent, multi-sourced lead contamination in Central Europe since the Bronze Age recorded in the Füramoos peat bog, Germany [BibTeX]	2021	Anthropocene Vol. 36, pp. 100310	article	DOI
BibTeX: @article{Kern2021, author = {Oliver A. Kern and Andreas Koutsodendris and Finn Süfke and Marcus Gutjahr and Bertil Mächtle and Jörg Pross}, title = {Persistent, multi-sourced lead contamination in Central Europe since the Bronze Age recorded in the Füramoos peat bog, Germany}, journal = {Anthropocene}, publisher = {Elsevier BV}, year = {2021}, volume = {36}, pages = {100310}, doi = {https://doi.org/10.1016/j.ancene.2021.100310} }
Kesch, C., Radtke, J.-P., Wintsche, A., Wiesenfarth, M., Luttje, M., Gasch, C., Dieffenbacher, S., Pecqueux, C., Teber, D., Hatiboglu, G., Nyarangi-Dix, J., Simpfendörfer, T., Schönberg, G., Dimitrakopoulou-Strauss, A., Freitag, M., Duensing, A., Grüllich, C., Jäger, D., Götz, M., Grabe, N., Schweiger, M.-R., Pahernik, S., Perner, S., Herpel, E., Roth, W., Wieczorek, K., Maier-Hein, K., Debus, J., Haberkorn, U., Giesel, F., Galle, J., Hadaschik, B., Schlemmer, H.-P., Hohenfellner, M., Bonekamp, D., Sültmann, H. and Duensing, S.	Correlation between genomic index lesions and mpMRI and 68Ga-PSMA-PET/CT imaging features in primary prostate cancer [BibTeX]	2018	Scientific Reports Vol. 8(1)	article	DOI
BibTeX: @article{Kesch2018, author = {Claudia Kesch and Jan-Philipp Radtke and Axel Wintsche and Manuel Wiesenfarth and Mariska Luttje and Claudia Gasch and Svenja Dieffenbacher and Carine Pecqueux and Dogu Teber and Gencay Hatiboglu and Joanne Nyarangi-Dix and Tobias Simpfendörfer and Gita Schönberg and Antonia Dimitrakopoulou-Strauss and Martin Freitag and Anette Duensing and Carsten Grüllich and Dirk Jäger and Michael Götz and Niels Grabe and Michal-Ruth Schweiger and Sascha Pahernik and Sven Perner and Esther Herpel and Wilfried Roth and Kathrin Wieczorek and Klaus Maier-Hein and Jürgen Debus and Uwe Haberkorn and Frederik Giesel and Jörg Galle and Boris Hadaschik and Heinz-Peter Schlemmer and Markus Hohenfellner and David Bonekamp and Holger Sültmann and Stefan Duensing}, title = {Correlation between genomic index lesions and mpMRI and 68Ga-PSMA-PET/CT imaging features in primary prostate cancer}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2018}, volume = {8}, number = {1}, doi = {https://doi.org/10.1038/s41598-018-35058-3} }
Kessler, L., Gao, R., Tetik-Elsherbiny, N., Lityagina, O., Zhailauova, A., Ren, Y., Trogisch, F.A., Cordero, J., Dou, Y., Wang, Y., Chichelnitskiy, E., Kraske, J.A., Schäfer, P.L., Wu, C.-C., Barreto, G., Potente, M., Wieland, T., Ola, R., Heineke, J. and Dobreva, G.	Rnf20 shapes the endothelial control of heart morphogenesis and function [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: SummaryDuring embryogenesis, distinct cardiac cell types form, which shape the structural and functional properties of the heart. How their activity is coordinated is largely unknown. Here we show that Rnf20 is a multifaceted regulator of cardiac morphogenesis and function. On the one hand, Rnf20 controls extracellular matrix dynamics and endothelial-cardiomyocyte crosstalk essential for second heart field development. On the other hand, it safeguards endothelial cell identity and function by maintaining physiological angiocrine signaling and preventing endothelial-to-mesenchymal transition. Endothelial-specific deletion of Rnf20 led to ventricular septal defects, myocardial thinning and cardiac dysfunction as a result of aberrant signaling and excessive extracellular matrix deposition that induced precocious cardiomyocyte binucleation and irregular contractility. Furthermore, we uncovered upstream factors (e.g. Sox9) and multiple angiocrine and extracellular matrix molecules that alter cardiomyocyte functionality upon endothelial Rnf20 loss. In summary, our work identifies a novel, endothelial-specific role of Rnf20 in regulating cardiac morphogenesis and function.
BibTeX: @article{Kessler2022, author = {Linda Kessler, Rui Gao, Nalan Tetik-Elsherbiny, Olga Lityagina, Azhar Zhailauova, Yonggang Ren, Felix A. Trogisch, Julio Cordero, Yanliang Dou, Yinuo Wang, Evgeny Chichelnitskiy, Joscha Alexander Kraske, Patricia Laura Schäfer, Chi-Chung Wu, Guillermo Barreto, Michael Potente, Thomas Wieland, Roxana Ola, Joerg Heineke, Gergana Dobreva}, title = {Rnf20 shapes the endothelial control of heart morphogenesis and function}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.09.16.508288} }
Kharazmi, E., Scherer, D., Boekstegers, F., Liang, Q., Sundquist, K., Sundquist, J., Fallah, M. and Bermejo, J.L.	Gallstones, Cholecystectomy, and Kidney Cancer: Observational and Mendelian Randomization Results Based on Large Cohorts [BibTeX]	2023	Gastroenterology Vol. 165(1), pp. 218-227.e8	article	DOI
BibTeX: @article{Kharazmi2023, author = {Elham Kharazmi and Dominique Scherer and Felix Boekstegers and Qunfeng Liang and Kristina Sundquist and Jan Sundquist and Mahdi Fallah and Justo Lorenzo Bermejo}, title = {Gallstones, Cholecystectomy, and Kidney Cancer: Observational and Mendelian Randomization Results Based on Large Cohorts}, journal = {Gastroenterology}, publisher = {Elsevier BV}, year = {2023}, volume = {165}, number = {1}, pages = {218--227.e8}, doi = {https://doi.org/10.1053/j.gastro.2023.03.227} }
Kilian, M., Sheinin, R., Tan, C.L., Friedrich, M., Krämer, C., Kaminitz, A., Sanghvi, K., Lindner, K., Chih, Y.-C., Cichon, F., Richter, B., Jung, S., Jähne, K., Ratliff, M., Prins, R.M., Etminan, N., von Deimling, A., Wick, W., Madi, A., Bunse, L. and Platten, M.	MHC class II-restricted antigen presentation is required to prevent dysfunction of cytotoxic T cells by blood-borne myeloids in brain tumors [BibTeX]	2023	Cancer Cell Vol. 41(2), pp. 235-251.e9	article	DOI URL
BibTeX: @article{Kilian2023, author = {Michael Kilian, Ron Sheinin, Chin Leng Tan, Mirco Friedrich, Christopher Krämer, Ayelet Kaminitz, Khwab Sanghvi, Katharina Lindner, Yu-Chan Chih, Frederik Cichon, Benjamin Richter, Stefanie Jung, Kristine Jähne, Miriam Ratliff, Robert M. Prins, Nima Etminan, Andreas von Deimling, Wolfgang Wick, Asaf Madi, Lukas Bunse, Michael Platten}, title = {MHC class II-restricted antigen presentation is required to prevent dysfunction of cytotoxic T cells by blood-borne myeloids in brain tumors}, journal = {Cancer Cell}, publisher = {Elsevier BV}, year = {2023}, volume = {41}, number = {2}, pages = {235--251.e9}, url = {https://api.elsevier.com/content/article/PII:S1535610822005931?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.ccell.2022.12.007} }
Kišonaitė, M., Wild, K., Lapouge, K., Ruppert, T. and Sinning, I.	High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation [BibTeX]	2022	Nature Communications Vol. 13(1)	article	DOI
BibTeX: @article{Kisonaite2022, author = {Miglė Kišonaitė and Klemens Wild and Karine Lapouge and Thomas Ruppert and Irmgard Sinning}, title = {High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {13}, number = {1}, doi = {https://doi.org/10.1038/s41467-022-27967-9} }
Kišonaitė, M., Wild, K., Lapouge, K., Gesé, G.V., Kellner, N., Hurt, E. and Sinning, I.	Structural inventory of cotranslational protein folding by the eukaryotic RAC complex [Abstract] [BibTeX]	2023	Nature Structural & Molecular Biology Vol. 30(5), pp. 670-677	article	DOI URL
Abstract: AbstractThe challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with the Hsp70 protein Ssb in fungi, and consists of the non-canonical Hsp70 Ssz1 and the J domain protein Zuotin (Zuo1). Here we determine cryo-EM structures of Chaetomium thermophilum RAC bound to 80S ribosomes. RAC adopts two distinct conformations accommodating continuous ribosomal rotation by a flexible lever arm. It is held together by a tight interaction between the Ssz1 substrate-binding domain and the Zuo1 N terminus, and additional contacts between the Ssz1 nucleotide-binding domain and Zuo1 J- and Zuo1 homology domains, which form a rigid unit. The Zuo1 HPD motif conserved in J-proteins is masked in a non-canonical interaction by the Ssz1 nucleotide-binding domain, and allows the positioning of Ssb for activation by Zuo1. Overall, we provide the basis for understanding how RAC cooperates with Ssb in a dynamic nascent chain interaction and protein folding.
BibTeX: @article{Kisonaite2023, author = {Miglė Kišonaitė, Klemens Wild, Karine Lapouge, Genís Valentín Gesé, Nikola Kellner, Ed Hurt, Irmgard Sinning}, title = {Structural inventory of cotranslational protein folding by the eukaryotic RAC complex}, journal = {Nature Structural & Molecular Biology}, publisher = {Springer Science and Business Media LLC}, year = {2023}, volume = {30}, number = {5}, pages = {670--677}, url = {https://www.nature.com/articles/s41594-023-00973-1.pdf}, doi = {https://doi.org/10.1038/s41594-023-00973-1} }
	Zeichentragende Artefakte im sakralen Raum [BibTeX]	2018		book	DOI
BibTeX: @book{Kiyanrad2018,, title = {Zeichentragende Artefakte im sakralen Raum}, publisher = {De Gruyter}, year = {2018}, doi = {https://doi.org/10.1515/9783110619928} }
	Bild und Schrift auf 'magischen' Artefakten [BibTeX]	2018		book	DOI
BibTeX: @book{Kiyanrad2018a,, title = {Bild und Schrift auf 'magischen' Artefakten}, publisher = {De Gruyter}, year = {2018}, doi = {https://doi.org/10.1515/9783110604337} }
Klein, S., Cortese, M., Winter, S.L., Wachsmuth-Melm, M., Neufeldt, C.J., Cerikan, B., Stanifer, M.L., Boulant, S., Bartenschlager, R. and Chlanda, P.	SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Klein2020, author = {Steffen Klein and Mirko Cortese and Sophie L. Winter and Moritz Wachsmuth-Melm and Christopher J. Neufeldt and Berati Cerikan and Megan L. Stanifer and Steeve Boulant and Ralf Bartenschlager and Petr Chlanda}, title = {SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-19619-7} }
Klein, S., Wachsmuth-Melm, M., Winter, S.L., Kolovou, A. and Chlanda, P.	Cryo-correlative light and electron microscopy workflow for cryo-focused ion beam milled adherent cells [BibTeX]	2021	Methods in Cell Biology, pp. 273-302	incollection	DOI
BibTeX: @incollection{Klein2021, author = {Steffen Klein and Moritz Wachsmuth-Melm and Sophie L. Winter and Androniki Kolovou and Petr Chlanda}, title = {Cryo-correlative light and electron microscopy workflow for cryo-focused ion beam milled adherent cells}, booktitle = {Methods in Cell Biology}, publisher = {Elsevier}, year = {2021}, pages = {273--302}, doi = {https://doi.org/10.1016/bs.mcb.2020.12.009} }
Klein, S., Wimmer, B.H., Winter, S.L., Kolovou, A., Laketa, V. and Chlanda, P.	Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies [BibTeX]	2021	Communications Biology Vol. 4(1)	article	DOI
BibTeX: @article{Klein2021a, author = {Steffen Klein and Benedikt H. Wimmer and Sophie L. Winter and Androniki Kolovou and Vibor Laketa and Petr Chlanda}, title = {Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies}, journal = {Communications Biology}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {4}, number = {1}, doi = {https://doi.org/10.1038/s42003-020-01567-z} }
Klein, S., Golani, G., Lolicato, F., Lahr, C., Beyer, D., Herrmann, A., Wachsmuth-Melm, M., Reddmann, N., Brecht, R., Hosseinzadeh, M., Kolovou, A., Makroczyova, J., Peterl, S., Schorb, M., Schwab, Y., Brügger, B., Nickel, W., Schwarz, U.S. and Chlanda, P.	IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion [BibTeX]	2023	Cell Host &ampmathsemicolon Microbe Vol. 31(4), pp. 616-633.e20	article	DOI
BibTeX: @article{Klein2023, author = {Steffen Klein and Gonen Golani and Fabio Lolicato and Carmen Lahr and Daniel Beyer and Alexia Herrmann and Moritz Wachsmuth-Melm and Nina Reddmann and Romy Brecht and Mehdi Hosseinzadeh and Androniki Kolovou and Jana Makroczyova and Sarah Peterl and Martin Schorb and Yannick Schwab and Britta Brügger and Walter Nickel and Ulrich S. Schwarz and Petr Chlanda}, title = {IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion}, journal = {Cell Host &ampmathsemicolon Microbe}, publisher = {Elsevier BV}, year = {2023}, volume = {31}, number = {4}, pages = {616--633.e20}, doi = {https://doi.org/10.1016/j.chom.2023.03.005} }
Klessen, R.S.	Invertible Neural Networks in Astrophysics [Abstract] [BibTeX]	2022	EPJ Web of Conferences Vol. 265, pp. 00009	article	DOI
Abstract: Modern machine learning techniques have become indispensable in many fields of astronomy and astrophysics. Here we introduce a specific class of methods, invertible neural networks, and discuss two specific applications, the prediction of stellar parameters from photometric observations and the study of stellar feedback processes from on emission lines.
BibTeX: @article{Klessen2022, author = {Ralf S. Klessen}, title = {Invertible Neural Networks in Astrophysics}, journal = {EPJ Web of Conferences}, publisher = {EDP Sciences}, year = {2022}, volume = {265}, pages = {00009}, doi = {https://doi.org/10.1051/epjconf/202226500009} }
Klevanski, M., Herrmannsdoerfer, F., Sass, S., Venkataramani, V., Heilemann, M. and Kuner, T.	Automated highly multiplexed super-resolution imaging of protein nano-architecture in cells and tissues [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Klevanski2020, author = {Maja Klevanski and Frank Herrmannsdoerfer and Steffen Sass and Varun Venkataramani and Mike Heilemann and Thomas Kuner}, title = {Automated highly multiplexed super-resolution imaging of protein nano-architecture in cells and tissues}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-15362-1} }
Klosner, J., Agelopoulos, K., Rohde, C., Göllner, S., Schliemann, C., Berdel, W.E. and Müller-Tidow, C.	Integrated RNAi Screening Identifies The NEDDylation Pathway As A Synergistic Partner of Azacytidine In Acute Myeloid Leukemia [BibTeX]	2021		article	DOI
BibTeX: @article{Klosner2021, author = {Justine Klosner and Konstantin Agelopoulos and Christian Rohde and Stefanie Göllner and Christoph Schliemann and Wolfgang E. Berdel and Carsten Müller-Tidow}, title = {Integrated RNAi Screening Identifies The NEDDylation Pathway As A Synergistic Partner of Azacytidine In Acute Myeloid Leukemia}, publisher = {Research Square Platform LLC}, year = {2021}, doi = {https://doi.org/10.21203/rs.3.rs-647282/v1} }
Kmietczyk, V., Riechert, E., Kalinski, L., Boileau, E., Malovrh, E., Malone, B., Gorska, A., Hofmann, C., Varma, E., Jürgensen, L., Kamuf-Schenk, V., Altmüller, J., Tappu, R., Busch, M., Most, P., Katus, H.A., Dieterich, C. and Völkers, M.	m6A-mRNA methylation regulates cardiac gene expression and cellular growth [BibTeX]	2019	Life Science Alliance Vol. 2(2), pp. e201800233	article	DOI
BibTeX: @article{Kmietczyk2019, author = {Vivien Kmietczyk and Eva Riechert and Laura Kalinski and Etienne Boileau and Ellen Malovrh and Brandon Malone and Agnieszka Gorska and Christoph Hofmann and Eshita Varma and Lonny Jürgensen and Verena Kamuf-Schenk and Janine Altmüller and Rewati Tappu and Martin Busch and Patrick Most and Hugo A Katus and Christoph Dieterich and Mirko Völkers}, title = {m6A-mRNA methylation regulates cardiac gene expression and cellular growth}, journal = {Life Science Alliance}, publisher = {Life Science Alliance, LLC}, year = {2019}, volume = {2}, number = {2}, pages = {e201800233}, doi = {https://doi.org/10.26508/lsa.201800233} }
Koch, P.-S., Sandorski, K., Heil, J., Schmid, C.D., Kürschner, S.W., Hoffmann, J., Winkler, M., Staniczek, T., de la Torre, C., Sticht, C., Schledzewski, K., Taketo, M.M., Trogisch, F.A., Heineke, J., Géraud, C., Goerdt, S. and Olsavszky, V.	Imbalanced Activation of Wnt-/upbeta-Catenin-Signaling in Liver Endothelium Alters Normal Sinusoidal Differentiation [BibTeX]	2021	Frontiers in Physiology Vol. 12	article	DOI
BibTeX: @article{Koch2021, author = {Philipp-Sebastian Koch and Kajetan Sandorski and Joschka Heil and Christian D. Schmid and Sina W. Kürschner and Johannes Hoffmann and Manuel Winkler and Theresa Staniczek and Carolina de la Torre and Carsten Sticht and Kai Schledzewski and Makoto Mark Taketo and Felix A. Trogisch and Joerg Heineke and Cyrill Géraud and Sergij Goerdt and Victor Olsavszky}, title = {Imbalanced Activation of Wnt-/upbeta-Catenin-Signaling in Liver Endothelium Alters Normal Sinusoidal Differentiation}, journal = {Frontiers in Physiology}, publisher = {Frontiers Media SA}, year = {2021}, volume = {12}, doi = {https://doi.org/10.3389/fphys.2021.722394} }
Kock, S.T., Schittek, K., Mächtle, B., Maldonado, A., Vos, H., Lupo, L.C., Kulemeyer, J.J., Wissel, H., Schäbitz, F. and Lücke, A.	Multi-Centennial-Scale Variations of South American Summer Monsoon Intensity in the Southern Central Andes (24–27textdegreeS) During the Late Holocene [BibTeX]	2020	Geophysical Research Letters Vol. 47(4)	article	DOI
BibTeX: @article{Kock2020, author = {Sebastian T. Kock and Karsten Schittek and Bertil Mächtle and Antonio Maldonado and Heinz Vos and Liliana C. Lupo and Julio J. Kulemeyer and Holger Wissel and Frank Schäbitz and Andreas Lücke}, title = {Multi-Centennial-Scale Variations of South American Summer Monsoon Intensity in the Southern Central Andes (24–27textdegreeS) During the Late Holocene}, journal = {Geophysical Research Letters}, publisher = {American Geophysical Union (AGU)}, year = {2020}, volume = {47}, number = {4}, doi = {https://doi.org/10.1029/2019gl084157} }
Koehler, S., Hussain, T., Blair, Z., Huffaker, T., Ritzmann, F., Tandon, A., Pickardt, T., Sarikouch, S., Latus, H., Greil, G., Wolf, I. and Engelhardt, S.	Unsupervised Domain Adaptation From Axial to Short-Axis Multi-Slice Cardiac MR Images by Incorporating Pretrained Task Networks [BibTeX]	2021	IEEE Transactions on Medical Imaging Vol. 40(10), pp. 2939-2953	article	DOI URL
BibTeX: @article{Koehler2021, author = {Sven Koehler, Tarique Hussain, Zach Blair, Tyler Huffaker, Florian Ritzmann, Animesh Tandon, Thomas Pickardt, Samir Sarikouch, Heiner Latus, Gerald Greil, Ivo Wolf, Sandy Engelhardt}, title = {Unsupervised Domain Adaptation From Axial to Short-Axis Multi-Slice Cardiac MR Images by Incorporating Pretrained Task Networks}, journal = {IEEE Transactions on Medical Imaging}, publisher = {Institute of Electrical and Electronics Engineers (IEEE)}, year = {2021}, volume = {40}, number = {10}, pages = {2939--2953}, url = {http://xplorestaging.ieee.org/ielx7/42/9552972/09328840.pdf?arnumber=9328840}, doi = {https://doi.org/10.1109/TMI.2021.3052972} }
Koehler, S., Hussain, T., Hussain, H., Young, D., Sarikouch, S., Pickardt, T., Greil, G. and Engelhardt, S.	Self-supervised Motion Descriptor for Cardiac Phase Detection in 4D CMR Based on Discrete Vector Field Estimations [BibTeX]	2022	Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers	incollection	DOI
BibTeX: @incollection{Koehler2022, author = {Sven Koehler, Tarique Hussain, Hamza Hussain, Daniel Young, Samir Sarikouch, Thomas Pickardt, Gerald Greil, Sandy Engelhardt}, title = {Self-supervised Motion Descriptor for Cardiac Phase Detection in 4D CMR Based on Discrete Vector Field Estimations}, booktitle = {Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers}, publisher = {Springer Nature Switzerland}, year = {2022}, doi = {https://doi.org/10.1007/978-3-031-23443-9_7} }
Koehler, S., Sharan, L., Kuhm, J., Ghanaat, A., Gordejeva, J., Simon, N.K., Grell, N.M., André, F. and Engelhardt, S.	Comparison of Evaluation Metrics for Landmark Detection in CMR Images [BibTeX]	2022	Informatik aktuell	incollection	DOI
BibTeX: @incollection{Koehler2022a, author = {Sven Koehler, Lalith Sharan, Julian Kuhm, Arman Ghanaat, Jelizaveta Gordejeva, Nike K. Simon, Niko M. Grell, Florian André, Sandy Engelhardt}, title = {Comparison of Evaluation Metrics for Landmark Detection in CMR Images}, booktitle = {Informatik aktuell}, publisher = {Springer Fachmedien Wiesbaden}, year = {2022}, doi = {https://doi.org/10.1007/978-3-658-36932-3_43} }
Köntges, W., Perkhun, P., Schröder, R., Alkarsifi, R., Margeat, O., Videlot-Ackermann, C., Ackermann, J. and Pfannmöller, M.	Real-space correlation of crystallinity and material phase distribution in non-fullerene acceptor blends [BibTeX]	2019		inproceedings
BibTeX: @inproceedings{Koentges2019, author = {Köntges, Wolfgang and Perkhun, Pavlo and Schröder, Rasmus and Alkarsifi, Riva and Margeat, Olivier and Videlot-Ackermann, Christine and Ackermann, Jörg and Pfannmöller, Martin}, title = {Real-space correlation of crystallinity and material phase distribution in non-fullerene acceptor blends}, year = {2019} }
Köntges, W., Perkhun, P., Schröder, R., Barulina, E., Margeat, O., Videlot-Ackermann, C., Ackermann, J. and Pfannmöller, M.	Optimal Interfacial Composition and Crystallinity of Non-Fullerene Acceptor Blends for Organic Photovoltaics [BibTeX]	2019		inproceedings	DOI
BibTeX: @inproceedings{Koentges2019a, author = {Köntges, Wolfgang and Perkhun, Pavlo and Schröder, Rasmus and Barulina, Elena and Margeat, Olivier and Videlot-Ackermann, Christine and Ackermann, Jörg and Pfannmöller, Martin}, title = {Optimal Interfacial Composition and Crystallinity of Non-Fullerene Acceptor Blends for Organic Photovoltaics}, year = {2019}, doi = {https://doi.org/10.29363/nanoge.ngfm.2019.200} }
Köntges, W., Perkhun, P., Kammerer, J., Alkarsifi, R., Würfel, U., Margeat, O., Videlot-Ackermann, C., Simon, J.-J., Schröder, R.R., Ackermann, J. and Pfannmöller, M.	Visualizing morphological principles for efficient photocurrent generation in organic non-fullerene acceptor blends [BibTeX]	2020	Energy & Environmental Science Vol. 13(4), pp. 1259-1268	article	DOI
BibTeX: @article{Koentges2020, author = {Wolfgang Köntges and Pavlo Perkhun and Jochen Kammerer and Riva Alkarsifi and Uli Würfel and Olivier Margeat and Christine Videlot-Ackermann and Jean-Jacques Simon and Rasmus R. Schröder and Jörg Ackermann and Martin Pfannmöller}, title = {Visualizing morphological principles for efficient photocurrent generation in organic non-fullerene acceptor blends}, journal = {Energy & Environmental Science}, publisher = {Royal Society of Chemistry (RSC)}, year = {2020}, volume = {13}, number = {4}, pages = {1259--1268}, doi = {https://doi.org/10.1039/c9ee03535d} }
Kong, S., Arce, H.G., Feddersen, J.R., Carpenter, J.M., Nakamura, F., Shimajiri, Y., Isella, A., Ossenkopf-Okada, V., Sargent, A.I., Sánchez-Monge, Á., Suri, S.T., Kauffmann, J., Pillai, T., Pineda, J.E., Koda, J., Bally, J., Lis, D.C., Padoan, P., Klessen, R., Mairs, S., Goodman, A., Goldsmith, P., McGehee, P., Schilke, P., Teuben, P.J., Maureira, M.J., Hara, C., Ginsburg, A., Burkhart, B., Smith, R.J., Schmiedeke, A., Pineda, J.L., Ishii, S., Sasaki, K., Kawabe, R., Urasawa, Y., Oyamada, S. and Tanabe, Y.	The CARMA-NRO Orion Survey [BibTeX]	2018	The Astrophysical Journal Supplement Series Vol. 236(2), pp. 25	article	DOI
BibTeX: @article{Kong2018, author = {Shuo Kong and Héctor G. Arce and Jesse R. Feddersen and John M. Carpenter and Fumitaka Nakamura and Yoshito Shimajiri and Andrea Isella and Volker Ossenkopf-Okada and Anneila I. Sargent and Álvaro Sánchez-Monge and Sümeyye T. Suri and Jens Kauffmann and Thushara Pillai and Jaime E. Pineda and Jin Koda and John Bally and Dariusz C. Lis and Paolo Padoan and Ralf Klessen and Steve Mairs and Alyssa Goodman and Paul Goldsmith and Peregrine McGehee and Peter Schilke and Peter J. Teuben and Mar\ia José Maureira and Chihomi Hara and Adam Ginsburg and Blakesley Burkhart and Rowan J. Smith and Anika Schmiedeke and Jorge L. Pineda and Shun Ishii and Kazushige Sasaki and Ryohei Kawabe and Yumiko Urasawa and Shuri Oyamada and Yoshihiro Tanabe}, title = {The CARMA-NRO Orion Survey}, journal = {The Astrophysical Journal Supplement Series}, publisher = {American Astronomical Society}, year = {2018}, volume = {236}, number = {2}, pages = {25}, doi = {https://doi.org/10.3847/1538-4365/aabafc} }
Kong, S., Arce, H.G., Sargent, A.I., Mairs, S., Klessen, R.S., Bally, J., Padoan, P., Smith, R.J., Maureira, M.J., Carpenter, J.M., Ginsburg, A., Stutz, A.M., Goldsmith, P., Meingast, S., McGehee, P., Sánchez-Monge, Á., Suri, S., Pineda, J.E., Alves, J., Feddersen, J.R., Kauffmann, J. and Schilke, P.	The CARMA-NRO Orion Survey: Core Emergence and Kinematics in the Orion A Cloud [BibTeX]	2019	The Astrophysical Journal Vol. 882(1), pp. 45	article	DOI
BibTeX: @article{Kong2019, author = {Shuo Kong and Héctor G. Arce and Anneila I. Sargent and Steve Mairs and Ralf S. Klessen and John Bally and Paolo Padoan and Rowan J. Smith and Mar\ia José Maureira and John M. Carpenter and Adam Ginsburg and Amelia M. Stutz and Paul Goldsmith and Stefan Meingast and Peregrine McGehee and Álvaro Sánchez-Monge and Sümeyye Suri and Jaime E. Pineda and João Alves and Jesse R. Feddersen and Jens Kauffmann and Peter Schilke}, title = {The CARMA-NRO Orion Survey: Core Emergence and Kinematics in the Orion A Cloud}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2019}, volume = {882}, number = {1}, pages = {45}, doi = {https://doi.org/10.3847/1538-4357/ab311e} }
Kong, S., Ossenkopf-Okada, V., Arce, H.G., Klessen, R.S. and Xu, D.	CMR Exploration. I. Filament Structure with Synthetic Observations [BibTeX]	2023	The Astrophysical Journal Supplement Series Vol. 265(2), pp. 58	article	DOI
BibTeX: @article{Kong2023, author = {Shuo Kong and Volker Ossenkopf-Okada and Héctor G. Arce and Ralf S. Klessen and Duo Xu}, title = {CMR Exploration. I. Filament Structure with Synthetic Observations}, journal = {The Astrophysical Journal Supplement Series}, publisher = {American Astronomical Society}, year = {2023}, volume = {265}, number = {2}, pages = {58}, doi = {https://doi.org/10.3847/1538-4365/acbfb0} }
	Material Aspects of Reading in Ancient and Medieval Cultures [BibTeX]	2020		book	DOI
BibTeX: @book{Krauss2020,, title = {Material Aspects of Reading in Ancient and Medieval Cultures}, publisher = {De Gruyter}, year = {2020}, doi = {https://doi.org/10.1515/9783110639247} }
Kriegsmann, K., Kriegsmann, M., Cremer, M., Schmitt, M., Dreger, P., Goldschmidt, H., Müller-Tidow, C. and Hundemer, M.	Cell-based immunotherapy approaches for multiple myeloma [BibTeX]	2018	British Journal of Cancer Vol. 120(1), pp. 38-44	article	DOI
BibTeX: @article{Kriegsmann2018, author = {Katharina Kriegsmann and Mark Kriegsmann and Martin Cremer and Michael Schmitt and Peter Dreger and Hartmut Goldschmidt and Carsten Müller-Tidow and Michael Hundemer}, title = {Cell-based immunotherapy approaches for multiple myeloma}, journal = {British Journal of Cancer}, publisher = {Springer Science and Business Media LLC}, year = {2018}, volume = {120}, number = {1}, pages = {38--44}, doi = {https://doi.org/10.1038/s41416-018-0346-9} }
Kriegsmann, K., Baertsch, M.-A., Awwad, M.H.S., Merz, M., Hose, D., Seckinger, A., Jauch, A., Becker, N., Benner, A., Raab, M.S., Hillengass, J., Bertsch, U., Dürig, J., Salwender, H.J., Hänel, M., Fenk, R., Munder, M., Weisel, K., Müller-Tidow, C., Goldschmidt, H. and Hundemer, M.	Cereblon-binding proteins expression levels correlate with hyperdiploidy in newly diagnosed multiple myeloma patients [BibTeX]	2019	Blood Cancer Journal Vol. 9(2)	article	DOI
BibTeX: @article{Kriegsmann2019, author = {Katharina Kriegsmann and Marc-Andrea Baertsch and Mohamed H. S. Awwad and Maximilian Merz and Dirk Hose and Anja Seckinger and Anna Jauch and Natalia Becker and Axel Benner and Marc S. Raab and Jens Hillengass and Uta Bertsch and Jan Dürig and Hans Jürgen Salwender and Mathias Hänel and Roland Fenk and Markus Munder and Katja Weisel and Carsten Müller-Tidow and Hartmut Goldschmidt and Michael Hundemer}, title = {Cereblon-binding proteins expression levels correlate with hyperdiploidy in newly diagnosed multiple myeloma patients}, journal = {Blood Cancer Journal}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {9}, number = {2}, doi = {https://doi.org/10.1038/s41408-019-0174-z} }
Kriegsmann, M., Haag, C., Weis, C.-A., Steinbuss, G., Warth, A., Zgorzelski, C., Muley, T., Winter, H., Eichhorn, M., Eichhorn, F., Kriegsmann, J., Christopoulos, P., Thomas, M., Witzens-Harig, M., Sinn, P., von Winterfeld, M., Heussel, C., Herth, F., Klauschen, F., Stenzinger, A. and Kriegsmann, K.	Deep Learning for the Classification of Small-Cell and Non-Small-Cell Lung Cancer [BibTeX]	2020	Cancers Vol. 12(6), pp. 1604	article	DOI
BibTeX: @article{Kriegsmann2020, author = {Mark Kriegsmann and Christian Haag and Cleo-Aron Weis and Georg Steinbuss and Arne Warth and Christiane Zgorzelski and Thomas Muley and Hauke Winter and Martin Eichhorn and Florian Eichhorn and Joerg Kriegsmann and Petros Christopoulos and Michael Thomas and Mathias Witzens-Harig and Peter Sinn and Moritz von Winterfeld and Claus Heussel and Felix Herth and Frederick Klauschen and Albrecht Stenzinger and Katharina Kriegsmann}, title = {Deep Learning for the Classification of Small-Cell and Non-Small-Cell Lung Cancer}, journal = {Cancers}, publisher = {MDPI AG}, year = {2020}, volume = {12}, number = {6}, pages = {1604}, doi = {https://doi.org/10.3390/cancers12061604} }
Kriegsmann, M., Kriegsmann, K., Steinbuss, G., Zgorzelski, C., Kraft, A. and Gaida, M.M.	Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma [BibTeX]	2021	International Journal of Molecular Sciences Vol. 22(10), pp. 5385	article	DOI
BibTeX: @article{Kriegsmann2021, author = {Mark Kriegsmann and Katharina Kriegsmann and Georg Steinbuss and Christiane Zgorzelski and Anne Kraft and Matthias M. Gaida}, title = {Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2021}, volume = {22}, number = {10}, pages = {5385}, doi = {https://doi.org/10.3390/ijms22105385} }
Kriegsmann, K., Lobers, F., Zgorzelski, C., Kriegsmann, J., Janßen, C., Meliß, R.R., Muley, T., Sack, U., Steinbuss, G. and Kriegsmann, M.	Deep learning for the detection of anatomical tissue structures and neoplasms of the skin on scanned histopathological tissue sections [Abstract] [BibTeX]	2022	Frontiers in Oncology Vol. 12	article	DOI
Abstract: Basal cell carcinoma (BCC), squamous cell carcinoma (SqCC) and melanoma are among the most common cancer types. Correct diagnosis based on histological evaluation after biopsy or excision is paramount for adequate therapy stratification. Deep learning on histological slides has been suggested to complement and improve routine diagnostics, but publicly available curated and annotated data and usable models trained to distinguish common skin tumors are rare and often lack heterogeneous non-tumor categories. A total of 16 classes from 386 cases were manually annotated on scanned histological slides, 129,364 100 x 100 µm ( 395 x 395 px) image tiles were extracted and split into a training, validation and test set. An EfficientV2 neuronal network was trained and optimized to classify image categories. Cross entropy loss, balanced accuracy and Matthews correlation coefficient were used for model evaluation. Image and patient data were assessed with confusion matrices. Application of the model to an external set of whole slides facilitated localization of melanoma and non-tumor tissue. Automated differentiation of BCC, SqCC, melanoma, naevi and non-tumor tissue structures was possible, and a high diagnostic accuracy was achieved in the validation (98%) and test (97%) set. In summary, we provide a curated dataset including the most common neoplasms of the skin and various anatomical compartments to enable researchers to train, validate and improve deep learning models. Automated classification of skin tumors by deep learning techniques is possible with high accuracy, facilitates tumor localization and has the potential to support and improve routine diagnostics.
BibTeX: @article{Kriegsmann2022, author = {Katharina Kriegsmann, Frithjof Lobers, Christiane Zgorzelski, Jörg Kriegsmann, Charlotte Janßen, Rolf Rüdinger Meliß, Thomas Muley, Ulrich Sack, Georg Steinbuss, Mark Kriegsmann}, title = {Deep learning for the detection of anatomical tissue structures and neoplasms of the skin on scanned histopathological tissue sections}, journal = {Frontiers in Oncology}, publisher = {Frontiers Media SA}, year = {2022}, volume = {12}, doi = {https://doi.org/10.3389/fonc.2022.1022967} }
Kriegsmann, M., Kriegsmann, K., Steinbuss, G., Zgorzelski, C., Albrecht, T., Heinrich, S., Farkas, S., Roth, W., Dang, H., Hausen, A. and Gaida, M.M.	Implementation of deep learning in liver pathology optimizes diagnosis of benign lesions and adenocarcinoma metastasis [BibTeX]	2023	Clinical and Translational Medicine Vol. 13(7)	article	DOI
BibTeX: @article{Kriegsmann2023, author = {Mark Kriegsmann and Katharina Kriegsmann and Georg Steinbuss and Christiane Zgorzelski and Thomas Albrecht and Stefan Heinrich and Stefan Farkas and Wilfried Roth and Hien Dang and Anne Hausen and Matthias M. Gaida}, title = {Implementation of deep learning in liver pathology optimizes diagnosis of benign lesions and adenocarcinoma metastasis}, journal = {Clinical and Translational Medicine}, publisher = {Wiley}, year = {2023}, volume = {13}, number = {7}, doi = {https://doi.org/10.1002/ctm2.1299} }
Ksoll, V.F., Gouliermis, D.A., Klessen, R.S., Grebel, E.K., Sabbi, E., Anderson, J., Lennon, D.J., Cignoni, M., de Marchi, G., Smith, L.J., Tosi, M. and van der Marel, R.P.	Hubble Tarantula Treasury Project – VI. Identification of Pre–Main-Sequence Stars using Machine Learning techniques [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 479(2), pp. 2389-2414	article	DOI
BibTeX: @article{Ksoll2018, author = {Victor F Ksoll and Dimitrios A Gouliermis and Ralf S Klessen and Eva K Grebel and Elena Sabbi and Jay Anderson and Daniel J Lennon and Michele Cignoni and Guido de Marchi and Linda J Smith and Monica Tosi and Roeland P van der Marel}, title = {Hubble Tarantula Treasury Project – VI. Identification of Pre–Main-Sequence Stars using Machine Learning techniques}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {479}, number = {2}, pages = {2389--2414}, doi = {https://doi.org/10.1093/mnras/sty1317} }
Kubíková, J., Ubartaitė, G., Metz, J. and Jeske, M.	Structural basis for binding of Smaug to the GPCR Smoothened and to the germline inducer Oskar [Abstract] [BibTeX]	2023	bioRxiv	article	DOI
Abstract: ABSTRACTDrosophilaSmaug and its orthologs comprise a family of mRNA repressor proteins that exhibit various functions during animal development. Smaug proteins contain a characteristic RNA-binding sterile-α motif (SAM) domain and a conserved but uncharacterized N-terminal domain (NTD). Here, we resolved the crystal structure of the NTD of the human SAM domain-containing protein 4A (SAMD4A, a.k.a. Smaug1) to 2.0 Å resolution, which revealed its composition of a homodimerization D-subdomain and a subdomain with similarity to a PHAT domain. Furthermore, we show thatDrosophilaSmaug directly interacts with theDrosophilagermline inducer Oskar and with the Hedgehog signaling transducer Smoothened through its D-PHAT domain. We determined the crystal structure of the D-PHAT domain of Smaug in complex with a Smoothened α-helical peptide to 1.61 Å resolution. The peptide binds within a groove that is formed by both the D- and PHAT subdomains. Structural modeling supported by experimental data suggested that an α-helix within the disordered region of Oskar binds to the D-PHAT domain in a mode similar to Smoothened. Together, our data uncover the N-terminal D-PHAT domain of Smaug as peptide-binding domain.
BibTeX: @article{Kubikova2023, author = {Jana Kubíková, Gabrielė Ubartaitė, Jutta Metz, Mandy Jeske}, title = {Structural basis for binding of Smaug to the GPCR Smoothened and to the germline inducer Oskar}, journal = {bioRxiv}, year = {2023}, doi = {https://doi.org/10.1101/2023.02.19.529116} }
Kub\iková, J., Ubartaitė, G., Metz, J. and Jeske, M.	Structural basis for binding of lessigreaterDrosophilaless/igreater Smaug to the GPCR Smoothened and to the germline inducer Oskar [BibTeX]	2023	Proceedings of the National Academy of Sciences Vol. 120(32)	article	DOI
BibTeX: @article{Kubikova2023a, author = {Jana Kub\iková and Gabrielė Ubartaitė and Jutta Metz and Mandy Jeske}, title = {Structural basis for binding of lessigreaterDrosophilaless/igreater Smaug to the GPCR Smoothened and to the germline inducer Oskar}, journal = {Proceedings of the National Academy of Sciences}, publisher = {Proceedings of the National Academy of Sciences}, year = {2023}, volume = {120}, number = {32}, doi = {https://doi.org/10.1073/pnas.2304385120} }
	Zerstörung von Geschriebenem [BibTeX]	2019		book	DOI
BibTeX: @book{KuehneWespi2019,, title = {Zerstörung von Geschriebenem}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110629040} }
Kupke, T., Götz, R.M., Richter, F.M., Beck, R., Lolicato, F., Nickel, W., Hopf, C. and Brügger, B.	In vivo characterization of the bacterial intramembrane-cleaving protease RseP using the heme binding tag-based assay iCliPSpy [BibTeX]	2023	Communications Biology Vol. 6(1)	article	DOI
BibTeX: @article{Kupke2023, author = {Thomas Kupke and Rabea M. Götz and Florian M. Richter and Rainer Beck and Fabio Lolicato and Walter Nickel and Carsten Hopf and Britta Brügger}, title = {In vivo characterization of the bacterial intramembrane-cleaving protease RseP using the heme binding tag-based assay iCliPSpy}, journal = {Communications Biology}, publisher = {Springer Science and Business Media LLC}, year = {2023}, volume = {6}, number = {1}, doi = {https://doi.org/10.1038/s42003-023-04654-z} }
Kurth, M., Beck, R., Aponte-Santamaria, C. and Brügger, B.	Molecular Dynamics Simulation and Photo-Crosslinking Reveal a Specific Cholesterol Binding Site for the Metabotropic Glutamate Receptor 2 [BibTeX]	2019	Biophysical Journal Vol. 116, pp. 41a-42a	article	DOI
BibTeX: @article{Kurth2019, author = {Kurth, Markus and Beck, Rainer and Aponte-Santamaria, Camilo and Brügger, Britta}, title = {Molecular Dynamics Simulation and Photo-Crosslinking Reveal a Specific Cholesterol Binding Site for the Metabotropic Glutamate Receptor 2}, journal = {Biophysical Journal}, year = {2019}, volume = {116}, pages = {41a--42a}, doi = {https://doi.org/10.1016/j.bpj.2018.11.268} }
Kurth, M., Lolicato, F., Sandoval-Perez, A., Amaya-Espinosa, H., Teslenko, A., Sinning, I., Beck, R., Brügger, B. and Aponte-Santamar\ia, C.	Cholesterol Localization around the Metabotropic Glutamate Receptor 2 [BibTeX]	2020	The Journal of Physical Chemistry B Vol. 124(41), pp. 9061-9078	article	DOI
BibTeX: @article{Kurth2020, author = {Markus Kurth and Fabio Lolicato and Angelica Sandoval-Perez and Helman Amaya-Espinosa and Alexandra Teslenko and Irmgard Sinning and Rainer Beck and Britta Brügger and Camilo Aponte-Santamar\ia}, title = {Cholesterol Localization around the Metabotropic Glutamate Receptor 2}, journal = {The Journal of Physical Chemistry B}, publisher = {American Chemical Society (ACS)}, year = {2020}, volume = {124}, number = {41}, pages = {9061--9078}, doi = {https://doi.org/10.1021/acs.jpcb.0c05264} }
Lannig, S., Schmied, C.-M., Prüfer, M., Kunkel, P., Strohmaier, R., Strobel, H., Gasenzer, T., Kevrekidis, P.G. and Oberthaler, M.K.	Collisions of Three-Component Vector Solitons in Bose-Einstein Condensates [BibTeX]	2020	Physical Review Letters Vol. 125(17), pp. 170401	article	DOI
BibTeX: @article{Lannig2020, author = {Stefan Lannig and Christian-Marcel Schmied and Maximilian Prüfer and Philipp Kunkel and Robin Strohmaier and Helmut Strobel and Thomas Gasenzer and Panayotis G. Kevrekidis and Markus K. Oberthaler}, title = {Collisions of Three-Component Vector Solitons in Bose-Einstein Condensates}, journal = {Physical Review Letters}, publisher = {American Physical Society (APS)}, year = {2020}, volume = {125}, number = {17}, pages = {170401}, doi = {https://doi.org/10.1103/physrevlett.125.170401} }
Lannig, S., Prüfer, M., Deller, Y., Siovitz, I., Dreher, J., Gasenzer, T., Strobel, H. and Oberthaler, M.K.	Observation of two non-thermal fixed points for the same microscopic symmetry [BibTeX]	2023		misc	DOI
BibTeX: @misc{Lannig2023, author = {Lannig, Stefan and Prüfer, Maximilian and Deller, Yannick and Siovitz, Ido and Dreher, Jan and Gasenzer, Thomas and Strobel, Helmut and Oberthaler, Markus K.}, title = {Observation of two non-thermal fixed points for the same microscopic symmetry}, publisher = {arXiv}, year = {2023}, doi = {https://doi.org/10.48550/ARXIV.2306.16497} }
Larson, K.L., Lee, J.C., Thilker, D.A., Whitmore, B.C., Deger, S., Lilly, J., Chandar, R., Dale, D.A., Bigiel, F., Grasha, K., Groves, B., Hannon, S., Klessen, R.S., Kreckel, K., Kruijssen, J.M.D., Leroy, A.K., Pan, H.-A., Rosolowsky, E., Schinnerer, E., Schruba, A., Watkins, E.J. and Williams, T.G.	Multiscale stellar associations across the star formation hierarchy in PHANGS–HST nearby galaxies: methodology and properties [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 523(4), pp. 6061-6081	article	DOI
BibTeX: @article{Larson2023, author = {Kirsten L Larson and Janice C Lee and David A Thilker and Bradley C Whitmore and Sinan Deger and James Lilly and Rupali Chandar and Daniel A Dale and Frank Bigiel and Kathryn Grasha and Brent Groves and Stephen Hannon and Ralf S Klessen and Kathryn Kreckel and J M Diederik Kruijssen and Adam K Leroy and Hsi-An Pan and Erik Rosolowsky and Eva Schinnerer and Andreas Schruba and Elizabeth J Watkins and Thomas G Williams}, title = {Multiscale stellar associations across the star formation hierarchy in PHANGS–HST nearby galaxies: methodology and properties}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {523}, number = {4}, pages = {6061--6081}, doi = {https://doi.org/10.1093/mnras/stad1600} }
Lau, B., Cheng, J., Flemming, D., Venuta, G.L., Berninghausen, O., Beckmann, R. and Hurt, E.	Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome [BibTeX]	2021	Molecular Cell Vol. 81, pp. 293-303.e4	article	DOI
BibTeX: @article{Lau2021, author = {Benjamin Lau and Jingdong Cheng and Dirk Flemming and Giuseppe La Venuta and Otto Berninghausen and Roland Beckmann and Ed Hurt}, title = {Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2021}, volume = {81}, pages = {293--303.e4}, doi = {https://doi.org/10.1016/j.molcel.2020.11.009} }
Lau, B., Beine-Golovchuk, O., Kornprobst, M., Cheng, J., Kressler, D., Jády, B., Kiss, T., Beckmann, R. and Hurt, E.	Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release [BibTeX]	2022	Cell Reports Vol. 41(8), pp. 111684	article	DOI URL
BibTeX: @article{Lau2022, author = {Benjamin Lau, Olga Beine-Golovchuk, Markus Kornprobst, Jingdong Cheng, Dieter Kressler, Beáta Jády, Tamás Kiss, Roland Beckmann, Ed Hurt}, title = {Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release}, journal = {Cell Reports}, publisher = {Elsevier BV}, year = {2022}, volume = {41}, number = {8}, pages = {111684}, url = {https://api.elsevier.com/content/article/PII:S2211124722015583?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.celrep.2022.111684} }
Laves, M.-H., Tölle, M., Schlaefer, A. and Engelhardt, S.	Posterior temperature optimized Bayesian models for inverse problems in medical imaging [BibTeX]	2022	Medical Image Analysis Vol. 78, pp. 102382	article	DOI URL
BibTeX: @article{Laves2022, author = {Max-Heinrich Laves, Malte Tölle, Alexander Schlaefer, Sandy Engelhardt}, title = {Posterior temperature optimized Bayesian models for inverse problems in medical imaging}, journal = {Medical Image Analysis}, publisher = {Elsevier BV}, year = {2022}, volume = {78}, pages = {102382}, url = {https://api.elsevier.com/content/article/PII:S1361841522000342?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.media.2022.102382} }
Layer, D., Kopp, J., Fontanillo, M., Köhn, M., Lapouge, K. and Sinning, I.	Structural basis of Naa20 activity towards a canonical NatB substrate [BibTeX]	2021	Communications Biology Vol. 4(1)	article	DOI
BibTeX: @article{Layer2021, author = {Dominik Layer and Jürgen Kopp and Miriam Fontanillo and Maja Köhn and Karine Lapouge and Irmgard Sinning}, title = {Structural basis of Naa20 activity towards a canonical NatB substrate}, journal = {Communications Biology}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {4}, number = {1}, doi = {https://doi.org/10.1038/s42003-020-01546-4} }
Legnar, M., Daumke, P., Hesser, J., Porubsky, S., Popovic, Z., Bindzus, J.N., Siemoneit, J.-H.H. and Weis, C.-A.	Natural Language Processing in Diagnostic Texts from Nephropathology [Abstract] [BibTeX]	2022	Diagnostics Vol. 12(7), pp. 1726	article	DOI URL
Abstract: Introduction: This study investigates whether it is possible to predict a final diagnosis based on a written nephropathological description—as a surrogate for image analysis—using various NLP methods. Methods: For this work, 1107 unlabelled nephropathological reports were included. (i) First, after separating each report into its microscopic description and diagnosis section, the diagnosis sections were clustered unsupervised to less than 20 diagnostic groups using different clustering techniques. (ii) Second, different text classification methods were used to predict the diagnostic group based on the microscopic description section. Results: The best clustering results (i) could be achieved with HDBSCAN, using BoW-based feature extraction methods. Based on keywords, these clusters can be mapped to certain diagnostic groups. A transformer encoder-based approach as well as an SVM worked best regarding diagnosis prediction based on the histomorphological description (ii). Certain diagnosis groups reached F1-scores of up to 0.892 while others achieved weak classification metrics. Conclusion: While textual morphological description alone enables retrieving the correct diagnosis for some entities, it does not work sufficiently for other entities. This is in accordance with a previous image analysis study on glomerular change patterns, where some diagnoses are associated with one pattern, but for others, there exists a complex pattern combination.
BibTeX: @article{Legnar2022, author = {Maximilian Legnar, Philipp Daumke, Jürgen Hesser, Stefan Porubsky, Zoran Popovic, Jan Niklas Bindzus, Joern-Helge Heinrich Siemoneit, Cleo-Aron Weis}, title = {Natural Language Processing in Diagnostic Texts from Nephropathology}, journal = {Diagnostics}, publisher = {MDPI AG}, year = {2022}, volume = {12}, number = {7}, pages = {1726}, url = {https://www.mdpi.com/2075-4418/12/7/1726/pdf}, doi = {https://doi.org/10.3390/diagnostics12071726} }
Leipziger, J.	Lesepraktiken im antiken Judentum [BibTeX]	2021		book	DOI
BibTeX: @book{Leipziger2021, author = {Jonas Leipziger}, title = {Lesepraktiken im antiken Judentum}, publisher = {De Gruyter}, year = {2021}, doi = {https://doi.org/10.1515/9783110732764} }
Lemp, J.M., Nuthanapati, M.P., Bärnighausen, T.W., Vollmer, S., Geldsetzer, P. and Jani, A.	Use of lifestyle interventions in primary care for individuals with newly diagnosed hypertension, hyperlipidaemia or obesity: a retrospective cohort study [BibTeX]	2022	Journal of the Royal Society of Medicine, pp. 014107682210773	article	DOI
BibTeX: @article{Lemp2022, author = {Julia M Lemp and Meghana Prasad Nuthanapati and Till W Bärnighausen and Sebastian Vollmer and Pascal Geldsetzer and Anant Jani}, title = {Use of lifestyle interventions in primary care for individuals with newly diagnosed hypertension, hyperlipidaemia or obesity: a retrospective cohort study}, journal = {Journal of the Royal Society of Medicine}, publisher = {SAGE Publications}, year = {2022}, pages = {014107682210773}, doi = {https://doi.org/10.1177/01410768221077381} }
Lerma-Martin, C., i-Mompel, P.B., Flores, R.O.R., Sekol, P., Hofmann, A., Thäwel, T., Riedl, C.J., Wünnemann, F., Ibarra-Arellano, M.A., Trobisch, T., Eisele, P., Schapiro, D., Haeussler, M., Hametner, S., Saez-Rodriguez, J. and Schirmer, L.	Spatial cell type mapping of multiple sclerosis lesions [BibTeX]	2022	bioRxiv	article	DOI
BibTeX: @article{LermaMartin2022, author = {Celia Lerma-Martin, Pau Badia-i-Mompel, Ricardo O. Ramirez Flores, Patricia Sekol, Annika Hofmann, Thomas Thäwel, Christian J. Riedl, Florian Wünnemann, Miguel A. Ibarra-Arellano, Tim Trobisch, Philipp Eisele, Denis Schapiro, Maximilian Haeussler, Simon Hametner, Julio Saez-Rodriguez, Lucas Schirmer}, title = {Spatial cell type mapping of multiple sclerosis lesions}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.11.03.514906} }
Lewis, S.C., McMillan, S.L.W., Low, M.-M.M., Cournoyer-Cloutier, C., Polak, B., Wilhelm, M.J.C., Tran, A., Sills, A., Zwart, S.P., Klessen, R.S. and Wall, J.E.	Early-forming Massive Stars Suppress Star Formation and Hierarchical Cluster Assembly [BibTeX]	2023	The Astrophysical Journal Vol. 944(2), pp. 211	article	DOI
BibTeX: @article{Lewis2023, author = {Sean C. Lewis and Stephen L. W. McMillan and Mordecai-Mark Mac Low and Claude Cournoyer-Cloutier and Brooke Polak and Martijn J. C. Wilhelm and Aaron Tran and Alison Sills and Simon Portegies Zwart and Ralf S. Klessen and Joshua E. Wall}, title = {Early-forming Massive Stars Suppress Star Formation and Hierarchical Cluster Assembly}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2023}, volume = {944}, number = {2}, pages = {211}, doi = {https://doi.org/10.3847/1538-4357/acb0c5} }
Li, T., Li, B., Sara, A., Ay, C., Leung, W.Y., Zhang, Y., Dong, Y., Liang, Q., Zhang, X., Weidner, P., Gutting, T., Behrens, H.-M., Röcken, C., Sung, J.J., Ebert, M.P., Yu, J. and Burgermeister, E.	Docking protein-1 promotes inflammatory macrophage signaling in gastric cancer [BibTeX]	2019	OncoImmunology Vol. 8(11), pp. e1649961	article	DOI
BibTeX: @article{Li2019, author = {Tong Li and Beifang Li and Asgharpour Sara and Christine Ay and Wing Yan Leung and Yanquan Zhang and Yujuan Dong and Qiaoyi Liang and Xiang Zhang and Philip Weidner and Tobias Gutting and Hans-Michael Behrens and Christoph Röcken and Joseph JY Sung and Matthias P. Ebert and Jun Yu and Elke Burgermeister}, title = {Docking protein-1 promotes inflammatory macrophage signaling in gastric cancer}, journal = {OncoImmunology}, publisher = {Informa UK Limited}, year = {2019}, volume = {8}, number = {11}, pages = {e1649961}, doi = {https://doi.org/10.1080/2162402x.2019.1649961} }
Li, H., Zech, J., Ludwig, C., Fendrich, S., Shapiro, A., Schultz, M. and Zipf, A.	Automatic mapping of national surface water with OpenStreetMap and Sentinel-2 MSI data using deep learning [BibTeX]	2021	International Journal of Applied Earth Observation and Geoinformation Vol. 104, pp. 102571	article	DOI
BibTeX: @article{Li2021, author = {Hao Li and Johannes Zech and Christina Ludwig and Sascha Fendrich and Aurelie Shapiro and Michael Schultz and Alexander Zipf}, title = {Automatic mapping of national surface water with OpenStreetMap and Sentinel-2 MSI data using deep learning}, journal = {International Journal of Applied Earth Observation and Geoinformation}, publisher = {Elsevier BV}, year = {2021}, volume = {104}, pages = {102571}, doi = {https://doi.org/10.1016/j.jag.2021.102571} }
Li, H., Zech, J., Hong, D., Ghamisi, P., Schultz, M. and Zipf, A.	Leveraging OpenStreetMap and Multimodal Remote Sensing Data with Joint Deep Learning for Wastewater Treatment Plants Detection [BibTeX]	2022	International Journal of Applied Earth Observation and Geoinformation Vol. 110, pp. 102804	article	DOI
BibTeX: @article{Li2022, author = {Hao Li and Johannes Zech and Danfeng Hong and Pedram Ghamisi and Michael Schultz and Alexander Zipf}, title = {Leveraging OpenStreetMap and Multimodal Remote Sensing Data with Joint Deep Learning for Wastewater Treatment Plants Detection}, journal = {International Journal of Applied Earth Observation and Geoinformation}, publisher = {Elsevier BV}, year = {2022}, volume = {110}, pages = {102804}, doi = {https://doi.org/10.1016/j.jag.2022.102804} }
Li, H., Herfort, B., Lautenbach, S., Chen, J. and Zipf, A.	Improving OpenStreetMap missing building detection using few-shot transfer learning in sub-Saharan Africa [BibTeX]	2022	Transactions in GIS	article	DOI
BibTeX: @article{Li2022a, author = {Hao Li and Benjamin Herfort and Sven Lautenbach and Jiaoyan Chen and Alexander Zipf}, title = {Improving OpenStreetMap missing building detection using few-shot transfer learning in sub-Saharan Africa}, journal = {Transactions in GIS}, publisher = {Wiley}, year = {2022}, doi = {https://doi.org/10.1111/tgis.12941} }
Liebers, N., Duell, J., Fitzgerald, D., Kerkhoff, A., Noerenberg, D., Kaebisch, E., Acker, F., Fuhrmann, S., Leng, C., Welslau, M., Chemnitz, J., Middeke, J.-M., Weber, T., Holtick, U., Trappe, R., Pfannes, R., Liersch, R., Spoer, C., Fuxius, S., Gebauer, N., Caillé, L., Geer, T., Koenecke, C., Keller, U., Claus, R., Mougiakakos, D., Mayer, S., Huettmann, A., Pott, C., Trummer, A., Wulf, G., Brunnberg, U., Bullinger, L., Hess, G., Mueller-Tidow, C., Glass, B., Lenz, G., Dreger, P. and Dietrich, S.	Polatuzumab vedotin as a salvage and bridging treatment in relapsed or refractory large B-cell lymphomas [BibTeX]	2021	Blood Advances Vol. 5(13), pp. 2707-2716	article	DOI
BibTeX: @article{Liebers2021, author = {Nora Liebers and Johannes Duell and Donnacha Fitzgerald and Andrea Kerkhoff and Daniel Noerenberg and Eva Kaebisch and Fabian Acker and Stephan Fuhrmann and Corinna Leng and Manfred Welslau and Jens Chemnitz and Jan-Moritz Middeke and Thomas Weber and Udo Holtick and Ralf Trappe and Roald Pfannes and Ruediger Liersch and Christian Spoer and Stefan Fuxius and Niklas Gebauer and Léandra Caillé and Thomas Geer and Christian Koenecke and Ulrich Keller and Rainer Claus and Dimitrios Mougiakakos and Stephanie Mayer and Andreas Huettmann and Christiane Pott and Arne Trummer and Gerald Wulf and Uta Brunnberg and Lars Bullinger and Georg Hess and Carsten Mueller-Tidow and Bertram Glass and Georg Lenz and Peter Dreger and Sascha Dietrich}, title = {Polatuzumab vedotin as a salvage and bridging treatment in relapsed or refractory large B-cell lymphomas}, journal = {Blood Advances}, publisher = {American Society of Hematology}, year = {2021}, volume = {5}, number = {13}, pages = {2707--2716}, doi = {https://doi.org/10.1182/bloodadvances.2020004155} }
Liebers, N., Speer, C., Benning, L., Bruch, P.-M., Kraemer, I., Meissner, J., Schnitzler, P., Kräusslich, H.-G., Dreger, P., Mueller-Tidow, C., Poschke, I. and Dietrich, S.	Humoral and cellular responses after COVID-19 vaccination in anti-CD20-treated lymphoma patients [BibTeX]	2022	Blood Vol. 139(1), pp. 142-147	article	DOI
BibTeX: @article{Liebers2022, author = {Nora Liebers and Claudius Speer and Louise Benning and Peter-Martin Bruch and Isabelle Kraemer and Julia Meissner and Paul Schnitzler and Hans-Georg Kräusslich and Peter Dreger and Carsten Mueller-Tidow and Isabel Poschke and Sascha Dietrich}, title = {Humoral and cellular responses after COVID-19 vaccination in anti-CD20-treated lymphoma patients}, journal = {Blood}, publisher = {American Society of Hematology}, year = {2022}, volume = {139}, number = {1}, pages = {142--147}, doi = {https://doi.org/10.1182/blood.2021013445} }
Linster, E., Layer, D., Bienvenut, W.V., Dinh, T.V., Weyer, F.A., Leemhuis, W., Brünje, A., Hoffrichter, M., Miklankova, P., Kopp, J., Lapouge, K., Sindlinger, J., Schwarzer, D., Meinnel, T., Finkemeier, I., Giglione, C., Hell, R., Sinning, I. and Wirtz, M.	The Arabidopsis N upalpha -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response [BibTeX]	2020	New Phytologist Vol. 228(2), pp. 554-569	article	DOI
BibTeX: @article{Linster2020, author = {Eric Linster and Dominik Layer and Willy V. Bienvenut and Trinh V. Dinh and Felix A. Weyer and Wiebke Leemhuis and Annika Brünje and Marion Hoffrichter and Pavlina Miklankova and Jürgen Kopp and Karine Lapouge and Julia Sindlinger and Dirk Schwarzer and Thierry Meinnel and Iris Finkemeier and Carmela Giglione and Ruediger Hell and Irmgard Sinning and Markus Wirtz}, title = {The Arabidopsis N upalpha -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response}, journal = {New Phytologist}, publisher = {Wiley}, year = {2020}, volume = {228}, number = {2}, pages = {554--569}, doi = {https://doi.org/10.1111/nph.16747} }
Lityagina, O. and Dobreva, G.	The LINC Between Mechanical Forces and Chromatin [BibTeX]	2021	Frontiers in Physiology Vol. 12	article	DOI
BibTeX: @article{Lityagina2021, author = {Olga Lityagina and Gergana Dobreva}, title = {The LINC Between Mechanical Forces and Chromatin}, journal = {Frontiers in Physiology}, publisher = {Frontiers Media SA}, year = {2021}, volume = {12}, doi = {https://doi.org/10.3389/fphys.2021.710809} }
Liu, P., Zupa, E., Neuner, A., Böhler, A., Loerke, J., Flemming, D., Ruppert, T., Rudack, T., Peter, C., Spahn, C., Gruss, O.J., Pfeffer, S. and Schiebel, E.	Insights into the assembly and activation of the microtubule nucleator upgamma-TuRC [BibTeX]	2019	Nature Vol. 578(7795), pp. 467-471	article	DOI
BibTeX: @article{Liu2019, author = {Peng Liu and Erik Zupa and Annett Neuner and Anna Böhler and Justus Loerke and Dirk Flemming and Thomas Ruppert and Till Rudack and Christoph Peter and Christian Spahn and Oliver J. Gruss and Stefan Pfeffer and Elmar Schiebel}, title = {Insights into the assembly and activation of the microtubule nucleator upgamma-TuRC}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {578}, number = {7795}, pages = {467--471}, doi = {https://doi.org/10.1038/s41586-019-1896-6} }
Liu, P., Würtz, M., Zupa, E., Pfeffer, S. and Schiebel, E.	Microtubule nucleation: The waltz between γ-tubulin ring complex and associated proteins [BibTeX]	2021	Current Opinion in Cell Biology Vol. 68, pp. 124-131	article	DOI URL
BibTeX: @article{Liu2021, author = {Peng Liu, Martin Würtz, Erik Zupa, Stefan Pfeffer, Elmar Schiebel}, title = {Microtubule nucleation: The waltz between γ-tubulin ring complex and associated proteins}, journal = {Current Opinion in Cell Biology}, publisher = {Elsevier BV}, year = {2021}, volume = {68}, pages = {124--131}, url = {https://api.elsevier.com/content/article/PII:S0955067420301393?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.ceb.2020.10.004} }
Lösel, P.D., van de Kamp, T., Jayme, A., Ershov, A., Faragó, T., Pichler, O., Jerome, N.T., Aadepu, N., Bremer, S., Chilingaryan, S.A., Heethoff, M., Kopmann, A., Odar, J., Schmelzle, S., Zuber, M., Wittbrodt, J., Baumbach, T. and Heuveline, V.	Introducing Biomedisa as an open-source online platform for biomedical image segmentation [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Loesel2020, author = {Philipp D. Lösel and Thomas van de Kamp and Alejandra Jayme and Alexey Ershov and Tomáš Faragó and Olaf Pichler and Nicholas Tan Jerome and Narendar Aadepu and Sabine Bremer and Suren A. Chilingaryan and Michael Heethoff and Andreas Kopmann and Janes Odar and Sebastian Schmelzle and Marcus Zuber and Joachim Wittbrodt and Tilo Baumbach and Vincent Heuveline}, title = {Introducing Biomedisa as an open-source online platform for biomedical image segmentation}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-19303-w} }
Lohmann, P.	Graffiti als Interaktionsform [BibTeX]	2017		book	DOI
BibTeX: @book{Lohmann2017, author = {Polly Lohmann}, title = {Graffiti als Interaktionsform}, publisher = {De Gruyter}, year = {2017}, doi = {https://doi.org/10.1515/9783110574289} }
Lolicato, F., Steringer, J., Saleppico, R., Beyer, D., Fernandez-Sobaberas, J., Unger, S., Klein, S., Riegerová, P., Wegehingel, S., Müller, H., Freund, C., Hof, M., Šachl, R., Chlanda, P., Vattulainen, I. and Nickel, W.	Disulfide bridge-dependent dimerization triggers FGF2 membrane translocation into the extracellular space [BibTeX]	2023		article	DOI
BibTeX: @article{Lolicato2023, author = {F Lolicato and JP Steringer and R Saleppico and D Beyer and J Fernandez-Sobaberas and S Unger and S Klein and P Riegerová and S Wegehingel and HM Müller and C Freund and M Hof and R Šachl and P Chlanda and I Vattulainen and W Nickel}, title = {Disulfide bridge-dependent dimerization triggers FGF2 membrane translocation into the extracellular space}, publisher = {eLife Sciences Publications, Ltd}, year = {2023}, doi = {https://doi.org/10.7554/elife.88579.1} }
Lucas, S., Kammerer, J., Pfannmöller, M., Schröder, R.R., He, Y., Li, N., Brabec, C.J., Leydecker, T., Samor\i, P., Marszalek, T., Pisula, W., Mena-Osteritz, E. and Bäuerle, P.	Molecular Donor–Acceptor Dyads for Efficient Single-Material Organic Solar Cells [BibTeX]	2020	Solar RRL Vol. 5(1), pp. 2000653	article	DOI
BibTeX: @article{Lucas2020, author = {Sebastian Lucas and Jochen Kammerer and Martin Pfannmöller and Rasmus R. Schröder and Yakun He and Ning Li and Christoph J. Brabec and Tim Leydecker and Paolo Samor\i and Tomasz Marszalek and Wojchiech Pisula and Elena Mena-Osteritz and Peter Bäuerle}, title = {Molecular Donor–Acceptor Dyads for Efficient Single-Material Organic Solar Cells}, journal = {Solar RRL}, publisher = {Wiley}, year = {2020}, volume = {5}, number = {1}, pages = {2000653}, doi = {https://doi.org/10.1002/solr.202000653} }
Lucic, B., Chen, H.-C., Kuzman, M., Zorita, E., Wegner, J., Minneker, V., Wang, W., Fronza, R., Laufs, S., Schmidt, M., Stadhouders, R., Roukos, V., Vlahovicek, K., Filion, G.J. and Lusic, M.	Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration [BibTeX]	2019	Nature Communications Vol. 10(1), pp. 4059	article	DOI
BibTeX: @article{Lucic2019, author = {Bojana Lucic and Heng-Chang Chen and Maja Kuzman and Eduard Zorita and Julia Wegner and Vera Minneker and Wei Wang and Raffaele Fronza and Stefanie Laufs and Manfred Schmidt and Ralph Stadhouders and Vassilis Roukos and Kristian Vlahovicek and Guillaume J. Filion and Marina Lusic}, title = {Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {10}, number = {1}, pages = {4059}, doi = {https://doi.org/10.1038/s41467-019-12046-3} }
Lucic, B., Wegner, J., Stanic, M., Jost, K.L. and Lusic, M.	3D Immuno-DNA Fluorescence In Situ Hybridization (FISH) for Detection of HIV-1 and Cellular Genes in Primary CD4mathplus T Cells [BibTeX]	2020	Methods in Molecular Biology, pp. 239-249	incollection	DOI
BibTeX: @incollection{Lucic2020, author = {Bojana Lucic and Julia Wegner and Mia Stanic and Katharina Laurence Jost and Marina Lusic}, title = {3D Immuno-DNA Fluorescence In Situ Hybridization (FISH) for Detection of HIV-1 and Cellular Genes in Primary CD4mathplus T Cells}, booktitle = {Methods in Molecular Biology}, publisher = {Springer US}, year = {2020}, pages = {239--249}, doi = {https://doi.org/10.1007/978-1-0716-0664-3_14} }
Lucic, B., de Castro, I.J. and Lusic, M.	Viruses in the Nucleus [BibTeX]	2021	Cold Spring Harbor Perspectives in Biology Vol. 13	article	DOI
BibTeX: @article{Lucic2021, author = {Bojana Lucic and Ines J. de Castro and Marina Lusic}, title = {Viruses in the Nucleus}, journal = {Cold Spring Harbor Perspectives in Biology}, publisher = {Cold Spring Harbor Laboratory}, year = {2021}, volume = {13}, doi = {https://doi.org/10.1101/cshperspect.a039446} }
Ludwig, C., Fendrich, S. and Zipf, A.	Regional variations of context-based association rules in OpenStreetMap [BibTeX]	2020	Transactions in GIS Vol. 25(2), pp. 602-621	article	DOI
BibTeX: @article{Ludwig2020, author = {Christina Ludwig and Sascha Fendrich and Alexander Zipf}, title = {Regional variations of context-based association rules in OpenStreetMap}, journal = {Transactions in GIS}, publisher = {Wiley}, year = {2020}, volume = {25}, number = {2}, pages = {602--621}, doi = {https://doi.org/10.1111/tgis.12694} }
Ludwig, C., Hecht, R., Lautenbach, S., Schorcht, M. and Zipf, A.	Mapping Public Urban Green Spaces Based on OpenStreetMap and Sentinel-2 Imagery Using Belief Functions [BibTeX]	2021	ISPRS International Journal of Geo-Information Vol. 10(4), pp. 251	article	DOI
BibTeX: @article{Ludwig2021, author = {Christina Ludwig and Robert Hecht and Sven Lautenbach and Martin Schorcht and Alexander Zipf}, title = {Mapping Public Urban Green Spaces Based on OpenStreetMap and Sentinel-2 Imagery Using Belief Functions}, journal = {ISPRS International Journal of Geo-Information}, publisher = {MDPI AG}, year = {2021}, volume = {10}, number = {4}, pages = {251}, doi = {https://doi.org/10.3390/ijgi10040251} }
Luo, F., Liu, X., Südhof, T.C. and Acuna, C.	Efficient stimulus-secretion coupling at ribbon synapses requires RIM-binding protein tethering of L-type Ca2mathpluschannels [BibTeX]	2017	Proceedings of the National Academy of Sciences Vol. 114(38), pp. E8081-E8090	article	DOI
BibTeX: @article{Luo2017, author = {Fujun Luo and Xinran Liu and Thomas C. Südhof and Claudio Acuna}, title = {Efficient stimulus-secretion coupling at ribbon synapses requires RIM-binding protein tethering of L-type Ca2mathpluschannels}, journal = {Proceedings of the National Academy of Sciences}, publisher = {Proceedings of the National Academy of Sciences}, year = {2017}, volume = {114}, number = {38}, pages = {E8081--E8090}, doi = {https://doi.org/10.1073/pnas.1702991114} }
Maconi, E., Soler, J.D., Reissl, S., Girichidis, P., Klessen, R.S., Hennebelle, P., Molinari, S., Testi, L., Smith, R.J., Sormani, M.C., Teh, J.W. and Traficante, A.	Modelling Local Bubble analogs: synthetic dust polarization maps [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 523(4), pp. 5995-6010	article	DOI
BibTeX: @article{Maconi2023, author = {E Maconi and J D Soler and S Reissl and P Girichidis and R S Klessen and P Hennebelle and S Molinari and L Testi and R J Smith and M C Sormani and J W Teh and A Traficante}, title = {Modelling Local Bubble analogs: synthetic dust polarization maps}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {523}, number = {4}, pages = {5995--6010}, doi = {https://doi.org/10.1093/mnras/stad1854} }
Magg, M., Hartwig, T., Agarwal, B., Frebel, A., Glover, S.C.O., Griffen, B.F. and Klessen, R.S.	Predicting the locations of possible long-lived low-mass first stars: importance of satellite dwarf galaxies [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 473(4), pp. 5308-5323	article	DOI
BibTeX: @article{Magg2018, author = {Magg, Mattis and Hartwig, Tilman and Agarwal, Bhaskar and Frebel, Anna and Glover, Simon C. O. and Griffen, Brendan F. and Klessen, Ralf S.}, title = {Predicting the locations of possible long-lived low-mass first stars: importance of satellite dwarf galaxies}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {473}, number = {4}, pages = {5308--5323}, doi = {https://doi.org/10.1093/mnras/stx2729} }
Magg, M., Klessen, R.S., Glover, S.C.O. and Li, H.	Observational constraints on the survival of pristine stars [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 487(1), pp. 486-490	article	DOI
BibTeX: @article{Magg2019, author = {Mattis Magg and Ralf S Klessen and Simon C O Glover and Haining Li}, title = {Observational constraints on the survival of pristine stars}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {487}, number = {1}, pages = {486--490}, doi = {https://doi.org/10.1093/mnras/stz1210} }
Magg, M., Schauer, A.T.P., Klessen, R.S., Glover, S.C.O., Tress, R.G. and Jaura, O.	Metal Mixing in Minihalos: The Descendants of Pair-instability Supernovae [BibTeX]	2022	The Astrophysical Journal Vol. 929(2), pp. 119	article	DOI
BibTeX: @article{Magg2022, author = {Mattis Magg and Anna T. P. Schauer and Ralf S. Klessen and Simon C. O. Glover and Robin G. Tress and Ondrej Jaura}, title = {Metal Mixing in Minihalos: The Descendants of Pair-instability Supernovae}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2022}, volume = {929}, number = {2}, pages = {119}, doi = {https://doi.org/10.3847/1538-4357/ac5aac} }
Magg, M., Reis, I., Fialkov, A., Barkana, R., Klessen, R.S., Glover, S.C.O., Chen, L.-H., Hartwig, T. and Schauer, A.T.P.	Effect of the cosmological transition to metal-enriched star formation on the hydrogen 21-cm signal [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 514(3), pp. 4433-4449	article	DOI
BibTeX: @article{Magg2022a, author = {Mattis Magg, Itamar Reis, Anastasia Fialkov, Rennan Barkana, Ralf S Klessen, Simon C O Glover, Li-Hsin Chen, Tilman Hartwig, Anna T P Schauer}, title = {Effect of the cosmological transition to metal-enriched star formation on the hydrogen 21-cm signal}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {514}, number = {3}, pages = {4433--4449}, doi = {https://doi.org/10.1093/mnras/stac1664} }
Maike Petersen, M.N.	Using an unmanned aerial system to analyse environmental impacts of charcoal production on tropical savanna ecosystems in northwestern Kenya [Abstract] [BibTeX]	2022	Environmental Monitoring and Assessment Vol. 194(9)	article	DOI
Abstract: AbstractIn many regions of Sub-Saharan Africa, charcoal plays an important role as energy source but is widely perceived as a major driver of deforestation and forest degradation. This narrative, however, is mostly based on research within primary production regions. Though space-borne remote sensing applications can be useful in monitoring such large-scale production modes, environmental effects of household-level production are less easy to assess. Therefore, the present study employs an unmanned aerial system (UAS) to assess the impact of small-scale charcoal production on the vegetation density in the immediate vicinity of production sites. The UAS data was complemented by field measurements and very high-resolution WordView-2 satellite imagery. This approach revealed only small differences between charcoal production sites and reference plots which were usually evened out after 20–25-m distance to the plot centre using a concentric ring analysis. Results further show that a distinction between different land-use practices is difficult, even with the high spatial resolution provided by a UAS. Thus, more research and new approaches are needed to evaluate the role of small-scale charcoal production in deforestation and forest degradation processes against the background of other human activities. However, to exploit the full potential of UAS for monitoring environmental effects in charcoal producing areas, official regulations need to be clearer and more reliable.
BibTeX: @article{MaikePetersen2022, author = {Maike Petersen, Marcus Nüsser}, title = {Using an unmanned aerial system to analyse environmental impacts of charcoal production on tropical savanna ecosystems in northwestern Kenya}, journal = {Environmental Monitoring and Assessment}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {194}, number = {9}, doi = {https://doi.org/10.1007/s10661-022-10241-2} }
Majeed, U., Rashid, I., Sattar, A., Allen, S., Stoffel, M., Nüsser, M. and Schmidt, S.	Recession of Gya Glacier and the 2014 glacial lake outburst flood in the Trans-Himalayan region of Ladakh, India [BibTeX]	2021	Science of The Total Environment Vol. 756, pp. 144008	article	DOI
BibTeX: @article{Majeed2021, author = {Ulfat Majeed and Irfan Rashid and Ashim Sattar and Simon Allen and Markus Stoffel and Marcus Nüsser and Susanne Schmidt}, title = {Recession of Gya Glacier and the 2014 glacial lake outburst flood in the Trans-Himalayan region of Ladakh, India}, journal = {Science of The Total Environment}, publisher = {Elsevier BV}, year = {2021}, volume = {756}, pages = {144008}, doi = {https://doi.org/10.1016/j.scitotenv.2020.144008} }
Malek, M., Wawrzyniak, A.M., Koch, P., Lüchtenborg, C., Hessenberger, M., Sachsenheimer, T., Jang, W., Brügger, B. and Haucke, V.	Inositol triphosphate-triggered calcium release blocks lipid exchange at endoplasmic reticulum-Golgi contact sites [BibTeX]	2021	Nature Communications Vol. 12(1)	article	DOI
BibTeX: @article{Malek2021, author = {Mouhannad Malek and Anna M. Wawrzyniak and Peter Koch and Christian Lüchtenborg and Manuel Hessenberger and Timo Sachsenheimer and Wonyul Jang and Britta Brügger and Volker Haucke}, title = {Inositol triphosphate-triggered calcium release blocks lipid exchange at endoplasmic reticulum-Golgi contact sites}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, doi = {https://doi.org/10.1038/s41467-021-22882-x} }
Mandowara, Y., Sormani, M.C., Sobacchi, E. and Klessen, R.S.	The physical origin and the properties of arm spurs/feathers in local simulations of the wiggle instability [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 513(4), pp. 5052-5075	article	DOI
BibTeX: @article{Mandowara2022, author = {Yash Mandowara and Mattia C Sormani and Emanuele Sobacchi and Ralf S Klessen}, title = {The physical origin and the properties of arm spurs/feathers in local simulations of the wiggle instability}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {513}, number = {4}, pages = {5052--5075}, doi = {https://doi.org/10.1093/mnras/stac1214} }
Manta, C.-P., Leibing, T., Friedrich, M., Nolte, H., Adrian, M., Schledzewski, K., Krzistetzko, J., Kirkamm, C., Schmid, C.D., Xi, Y., Stojanovic, A., Tonack, S., de la Torre, C., Hammad, S., Offermanns, S., Krüger, M., Cerwenka, A., Platten, M., Goerdt, S. and Géraud, C.	Targeting of Scavenger Receptors Stabilin-1 and Stabilin-2 Ameliorates Atherosclerosis by a Plasma Proteome Switch Mediating Monocyte/Macrophage Suppression [Abstract] [BibTeX]	2022	Circulation Vol. 146(23), pp. 1783-1799	article	DOI
Abstract: Background: Scavenger receptors Stabilin-1 (Stab1) and Stabilin-2 (Stab2) are preferentially expressed by liver sinusoidal endothelial cells. They mediate the clearance of circulating plasma molecules controlling distant organ homeostasis. Studies suggest that Stab1 and Stab2 may affect atherosclerosis. Although subsets of tissue macrophages also express Stab1, hematopoietic Stab1 deficiency does not modulate atherogenesis. Here, we comprehensively studied how targeting Stab1 and Stab2 affects atherosclerosis. Methods: ApoE-KO mice were interbred with Stab1-KO and Stab2-KO mice and fed a Western diet. For antibody targeting, Ldlr-KO mice were also used. Unbiased plasma proteomics were performed and independently confirmed. Ligand binding studies comprised glutathione-S-transferase–pulldown and endocytosis assays. Plasma proteome effects on monocytes were studied by single-cell RNA sequencing in vivo, and by gene expression analyses of Stabilin ligand–stimulated and plasma-stimulated bone marrow–derived monocytes/macrophages in vitro. Results: Spontaneous and Western diet–associated atherogenesis was significantly reduced in ApoE-Stab1-KO and ApoE-Stab2-KO mice. Similarly, inhibition of Stab1 or Stab2 by monoclonal antibodies significantly reduced Western diet–associated atherosclerosis in ApoE-KO and Ldlr-KO mice. Although neither plasma lipid levels nor circulating immune cell numbers were decisively altered, plasma proteomics revealed a switch in the plasma proteome, consisting of 231 dysregulated proteins comparing wildtype with Stab1/2-single and Stab1/2-double KO, and of 41 proteins comparing ApoE-, ApoE-Stab1-, and ApoE-Stab2-KO. Among this broad spectrum of common, but also disparate scavenger receptor ligand candidates, periostin, reelin, and TGFBi (transforming growth factor, β-induced), known to modulate atherosclerosis, were independently confirmed as novel circulating ligands of Stab1/2. Single-cell RNA sequencing of circulating myeloid cells of ApoE-, ApoE-Stab1-, and ApoE-Stab2-KO mice showed transcriptomic alterations in patrolling (Ccr2 – /Cx3cr1 ++ /Ly6C lo ) and inflammatory (Ccr2 + /Cx3cr1 + /Ly6C hi ) monocytes, including downregulation of proatherogenic transcription factor Egr1. In wildtype bone marrow–derived monocytes/macrophages, ligand exposure alone did not alter Egr1 expression in vitro. However, exposure to plasma from ApoE-Stab1-KO and ApoE-Stab2-KO mice showed a reverted proatherogenic macrophage activation compared with ApoE-KO plasma, including downregulation of Egr1 in vitro. Conclusions: Inhibition of Stab1/Stab2 mediates an anti-inflammatory switch in the plasma proteome, including direct Stabilin ligands. The altered plasma proteome suppresses both patrolling and inflammatory monocytes and, thus, systemically protects against atherogenesis. Altogether, anti-Stab1– and anti-Stab2–targeted therapies provide a novel approach for the future treatment of atherosclerosis.
BibTeX: @article{Manta2022, author = {Calin-Petru Manta, Thomas Leibing, Mirco Friedrich, Hendrik Nolte, Monica Adrian, Kai Schledzewski, Jessica Krzistetzko, Christof Kirkamm, Christian David Schmid, Yannick Xi, Ana Stojanovic, Sarah Tonack, Carolina de la Torre, Seddik Hammad, Stefan Offermanns, Marcus Krüger, Adelheid Cerwenka, Michael Platten, Sergij Goerdt, Cyrill Géraud}, title = {Targeting of Scavenger Receptors Stabilin-1 and Stabilin-2 Ameliorates Atherosclerosis by a Plasma Proteome Switch Mediating Monocyte/Macrophage Suppression}, journal = {Circulation}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, year = {2022}, volume = {146}, number = {23}, pages = {1783--1799}, doi = {https://doi.org/10.1161/CIRCULATIONAHA.121.058615} }
Marin, R., Cortez, D., Lamanna, F., Pradeepa, M.M., Leushkin, E., Julien, P., Liechti, A., Halbert, J., Brüning, T., Mössinger, K., Trefzer, T., Conrad, C., Kerver, H.N., Wade, J., Tschopp, P. and Kaessmann, H.	Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage [Abstract] [BibTeX]	2017	Genome research Vol. 27(12), pp. 1974-1987	article	DOI URL
Abstract: Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.
BibTeX: @article{Marin2017, author = {Marin, Ray and Cortez, Diego and Lamanna, Francesco and Pradeepa, Madapura M. and Leushkin, Evgeny and Julien, Philippe and Liechti, Angélica and Halbert, Jean and Brüning, Thoomke and Mössinger, Katharina and Trefzer, Timo and Conrad, Christian and Kerver, Halie N. and Wade, Juli and Tschopp, Patrick and Kaessmann, Henrik}, title = {Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage}, journal = {Genome research}, publisher = {Cold Spring Harbor Lab}, year = {2017}, volume = {27}, number = {12}, pages = {1974--1987}, url = {http://genome.cshlp.org/content/27/12/1974.abstract}, doi = {https://doi.org/10.1101/gr.223727.117} }
Martín-Cortecero, J., Isaías-Camacho, E.U., Boztepe, B., Ziegler, K., Mease, R.A. and Groh, A.	Monosynaptic trans-collicular pathways link mouse whisker circuits to integrate somatosensory and motor cortical signals [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: AbstractThe superior colliculus (SC), a conserved midbrain-node with extensive long-range connectivity throughout the brain, is a key structure for innate behaviors. Descending cortical pathways are increasingly recognized as central control points for SC-mediated behaviors, but how cortico-collicular pathways coordinate SC activity at the cellular level is poorly understood. Moreover, despite the known role of the SC as a multisensory integrator, the involvement of the SC in the somatosensory system is largely unexplored in comparison to its involvement in the visual and auditory systems. Here, we mapped the connectivity of the whisker-sensitive region of the SC in mice with trans-synaptic and intersectional tracing tools and in vivo electrophysiology. The results reveal a novel trans-collicular connectivity motif in which neurons in motor- and somatosensory cortices impinge onto the brainstem-SC-brainstem sensory-motor arc and onto SC-midbrain output pathways via only one synapse in the SC. Intersectional approaches and optogenetically assisted connectivity quantificationsin vivoreveal convergence of motor and somatosensory cortical input on individual SC neurons, providing a new framework for sensory-motor integration in the SC. More than a third of the cortical recipient neurons in the whisker SC are GABAergic neurons, which include a hitherto unknown population of GABAergic projection neurons targeting thalamic nuclei and the zona incerta. These results pinpoint a whisker region in the SC of mice as a node for the integration of somatosensory and motor cortical signals via parallel excitatory and inhibitory trans-collicular pathways which link cortical and subcortical whisker circuits for somato-motor integration.
BibTeX: @article{MartinCortecero2022, author = {Jesús Martín-Cortecero, Emilio Ulises Isaías-Camacho, Berin Boztepe, Katharina Ziegler, Rebecca Audrey Mease, Alexander Groh}, title = {Monosynaptic trans-collicular pathways link mouse whisker circuits to integrate somatosensory and motor cortical signals}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1371/journal.pbio.3002126} }
Marty-Lombardi, S., Lu, S., Ambroziak, W., Wende, H., Schrenk-Siemens, K., DePaoli-Roach, A.A., Hagenston, A.M., Tappe-Theodor, A., Simonetti, M., Kuner, R., Fleming, T. and Siemens, J.	Neuron-astrocyte metabolic coupling facilitates spinal plasticity and maintenance of persistent pain [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: AbstractLong-lasting pain stimuli can trigger maladaptive changes in the spinal cord, reminiscent of plasticity associated with memory formation. Metabolic coupling between astrocytes and neurons has been implicated in neuronal plasticity and memory formation in the CNS, but neither its involvement in pathological pain nor in spinal plasticity has been tested. Here, we report a novel form of neuroglia signaling involving spinal astrocytic glycogen dynamics triggered by persistent noxious stimulation via upregulation of the metabolic signaling molecule PTG exclusively in spinal astrocytes. PTG drove glycogen build-up in astrocytes, and blunting glycogen accumulation and turnover byPtggene deletion reduced pain-related behaviors and promoted faster recovery by shortening pain maintenance. Furthermore, mechanistic analyses revealed that glycogen dynamics is a critically required process for maintenance of pain by facilitating neuronal plasticity in spinal lamina 1 neurons. Finally, metabolic analysis indicated that glycolysis and lactate transfer between astrocytes and neurons fuels spinal neuron hyperexcitability.Spinal glycogen-metabolic cascades therefore hold therapeutic potential to alleviate pathological pain.
BibTeX: @article{MartyLombardi2022, author = {Sebastián Marty-Lombardi, Shiying Lu, Wojciech Ambroziak, Hagen Wende, Katrin Schrenk-Siemens, Anna A. DePaoli-Roach, Anna M. Hagenston, Anke Tappe-Theodor, Manuela Simonetti, Rohini Kuner, Thomas Fleming, Jan Siemens}, title = {Neuron-astrocyte metabolic coupling facilitates spinal plasticity and maintenance of persistent pain}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.12.03.518519} }
Maul, S., Miglus, P., Aguilar-Kons, J., al-Magasees, A., Fetner, R., Heiler, J., Stępniowski, F. and Tamm, A.	Erforschung des ekal mašarti auf Tell Nebi Yunus in Ninive 2018--2019 [BibTeX]	2020	Zeitschrift für Orient-Archäologie Vol. 13, pp. 128-213	article
BibTeX: @article{Maul2020, author = {Maul, SM and Miglus, PA and Aguilar-Kons, J and al-Magasees, A and Fetner, RA and Heiler, J and Stępniowski, FM and Tamm, A}, title = {Erforschung des ekal mašarti auf Tell Nebi Yunus in Ninive 2018--2019}, journal = {Zeitschrift für Orient-Archäologie}, year = {2020}, volume = {13}, pages = {128--213} }
Maul, S.M. and Miglus, P.	Verwüstung und Plünderung des letzten unerforschten assyrischen Königspalastes [BibTeX]	2021	B. Hemeier, I. Sabrine, Kulturraub – Fallbeispiele aus Syrien, Irak, Jemen, Ägypten und Libyen	article
BibTeX: @article{Maul2021, author = {Maul, S. M. and Miglus, P.}, title = {Verwüstung und Plünderung des letzten unerforschten assyrischen Königspalastes}, journal = {B. Hemeier, I. Sabrine, Kulturraub – Fallbeispiele aus Syrien, Irak, Jemen, Ägypten und Libyen}, year = {2021} }
Maul, S.	Die Wahrsagekunst des Alten Orients oder Von Sinn und Unsinn der Prognostik [BibTeX]	2021	Kann Wissenschaft in die Zukunft sehen? Prognosen in den Wissenschaften, Acta Historica Leopoldina 78, pp. 71–87	incollection	DOI
BibTeX: @incollection{Maul2021a, author = {Stefan Maul}, title = {Die Wahrsagekunst des Alten Orients oder Von Sinn und Unsinn der Prognostik}, booktitle = {Kann Wissenschaft in die Zukunft sehen? Prognosen in den Wissenschaften, Acta Historica Leopoldina 78}, publisher = {Deutsche Akademie der Naturforscher Leopoldina – Nationale Akademie der Wissenschaften, Wissenschaftliche Verlagsgesellschaft}, year = {2021}, pages = {71–87}, doi = {https://doi.org/10.11588/propylaeumdok.00004832} }
Maul, S.M. and Miglus, P.A.	Ninive. Verwüstung und Plünderung des letzten unerforschten assyrischen Königspalastes [BibTeX]	2021	Kulturraub – Fallbeispiele aus Syrien, Irak, Jemen, Ägypten und Libyen, pp. 186-190	incollection
BibTeX: @incollection{Maul2021b, author = {Maul, S. M.; Miglus, P. A.}, title = {Ninive. Verwüstung und Plünderung des letzten unerforschten assyrischen Königspalastes}, booktitle = {Kulturraub – Fallbeispiele aus Syrien, Irak, Jemen, Ägypten und Libyen}, year = {2021}, pages = {186-190} }
Maul, S.	Auf der Suche nach dem Ursprung – Vergangenheitskonstruktionen und der Alte Orient [BibTeX]	2022	Genese und Legitimation. „Intentionale Geschichte“ im interdisziplinären Gespräch, Texte und Materialien der Forschungsstätte der Evangelischen Studiengemeinschaft e.V. 1	incollection
BibTeX: @incollection{Maul2022, author = {Stefan Maul}, title = {Auf der Suche nach dem Ursprung – Vergangenheitskonstruktionen und der Alte Orient}, booktitle = {Genese und Legitimation. „Intentionale Geschichte“ im interdisziplinären Gespräch, Texte und Materialien der Forschungsstätte der Evangelischen Studiengemeinschaft e.V. 1}, year = {2022} }
Maul, S.	Altern und Altersvorsorge in einer frühen Hochkultur, in: A. Ho, Th. W. Holstein, H. Häfner (Hrsg.), Altern: Biologie und Chancen. Alter und Altern individuell, kollektiv und die Folgen, Schriften der Mathematisch-naturwissenschaftliche Klasse / Heidelberger Akademie der Wissenschaften 27, Wiesbaden 2022, 141–151 [BibTeX]	2022	Altern: Biologie und Chancen. Alter und Altern individuell, kollektiv und die Folgen, Schriften der Mathematisch-naturwissenschaftliche Klasse / Heidelberger Akademie der Wissenschaften 27, pp. 141–151	incollection
BibTeX: @incollection{Maul2022a, author = {Stefan Maul}, title = {Altern und Altersvorsorge in einer frühen Hochkultur, in: A. Ho, Th. W. Holstein, H. Häfner (Hrsg.), Altern: Biologie und Chancen. Alter und Altern individuell, kollektiv und die Folgen, Schriften der Mathematisch-naturwissenschaftliche Klasse / Heidelberger Akademie der Wissenschaften 27, Wiesbaden 2022, 141–151}, booktitle = {Altern: Biologie und Chancen. Alter und Altern individuell, kollektiv und die Folgen, Schriften der Mathematisch-naturwissenschaftliche Klasse / Heidelberger Akademie der Wissenschaften 27}, year = {2022}, pages = {141–151} }
Maul, S.	Aus Ruinen [BibTeX]	2023	Ruperto Carola, pp. Nr. 21 (2023): Anfang & Ende	article	DOI
BibTeX: @article{Maul2023, author = {Maul, Stefan}, title = {Aus Ruinen}, journal = {Ruperto Carola}, publisher = {Ruperto Carola}, year = {2023}, pages = {Nr. 21 (2023): Anfang & Ende}, doi = {https://doi.org/10.17885/HEIUP.RUCA.2023.21.24730} }
McDowell, M.A., Heimes, M., Fiorentino, F., Mehmood, S., Farkas, Á., Coy-Vergara, J., Wu, D., Bolla, J.R., Schmid, V., Heinze, R., Wild, K., Flemming, D., Pfeffer, S., Schwappach, B., Robinson, C.V. and Sinning, I.	Structural Basis of Tail-Anchored Membrane Protein Biogenesis by the GET Insertase Complex [BibTeX]	2020	Molecular Cell Vol. 80(1), pp. 72-86.e7	article	DOI
BibTeX: @article{McDowell2020, author = {Melanie A. McDowell and Michael Heimes and Francesco Fiorentino and Shahid Mehmood and Ákos Farkas and Javier Coy-Vergara and Di Wu and Jani Reddy Bolla and Volker Schmid and Roger Heinze and Klemens Wild and Dirk Flemming and Stefan Pfeffer and Blanche Schwappach and Carol V. Robinson and Irmgard Sinning}, title = {Structural Basis of Tail-Anchored Membrane Protein Biogenesis by the GET Insertase Complex}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2020}, volume = {80}, number = {1}, pages = {72--86.e7}, doi = {https://doi.org/10.1016/j.molcel.2020.08.012} }
Meißner, T., Rozhkov, V., Hesser, J., Nahm, W. and Loew, N.	Quantitative comparison of planar coded aperture imaging reconstruction methods [Abstract] [BibTeX]	2023	Journal of Instrumentation Vol. 18(01), pp. P01006	article	DOI
Abstract: Abstract Imaging distributions of radioactive sources plays a substantial role in nuclear medicine as well as in monitoring nuclear waste and its deposit. Coded Aperture Imaging (CAI) has been proposed as an alternative to parallel or pinhole collimators, but requires image reconstruction as an extra step. Multiple reconstruction methods with varying run time and computational complexity have been proposed. Yet, no quantitative comparison between the different reconstruction methods has been carried out so far. This paper focuses on a comparison based on three sets of hot-rod phantom images captured with an experimental γ-camera consisting of a Tungsten-based MURA mask with a 2 mm thick 256 × 256 pixelated CdTe semiconductor detector coupled to a Timepix© readout circuit. Analytical reconstruction methods, MURA Decoding, Wiener Filter and a convolutional Maximum Likelihood Expectation Maximization (MLEM) algorithm were compared to data-driven Convolutional Encoder-Decoder (CED) approaches. The comparison is based on the contrast-to-noise ratio as it has been previously used to assess reconstruction quality. For the given set-up, MURA Decoding, the most commonly used CAI reconstruction method, provides robust reconstructions despite the assumption of a linear model. For single image reconstruction, however, MLEM performed best of all analytical reconstruction methods, but took on average 45 times longer than MURA Decoding. The fastest reconstruction method is the Wiener Filter with a run time 4.3 times faster compared to MURA Decoding and a mediocre quality. The CED with a specifically tailored training set was able to succeed the most commonly used MURA decoding on average by a factor between 1.37 and 2.60 and an equal run time.
BibTeX: @article{Meissner2023, author = {T. Meißner, V. Rozhkov, J. Hesser, W. Nahm, N. Loew}, title = {Quantitative comparison of planar coded aperture imaging reconstruction methods}, journal = {Journal of Instrumentation}, publisher = {IOP Publishing}, year = {2023}, volume = {18}, number = {01}, pages = {P01006}, doi = {https://doi.org/10.1088/1748-0221/18/01/P01006} }
Mencacci, N.E., Brockmann, M.M., Dai, J., Pajusalu, S., Atasu, B., Campos, J., Pino, G., Gonzalez-Latapi, P., Patzke, C., Schwake, M., Tucci, A., Pittman, A., Simon-Sanchez, J., Carvill, G.L., Balint, B., Wiethoff, S., Warner, T.T., Papandreou, A., Soo, A., Rein, R., Kadastik-Eerme, L., Puusepp, S., Reinson, K., Tomberg, T., Hanagasi, H., Gasser, T., Bhatia, K.P., Kurian, M.A., Lohmann, E., Õunap, K., Rosenmund, C., Südhof, T.C., Wood, N.W., Krainc, D. and Acuna, C.	Biallelic variants in TSPOAP1, encoding the active-zone protein RIMBP1, cause autosomal recessive dystonia [BibTeX]	2021	Journal of Clinical Investigation Vol. 131(7)	article	DOI
BibTeX: @article{Mencacci2021, author = {Niccolò E. Mencacci and Marisa M. Brockmann and Jinye Dai and Sander Pajusalu and Burcu Atasu and Joaquin Campos and Gabriela Pino and Paulina Gonzalez-Latapi and Christopher Patzke and Michael Schwake and Arianna Tucci and Alan Pittman and Javier Simon-Sanchez and Gemma L. Carvill and Bettina Balint and Sarah Wiethoff and Thomas T. Warner and Apostolos Papandreou and Audrey Soo and Reet Rein and Liis Kadastik-Eerme and Sanna Puusepp and Karit Reinson and Tiiu Tomberg and Hasmet Hanagasi and Thomas Gasser and Kailash P. Bhatia and Manju A. Kurian and Ebba Lohmann and Katrin Õunap and Christian Rosenmund and Thomas C. Südhof and Nicholas W. Wood and Dimitri Krainc and Claudio Acuna}, title = {Biallelic variants in TSPOAP1, encoding the active-zone protein RIMBP1, cause autosomal recessive dystonia}, journal = {Journal of Clinical Investigation}, publisher = {American Society for Clinical Investigation}, year = {2021}, volume = {131}, number = {7}, doi = {https://doi.org/10.1172/jci140625} }
Metz, E.-M., Vardag, S.N., Basu, S., Jung, M., Ahrens, B., El-Madany, T., Sitch, S., Arora, V.K., Briggs, P.R., Friedlingstein, P., Goll, D.S., Jain, A.K., Kato, E., Lombardozzi, D., Nabel, J.E.M.S., Poulter, B., Séférian, R., Tian, H., Wiltshire, A., Yuan, W., Yue, X., Zaehle, S., Deutscher, N.M., Griffith, D.W.T. and Butz, A.	Soil respiration–driven CO ₂ pulses dominate Australia’s flux variability [Abstract] [BibTeX]	2023	Science Vol. 379(6639), pp. 1332-1335	article	DOI
Abstract: The Australian continent contributes substantially to the year-to-year variability of the global terrestrial carbon dioxide (CO 2 ) sink. However, the scarcity of in situ observations in remote areas prevents the deciphering of processes that force the CO 2 flux variability. In this study, by examining atmospheric CO 2 measurements from satellites in the period 2009–2018, we find recurrent end-of-dry-season CO 2 pulses over the Australian continent. These pulses largely control the year-to-year variability of Australia’s CO 2 balance. They cause two to three times larger seasonal variations compared with previous top-down inversions and bottom-up estimates. The pulses occur shortly after the onset of rainfall and are driven by enhanced soil respiration preceding photosynthetic uptake in Australia’s semiarid regions. The suggested continental-scale relevance of soil-rewetting processes has substantial implications for our understanding and modeling of global climate–carbon cycle feedbacks.
BibTeX: @article{Metz2023, author = {Eva-Marie Metz, Sanam N. Vardag, Sourish Basu, Martin Jung, Bernhard Ahrens, Tarek El-Madany, Stephen Sitch, Vivek K. Arora, Peter R. Briggs, Pierre Friedlingstein, Daniel S. Goll, Atul K. Jain, Etsushi Kato, Danica Lombardozzi, Julia E. M. S. Nabel, Benjamin Poulter, Roland Séférian, Hanqin Tian, Andrew Wiltshire, Wenping Yuan, Xu Yue, Sönke Zaehle, Nicholas M. Deutscher, David W. T. Griffith, André Butz}, title = {Soil respiration–driven CO ₂ pulses dominate Australia’s flux variability}, journal = {Science}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2023}, volume = {379}, number = {6639}, pages = {1332--1335}, doi = {https://doi.org/10.1126/science.add7833} }
Meurer, M., Duan, Y., Sass, E., Kats, I., Herbst, K., Buchmuller, B.C., Dederer, V., Huber, F., Kirrmaier, D., Štefl, M., Van Laer, K., Dick, T.P., Lemberg, M.K., Khmelinskii, A., Levy, E.D. and Knop, M.	Genome-wide C-SWAT library for high-throughput yeast genome tagging [Abstract] [BibTeX]	2018	Nature Methods Vol. 15(8), pp. 598-600	article	DOI
Abstract: Here we describe a C-SWAT library for high-throughput tagging of Saccharomyces cerevisiae open reading frames (ORFs). In 5,661 strains, we inserted an acceptor module after each ORF that can be efficiently replaced with tags or regulatory elements. We validated the library with targeted sequencing and tagged the proteome with bright fluorescent proteins to quantify the effect of heterologous transcription terminators on protein expression and to localize previously undetected proteins.
BibTeX: @article{Meurer2018, author = {Meurer, Matthias and Duan, Yuanqiang and Sass, Ehud and Kats, Ilia and Herbst, Konrad and Buchmuller, Benjamin C. and Dederer, Verena and Huber, Florian and Kirrmaier, Daniel and Štefl, Martin and Van Laer, Koen and Dick, Tobias P. and Lemberg, Marius K. and Khmelinskii, Anton and Levy, Emmanuel D. and Knop, Michael}, title = {Genome-wide C-SWAT library for high-throughput yeast genome tagging}, journal = {Nature Methods}, year = {2018}, volume = {15}, number = {8}, pages = {598--600}, doi = {https://doi.org/10.1038/s41592-018-0045-8} }
Miglus, P., Bürger, U., Fetner, R., Muehl, S. and Sollee, A.	Excavation at Bakr Awa 2010 and 2011 [BibTeX]	2013	Iraq Vol. 75, pp. 43-88	article	DOI
BibTeX: @article{Miglus2013, author = {Miglus, Peter and Bürger, Ulrike and Fetner, Rafal and Muehl, Simone and Sollee, Alexander}, title = {Excavation at Bakr Awa 2010 and 2011}, journal = {Iraq}, year = {2013}, volume = {75}, pages = {43--88}, doi = {https://doi.org/10.1017/S0021088900000413} }
Miglus, P.A.	Der altbabylonische Palast in Tuttul (Tall Biʿa): funktionale und historische Aspekte [BibTeX]	2019	Der Palast im antiken und islamischen Orient, 9. Internationales Colloquium der DOG, 30. März bis 1. April 2016, Frankfurt am Main, Internationale Colloquien der Deutschen Orient-Gesellschaft 9, pp. 139-150	incollection
BibTeX: @incollection{Miglus2019, author = {Peter A. Miglus}, title = {Der altbabylonische Palast in Tuttul (Tall Biʿa): funktionale und historische Aspekte}, booktitle = {Der Palast im antiken und islamischen Orient, 9. Internationales Colloquium der DOG, 30. März bis 1. April 2016, Frankfurt am Main, Internationale Colloquien der Deutschen Orient-Gesellschaft 9}, year = {2019}, pages = {139-150} }
Miglus, P.A.	Ein Ensemble ungewöhnlicher Reliefs im Militärpalast von Ninive [BibTeX]	2021	Zeitschrift für Assyriologie und vorderasiatische Archäologie Vol. 112(1), pp. 124-136	article	DOI
BibTeX: @article{Miglus2021, author = {Peter A. Miglus}, title = {Ein Ensemble ungewöhnlicher Reliefs im Militärpalast von Ninive}, journal = {Zeitschrift für Assyriologie und vorderasiatische Archäologie}, publisher = {Walter de Gruyter GmbH}, year = {2021}, volume = {112}, number = {1}, pages = {124--136}, doi = {https://doi.org/10.1515/za-2021-2007} }
Miglus, P.A.	Gedanken über die frühen Felsreliefs im Zagros-Gebirge [BibTeX]	2021	Altorientalische Variationen zum 90. Geburtstag von Eva Strommenger, Heidelberger Studien zum Alten Orient 17, pp. 53-78	incollection
BibTeX: @incollection{Miglus2021a, author = {Peter A. Miglus}, title = {Gedanken über die frühen Felsreliefs im Zagros-Gebirge}, booktitle = {Altorientalische Variationen zum 90. Geburtstag von Eva Strommenger, Heidelberger Studien zum Alten Orient 17}, year = {2021}, pages = {53--78} }
Miglus, P.A.	Die Große Mauer Salmanassars III. In Assur [BibTeX]	2021	Nomina in Aqua Scripta. Homenaje a Joaquín María Córdoba Zoilo, pp. 523-537	incollection
BibTeX: @incollection{Miglus2021b, author = {Peter A. Miglus}, title = {Die Große Mauer Salmanassars III. In Assur}, booktitle = {Nomina in Aqua Scripta. Homenaje a Joaquín María Córdoba Zoilo}, year = {2021}, pages = {523-537} }
Miglus, P.A.	Assyrien im Untergang – Das Jahr 614 v. Chr. Und der archäologische Befund [BibTeX]	2021	Befund und Historisierung. Dokumentation und ihre Interpretationsräume, Araxes I, pp. 7-9	incollection
BibTeX: @incollection{Miglus2021c, author = {Peter A. Miglus}, title = {Assyrien im Untergang – Das Jahr 614 v. Chr. Und der archäologische Befund}, booktitle = {Befund und Historisierung. Dokumentation und ihre Interpretationsräume, Araxes I}, year = {2021}, pages = {7-9} }
Miglus, P.A.	Retrospective of the new beginnings in Assur [BibTeX]	2022	50 Jahre Vorderasiatische Archäologie in München, Münchener Abhandlungen zum Alten Orient 7, pp. 221-223	incollection
BibTeX: @incollection{Miglus2022, author = {Miglus, P. A.}, title = {Retrospective of the new beginnings in Assur}, booktitle = {50 Jahre Vorderasiatische Archäologie in München, Münchener Abhandlungen zum Alten Orient 7}, publisher = {A. Otto, K. Kaniuth (Hrsg.)}, year = {2022}, pages = {221-223} }
Mikheev, A.N., Siovitz, I. and Gasenzer, T.	Universal dynamics and non-thermal fixed points in quantum fluids far from equilibrium [BibTeX]	2023		misc	DOI
BibTeX: @misc{Mikheev2023, author = {Mikheev, Aleksandr N. and Siovitz, Ido and Gasenzer, Thomas}, title = {Universal dynamics and non-thermal fixed points in quantum fluids far from equilibrium}, publisher = {arXiv}, year = {2023}, doi = {https://doi.org/10.48550/ARXIV.2304.12464} }
Mikheev, A.N., Siovitz, I. and Gasenzer, T.	Universal dynamics and non-thermal fixed points in quantum fluids far from equilibrium [BibTeX]	2023	The European Physical Journal Special Topics	article	DOI
BibTeX: @article{Mikheev2023a, author = {Aleksandr N. Mikheev and Ido Siovitz and Thomas Gasenzer}, title = {Universal dynamics and non-thermal fixed points in quantum fluids far from equilibrium}, journal = {The European Physical Journal Special Topics}, publisher = {Springer Science and Business Media LLC}, year = {2023}, doi = {https://doi.org/10.1140/epjs/s11734-023-00974-7} }
Mil, A., Zache, T.V., Hegde, A., Xia, A., Bhatt, R.P., Oberthaler, M.K., Hauke, P., Berges, J. and Jendrzejewski, F.	A scalable realization of local U(1) gauge invariance in cold atomic mixtures [BibTeX]	2020	Science Vol. 367(6482), pp. 1128-1130	article	DOI
BibTeX: @article{Mil2020, author = {Alexander Mil and Torsten V. Zache and Apoorva Hegde and Andy Xia and Rohit P. Bhatt and Markus K. Oberthaler and Philipp Hauke and Jürgen Berges and Fred Jendrzejewski}, title = {A scalable realization of local U(1) gauge invariance in cold atomic mixtures}, journal = {Science}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2020}, volume = {367}, number = {6482}, pages = {1128--1130}, doi = {https://doi.org/10.1126/science.aaz5312} }
Mittal, D., Mease, R., Kuner, T., Flor, H., Kuner, R. and Andoh, J.	Data management strategy for a collaborative research center [BibTeX]	2022	GigaScience Vol. 12	article	DOI
BibTeX: @article{Mittal2022, author = {Deepti Mittal and Rebecca Mease and Thomas Kuner and Herta Flor and Rohini Kuner and Jamila Andoh}, title = {Data management strategy for a collaborative research center}, journal = {GigaScience}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {12}, doi = {https://doi.org/10.1093/gigascience/giad049} }
Mitterer, V., Thoms, M., Buschauer, R., Berninghausen, O., Hurt, E. and Beckmann, R.	Concurrent remodelling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase [Abstract] [BibTeX]	2023	eLife Vol. 12	article	DOI URL
Abstract: Biogenesis intermediates of nucleolar ribosomal 60S precursor particles undergo a number of structural maturation steps before they transit to the nucleoplasm and are finally exported into the cytoplasm. The AAA+-ATPase Rea1 participates in the nucleolar exit by releasing the Ytm1–Erb1 heterodimer from the evolving pre-60S particle. Here, we show that the DEAD-box RNA helicase Spb4 with its interacting partner Rrp17 is further integrated into this maturation event. Spb4 binds to a specific class of late nucleolar pre-60S intermediates, whose cryo-EM structure revealed how its helicase activity facilitates melting and restructuring of 25S rRNA helices H62 and H63/H63a prior to Ytm1–Erb1 release. In vitro maturation of such Spb4-enriched pre-60S particles, incubated with purified Rea1 and its associated pentameric Rix1-complex in the presence of ATP, combined with cryo-EM analysis depicted the details of the Rea1-dependent large-scale pre-ribosomal remodeling. Our structural insights unveil how the Rea1 ATPase and Spb4 helicase remodel late nucleolar pre-60S particles by rRNA restructuring and dismantling of a network of several ribosomal assembly factors.
BibTeX: @article{Mitterer2023, author = {Valentin Mitterer, Matthias Thoms, Robert Buschauer, Otto Berninghausen, Ed Hurt, Roland Beckmann}, title = {Concurrent remodelling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2023}, volume = {12}, url = {https://cdn.elifesciences.org/articles/84877/elife-84877-v3.pdf}, doi = {https://doi.org/10.7554/eLife.84877} }
Mittler, B.	Vergessen? Verhasst? Verehrt? - Der Erinnerung zum Trotz: Die chinesische Revolution und warum China immer noch an Mao glaubt [BibTeX]	2019	Helmstedter Colloquien Heft 21 - Revolution! Verehrt – verhasst – vergessen, pp. 155-199	incollection
BibTeX: @incollection{Mittler2019, author = {Barbara Mittler}, title = {Vergessen? Verhasst? Verehrt? - Der Erinnerung zum Trotz: Die chinesische Revolution und warum China immer noch an Mao glaubt}, booktitle = {Helmstedter Colloquien Heft 21 - Revolution! Verehrt – verhasst – vergessen}, publisher = {Leipziger Universitätsverlag}, year = {2019}, pages = {155-199} }
Mittler, B.	Taxonomien und epistemische Gewalt: Zur Gefahr von Eindeutigem und vom Reden und Schweigen in autoritären Systemen [BibTeX]	2020	Herrschaft des Konkreten, pp. 161-191	incollection
BibTeX: @incollection{Mittler2020, author = {Barbara Mittler}, title = {Taxonomien und epistemische Gewalt: Zur Gefahr von Eindeutigem und vom Reden und Schweigen in autoritären Systemen}, booktitle = {Herrschaft des Konkreten}, publisher = {Wallstein Verlag}, year = {2020}, pages = {161-191} }
Mittler, B.	Noch einmal zu 100 Jahren Roter Oktober: Revolutionen und die Musik in China und der Welt [BibTeX]	2020	Oktoberrevolution 1917. Ereignis, Rezeption, künstlerische Deutung, pp. 267-285	incollection
BibTeX: @incollection{Mittler2020a, author = {Barbara Mittler}, title = {Noch einmal zu 100 Jahren Roter Oktober: Revolutionen und die Musik in China und der Welt}, booktitle = {Oktoberrevolution 1917. Ereignis, Rezeption, künstlerische Deutung}, publisher = {Winter Verlag}, year = {2020}, pages = {267-285} }
Mittler, B.	Vokabularien für eine globale Bibliothek – Von Transfer, Transformation und Transkulturalität [Abstract] [BibTeX]	2021	Bibliothek Forschung und Praxis Vol. 45(2), pp. 239-248	article	DOI
Abstract: ZusammenfassungBereits vor einem halben Jahrhundert hat Michel Foucault in seiner Ordnung der Dinge auf die Willkür und Macht von Ordnungssystemen hingewiesen. Dieser Beitrag versucht, Vorschläge für ein neues dialogisches Format zur Konzeption einer globalen Bibliothek zu machen, die von und mit dem, was in einem Ordnungssystem als „randständig“ in einem anderen jedoch „zentral“ erscheinen mag, gedacht wird. Diese globale Bibliothek als „geteiltes“ und nicht mehr „hierarchisiertes“ Welterbe setzt eine neue Sprache, neue Vokabularien voraus, die nicht nur diachron, sondern auch diatopisch angelegt sind, und immer bereits aus einer transkulturellen Perspektive betrachtet werden, die es erlaubt, die transformative Kraft von kulturellem Transfer konstruktiv und kreativ zu nutzen.
BibTeX: @article{Mittler2021, author = {Barbara Mittler}, title = {Vokabularien für eine globale Bibliothek – Von Transfer, Transformation und Transkulturalität}, journal = {Bibliothek Forschung und Praxis}, publisher = {Walter de Gruyter GmbH}, year = {2021}, volume = {45}, number = {2}, pages = {239--248}, doi = {https://doi.org/10.1515/bfp-2021-0021} }
Mittler, B.	“And suddenly the memory revealed itself….”—Making Sense of the Senses in History [BibTeX]	2022	Sensing China. Modern Transformations of Sensory Culture, pp. 276-287	incollection
BibTeX: @incollection{Mittler2022, author = {Barbara Mittler}, title = {“And suddenly the memory revealed itself….”—Making Sense of the Senses in History}, booktitle = {Sensing China. Modern Transformations of Sensory Culture}, publisher = {Routledge}, year = {2022}, pages = {276-287} }
	Chronologics. Periodisation in a Global Context [BibTeX]	2022		book
BibTeX: @book{Mittler2022a,, title = {Chronologics. Periodisation in a Global Context}, publisher = {Heidelberg University Publishing}, year = {2022} }
Mittler, B.	Konfuzianische Weltordnungen II: Von der Sorge um die Zukunft des eigenen Landes—ein Dialog mit Ying Wangs Of Detours and Updates, Beitrag zum Programmheft des KlangForum Heidelberg,13./14.5.2023, 10-19. [BibTeX]	2023		article
BibTeX: @article{Mittler2023, author = {Barbara Mittler}, title = {Konfuzianische Weltordnungen II: Von der Sorge um die Zukunft des eigenen Landes—ein Dialog mit Ying Wangs Of Detours and Updates, Beitrag zum Programmheft des KlangForum Heidelberg,13./14.5.2023, 10-19.}, year = {2023} }
Mittler, B.	UnSilencing—Das Schweigen beenden! Zum Jahreskonzept der Jungen Kantorei 2023, 5-10 [BibTeX]	2023		article
BibTeX: @article{Mittler2023a, author = {Barbara Mittler}, title = {UnSilencing—Das Schweigen beenden! Zum Jahreskonzept der Jungen Kantorei 2023, 5-10}, year = {2023} }
Mobasheri, A., Huang, H., Degrossi, L.C. and Zipf, A.	Enrichment of OpenStreetMap Data Completeness with Sidewalk Geometries Using Data Mining Techniques [Abstract] [BibTeX]	2018	Sensors Vol. 18(2)	article	DOI URL
Abstract: Tailored routing and navigation services utilized by wheelchair users require certain information about sidewalk geometries and their attributes to execute efficiently. Except some minor regions/cities, such detailed information is not present in current versions of crowdsourced mapping databases including OpenStreetMap. CAP4Access European project aimed to use (and enrich) OpenStreetMap for making it fit to the purpose of wheelchair routing. In this respect, this study presents a modified methodology based on data mining techniques for constructing sidewalk geometries using multiple GPS traces collected by wheelchair users during an urban travel experiment. The derived sidewalk geometries can be used to enrich OpenStreetMap to support wheelchair routing. The proposed method was applied to a case study in Heidelberg, Germany. The constructed sidewalk geometries were compared to an official reference dataset (``ground truth dataset''). The case study shows that the constructed sidewalk network overlays with 96% of the official reference dataset. Furthermore, in terms of positional accuracy, a low Root Mean Square Error (RMSE) value (0.93 m) is achieved. The article presents our discussion on the results as well as the conclusion and future research directions.
BibTeX: @article{Mobasheri2018, author = {Mobasheri, Amin and Huang, Haosheng and Degrossi, Lívia Castro and Zipf, Alexander}, title = {Enrichment of OpenStreetMap Data Completeness with Sidewalk Geometries Using Data Mining Techniques}, journal = {Sensors}, year = {2018}, volume = {18}, number = {2}, url = {https://www.mdpi.com/1424-8220/18/2/509}, doi = {https://doi.org/10.3390/s18020509} }
Mocnik, F.-B., Mobasheri, A. and Zipf, A.	Open source data mining infrastructure for exploring and analysing OpenStreetMap [Abstract] [BibTeX]	2018	Open Geospatial Data, Software and Standards Vol. 3(1), pp. 7	article	DOI
Abstract: OpenStreetMap and other Volunteered Geographic Information datasets have been explored in the last years, with the aim of understanding how their meaning is rendered, of assessing their quality, and of understanding the community-driven process that creates and maintains the data. Research mostly focuses either on the data themselves while ignoring the social processes behind, or solely discusses the community-driven process without making sense of the data at a larger scale. A holistic understanding that takes these and other aspects into account is, however, seldom gained. This article describes a server infrastructure to collect and process data about different aspects of OpenStreetMap. The resulting data are offered publicly in a common container format, which fosters the simultaneous examination of different aspects with the aim of gaining a more holistic view and facilitates the results' reproducibility. As an example of such uses, we discuss the project OSMvis. This project offers a number of visualizations, which use the datasets produced by the server infrastructure to explore and visually analyse different aspects of OpenStreetMap. While the server infrastructure can serve as a blueprint for similar endeavours, the created datasets are of interest themselves too.
BibTeX: @article{Mocnik2018, author = {Mocnik, Franz-Benjamin and Mobasheri, Amin and Zipf, Alexander}, title = {Open source data mining infrastructure for exploring and analysing OpenStreetMap}, journal = {Open Geospatial Data, Software and Standards}, year = {2018}, volume = {3}, number = {1}, pages = {7}, doi = {https://doi.org/10.1186/s40965-018-0047-6} }
Mohammadi, M.M., Abouissa, A., Isyatul, A., Xie, Y., Cordero, J., Shirvani, A., Gigina, A., Engelhardt, M., Trogisch, F.A., Geffers, R., Dobreva, G., Bauersachs, J. and Heineke, J.	Induction of cardiomyocyte proliferation and angiogenesis protects neonatal mice from pressure overload–associated maladaptation [BibTeX]	2019	JCI Insight Vol. 4(16)	article	DOI
BibTeX: @article{Mohammadi2019, author = {Mona Malek Mohammadi and Aya Abouissa and Azizah Isyatul and Yinou Xie and Julio Cordero and Amir Shirvani and Anna Gigina and Maren Engelhardt and Felix A. Trogisch and Robert Geffers and Gergana Dobreva and Johann Bauersachs and Joerg Heineke}, title = {Induction of cardiomyocyte proliferation and angiogenesis protects neonatal mice from pressure overload–associated maladaptation}, journal = {JCI Insight}, publisher = {American Society for Clinical Investigation}, year = {2019}, volume = {4}, number = {16}, doi = {https://doi.org/10.1172/jci.insight.128336} }
Mohammadi, M.M., Abouissa, A. and Heineke, J.	A surgical mouse model of neonatal pressure overload by transverse aortic constriction [BibTeX]	2020	Nature Protocols Vol. 16(2), pp. 775-790	article	DOI URL
BibTeX: @article{Mohammadi2020, author = {Mona Malek Mohammadi, Aya Abouissa, Joerg Heineke}, title = {A surgical mouse model of neonatal pressure overload by transverse aortic constriction}, journal = {Nature Protocols}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {16}, number = {2}, pages = {775--790}, url = {http://www.nature.com/articles/s41596-020-00434-9.pdf}, doi = {https://doi.org/10.1038/s41596-020-00434-9} }
Monji-Azad, S., Hesser, J. and Löw, N.	A review of non-rigid transformations and learning-based 3D point cloud registration methods [BibTeX]	2023	ISPRS Journal of Photogrammetry and Remote Sensing Vol. 196, pp. 58-72	article	DOI URL
BibTeX: @article{MonjiAzad2023, author = {Sara Monji-Azad, Jürgen Hesser, Nikolas Löw}, title = {A review of non-rigid transformations and learning-based 3D point cloud registration methods}, journal = {ISPRS Journal of Photogrammetry and Remote Sensing}, publisher = {Elsevier BV}, year = {2023}, volume = {196}, pages = {58--72}, url = {https://api.elsevier.com/content/article/PII:S0924271622003380?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.isprsjprs.2022.12.023} }
	Les usages de la temporalité dans les sciences sociales / Vom Umgang mit Temporalität in den Sozial- und Geisteswissenschaften [BibTeX]	2019		book
BibTeX: @book{Monnet2019,, title = {Les usages de la temporalité dans les sciences sociales / Vom Umgang mit Temporalität in den Sozial- und Geisteswissenschaften}, publisher = {Verlag Dr. Dieter Winkler}, year = {2019} }
Mossel, D.M., Moganti, K., Riabov, V., Weiss, C., Kopf, S., Cordero, J., Dobreva, G., Rots, M.G., Klüter, H., Harmsen, M.C. and Kzhyshkowska, J.	Epigenetic Regulation of S100A9 and S100A12 Expression in Monocyte-Macrophage System in Hyperglycemic Conditions [BibTeX]	2020	Vol. 11	article	DOI
BibTeX: @article{Mossel2020, author = {Dieuwertje M. Mossel and Kondaiah Moganti and Vladimir Riabov and Christel Weiss and Stefan Kopf and Julio Cordero and Gergana Dobreva and Marianne G. Rots and Harald Klüter and Martin C. Harmsen and Julia Kzhyshkowska}, title = {Epigenetic Regulation of S100A9 and S100A12 Expression in Monocyte-Macrophage System in Hyperglycemic Conditions}, publisher = {Frontiers Media SA}, year = {2020}, volume = {11}, doi = {https://doi.org/10.3389/fimmu.2020.01071} }
Mougiakakos, D., Bach, C., Böttcher, M., Beier, F., Röhner, L., Stoll, A., Rehli, M., Gebhard, C., Lischer, C., Eberhardt, M., Vera, J., Büttner-Herold, M., Bitterer, K., Balzer, H., Leffler, M., Jitschin, S., Hundemer, M., Awwad, M.H., Busch, M., Stenger, S., Völkl, S., Schütz, C., Krönke, J., Mackensen, A. and Bruns, H.	The IKZF1–IRF4/IRF5 Axis Controls Polarization of Myeloma-Associated Macrophages [BibTeX]	2021	Cancer Immunology Research Vol. 9(3), pp. 265-278	article	DOI
BibTeX: @article{Mougiakakos2021, author = {Dimitrios Mougiakakos and Christian Bach and Martin Böttcher and Fabian Beier and Linda Röhner and Andrej Stoll and Michael Rehli and Claudia Gebhard and Christopher Lischer and Martin Eberhardt and Julio Vera and Maike Büttner-Herold and Katrin Bitterer and Heidi Balzer and Magdalena Leffler and Simon Jitschin and Michael Hundemer and Mohamed H.S. Awwad and Martin Busch and Steffen Stenger and Simon Völkl and Christian Schütz and Jan Krönke and Andreas Mackensen and Heiko Bruns}, title = {The IKZF1–IRF4/IRF5 Axis Controls Polarization of Myeloma-Associated Macrophages}, journal = {Cancer Immunology Research}, publisher = {American Association for Cancer Research (AACR)}, year = {2021}, volume = {9}, number = {3}, pages = {265--278}, doi = {https://doi.org/10.1158/2326-6066.cir-20-0555} }
Muckenhuber, M., Seufert, I., Müller-Ott, K., Mallm, J.-P., Klett, L.C., Knotz, C., Hechler, J., Kepper, N., Erdel, F. and Rippe, K.	Epigenetic signals that direct cell type–specific interferon beta response in mouse cells [Abstract] [BibTeX]	2023	Life Science Alliance Vol. 6(4), pp. e202201823	article	DOI
Abstract: The antiviral response induced by type I interferon (IFN) via the JAK-STAT signaling cascade activates hundreds of IFN-stimulated genes (ISGs) across human and mouse tissues but varies between cell types. However, the links between the underlying epigenetic features and the ISG profile are not well understood. We mapped ISGs, binding sites of the STAT1 and STAT2 transcription factors, chromatin accessibility, and histone H3 lysine modification by acetylation (ac) and mono-/tri-methylation (me1, me3) in mouse embryonic stem cells and fibroblasts before and after IFNβ treatment. A large fraction of ISGs and STAT-binding sites was cell type specific with promoter binding of a STAT1/2 complex being a key driver of ISGs. Furthermore, STAT1/2 binding to putative enhancers induced ISGs as inferred from a chromatin co-accessibility analysis. STAT1/2 binding was dependent on the chromatin context and positively correlated with preexisting H3K4me1 and H3K27ac marks in an open chromatin state, whereas the presence of H3K27me3 had an inhibitory effect. Thus, chromatin features present before stimulation represent an additional regulatory layer for the cell type–specific antiviral response.
BibTeX: @article{Muckenhuber2023, author = {Markus Muckenhuber, Isabelle Seufert, Katharina Müller-Ott, Jan-Philipp Mallm, Lara C Klett, Caroline Knotz, Jana Hechler, Nick Kepper, Fabian Erdel, Karsten Rippe}, title = {Epigenetic signals that direct cell type–specific interferon beta response in mouse cells}, journal = {Life Science Alliance}, publisher = {Life Science Alliance, LLC}, year = {2023}, volume = {6}, number = {4}, pages = {e202201823}, doi = {https://doi.org/10.26508/lsa.202201823} }
Müller, T.G., Zila, V., Peters, K., Schifferdecker, S., Stanic, M., Lucic, B., Laketa, V., Lusic, M., Müller, B. and Kräusslich, H.-G.	HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells [Abstract] [BibTeX]	2021	eLife Vol. 10	article	DOI URL
Abstract: HIV-1 replication commences inside the cone-shaped viral capsid, but timing, localization, and mechanism of uncoating are under debate. We adapted a strategy to visualize individual reverse-transcribed HIV-1 cDNA molecules and their association with viral and cellular proteins using fluorescence and correlative-light-and-electron-microscopy (CLEM). We specifically detected HIV-1 cDNA inside nuclei, but not in the cytoplasm. Nuclear cDNA initially co-localized with a fluorescent integrase fusion (IN-FP) and the viral CA (capsid) protein, but cDNA-punctae separated from IN-FP/CA over time. This phenotype was conserved in primary HIV-1 target cells, with nuclear HIV-1 complexes exhibiting strong CA-signals in all cell types. CLEM revealed cone-shaped HIV-1 capsid-like structures and apparently broken capsid-remnants at the position of IN-FP signals and elongated chromatin-like structures in the position of viral cDNA punctae lacking IN-FP. Our data argue for nuclear uncoating by physical disruption rather than cooperative disassembly of the CA-lattice, followed by physical separation from the pre-integration complex.
BibTeX: @article{Mueller2021, author = {Thorsten G Müller, Vojtech Zila, Kyra Peters, Sandra Schifferdecker, Mia Stanic, Bojana Lucic, Vibor Laketa, Marina Lusic, Barbara Müller, Hans-Georg Kräusslich}, title = {HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2021}, volume = {10}, url = {https://cdn.elifesciences.org/articles/64776/elife-64776-v2.pdf}, doi = {https://doi.org/10.7554/eLife.64776} }
Münning, M.	Sound, Meaning, Shape [BibTeX]	2022		book	DOI
BibTeX: @book{Muenning2022, author = {Münning, Mariana}, title = {Sound, Meaning, Shape}, publisher = {Heidelberg Asian Studies Publishing}, year = {2022}, doi = {https://doi.org/10.11588/HASP.939} }
Munkhjargal, M., Yadamsuren, G., Yamkhin, J. and Menzel, L.	The Combination of Wildfire and Changing Climate Triggers Permafrost Degradation in the Khentii Mountains, Northern Mongolia [BibTeX]	2020	Atmosphere Vol. 11(2), pp. 155	article	DOI
BibTeX: @article{Munkhjargal2020, author = {Munkhdavaa Munkhjargal and Gansukh Yadamsuren and Jambaljav Yamkhin and Lucas Menzel}, title = {The Combination of Wildfire and Changing Climate Triggers Permafrost Degradation in the Khentii Mountains, Northern Mongolia}, journal = {Atmosphere}, publisher = {MDPI AG}, year = {2020}, volume = {11}, number = {2}, pages = {155}, doi = {https://doi.org/10.3390/atmos11020155} }
Munkhjargal, M., Yadamsuren, G., Yamkhin, J. and Menzel, L.	Ground surface temperature variability and permafrost distribution over mountainous terrain in northern Mongolia [BibTeX]	2020	Arctic, Antarctic, and Alpine Research Vol. 52(1), pp. 13-26	article	DOI
BibTeX: @article{Munkhjargal2020a, author = {Munkhdavaa Munkhjargal and Gansukh Yadamsuren and Jambaljav Yamkhin and Lucas Menzel}, title = {Ground surface temperature variability and permafrost distribution over mountainous terrain in northern Mongolia}, journal = {Arctic, Antarctic, and Alpine Research}, publisher = {Informa UK Limited}, year = {2020}, volume = {52}, number = {1}, pages = {13--26}, doi = {https://doi.org/10.1080/15230430.2019.1704347} }
Murat, F., Mbengue, N., Winge, S.B., Trefzer, T., Leushkin, E., Sepp, M., Cardoso-Moreira, M., Schmidt, J., Schneider, C., Mößinger, K., Brüning, T., Lamanna, F., Belles, M.R., Conrad, C., Kondova, I., Bontrop, R., Behr, R., Khaitovich, P., Pääbo, S., Marques-Bonet, T., Grützner, F., Almstrup, K., Schierup, M.H. and Kaessmann, H.	The molecular evolution of spermatogenesis across mammals [BibTeX]	2022	Nature Vol. 613(7943), pp. 308-316	article	DOI URL
BibTeX: @article{Murat2022, author = {Florent Murat, Noe Mbengue, Sofia Boeg Winge, Timo Trefzer, Evgeny Leushkin, Mari Sepp, Margarida Cardoso-Moreira, Julia Schmidt, Celine Schneider, Katharina Mößinger, Thoomke Brüning, Francesco Lamanna, Meritxell Riera Belles, Christian Conrad, Ivanela Kondova, Ronald Bontrop, Rüdiger Behr, Philipp Khaitovich, Svante Pääbo, Tomas Marques-Bonet, Frank Grützner, Kristian Almstrup, Mikkel Heide Schierup, Henrik Kaessmann}, title = {The molecular evolution of spermatogenesis across mammals}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {613}, number = {7943}, pages = {308--316}, url = {https://www.nature.com/articles/s41586-022-05547-7.pdf}, doi = {https://doi.org/10.1038/s41586-022-05547-7} }
Narayanasamy, K.K., Stojic, A., Li, Y., Sass, S., Hesse, M.R., Deussner-Helfmann, N.S., Dietz, M.S., Kuner, T., Klevanski, M. and Heilemann, M.	Visualizing Synaptic Multi-Protein Patterns of Neuronal Tissue With DNA-Assisted Single-Molecule Localization Microscopy [BibTeX]	2021	Vol. 13	article	DOI
BibTeX: @article{Narayanasamy2021, author = {Kaarjel K. Narayanasamy and Aleksandar Stojic and Yunqing Li and Steffen Sass and Marina R. Hesse and Nina S. Deussner-Helfmann and Marina S. Dietz and Thomas Kuner and Maja Klevanski and Mike Heilemann}, title = {Visualizing Synaptic Multi-Protein Patterns of Neuronal Tissue With DNA-Assisted Single-Molecule Localization Microscopy}, publisher = {Frontiers Media SA}, year = {2021}, volume = {13}, doi = {https://doi.org/10.3389/fnsyn.2021.671288} }
Nickel, F., Studier-Fischer, A., Özdemir, B., Odenthal, J., Müller, L., Knödler, S., Kowalewski, K., Camplisson, I., Allers, M., Dietrich, M., Schmidt, K., Salg, G., Kenngott, H., Billeter, A., Gockel, I., Sagiv, C., Hadar, O., Gildenblat, J., Ayala, L., Seidlitz, S., Maier-Hein, L. and Müller-Stich, B.	Optimization of anastomotic technique and gastric conduit perfusion with hyperspectral imaging in an experimental model for minimally invasive esophagectomy [BibTeX]	2021		article	DOI
BibTeX: @article{Nickel2021, author = {F. Nickel and A. Studier-Fischer and B. Özdemir and J. Odenthal and L.R. Müller and S. Knödler and K.F. Kowalewski and I. Camplisson and M.M. Allers and M. Dietrich and K. Schmidt and G.A. Salg and H.G. Kenngott and A.T. Billeter and I. Gockel and C. Sagiv and O.E. Hadar and J. Gildenblat and L. Ayala and S. Seidlitz and L. Maier-Hein and B.P. Müller-Stich}, title = {Optimization of anastomotic technique and gastric conduit perfusion with hyperspectral imaging in an experimental model for minimally invasive esophagectomy}, publisher = {Cold Spring Harbor Laboratory}, year = {2021}, doi = {https://doi.org/10.1101/2021.10.03.462901} }
Nikola Kellner, E.H.	Transformation of Chaetomium thermophilum and Affinity Purification of Native Thermostable Protein Complexes [BibTeX]	2022	Methods in Molecular Biology	incollection	DOI
BibTeX: @incollection{NikolaKellner2022, author = {Nikola Kellner, Ed Hurt}, title = {Transformation of Chaetomium thermophilum and Affinity Purification of Native Thermostable Protein Complexes}, booktitle = {Methods in Molecular Biology}, publisher = {Springer US}, year = {2022}, doi = {https://doi.org/10.1007/978-1-0716-2337-4_2} }
Novack, T., Peters, R. and Zipf, A.	Graph-Based Matching of Points-of-Interest from Collaborative Geo-Datasets [Abstract] [BibTeX]	2018	ISPRS International Journal of Geo-Information Vol. 7(3)	article	DOI URL
Abstract: Several geospatial studies and applications require comprehensive semantic information from points-of-interest (POIs). However, this information is frequently dispersed across different collaborative mapping platforms. Surprisingly, there is still a research gap on the conflation of POIs from this type of geo-dataset. In this paper, we focus on the matching aspect of POI data conflation by proposing two matching strategies based on a graph whose nodes represent POIs and edges represent matching possibilities. We demonstrate how the graph is used for (1) dynamically defining the weights of the different POI similarity measures we consider; (2) tackling the issue that POIs should be left unmatched when they do not have a corresponding POI on the other dataset and (3) detecting multiple POIs from the same place in the same dataset and jointly matching these to the corresponding POI(s) from the other dataset. The strategies we propose do not require the collection of training samples or extensive parameter tuning. They were statistically compared with a ``naive'', though commonly applied, matching approach considering POIs collected from OpenStreetMap and Foursquare from the city of London (England). In our experiments, we sequentially included each of our methodological suggestions in the matching procedure and each of them led to an increase in the accuracy in comparison to the previous results. Our best matching result achieved an overall accuracy of 91%, which is more than 10% higher than the accuracy achieved by the baseline method.
BibTeX: @article{Novack2018, author = {Novack, Tessio and Peters, Robin and Zipf, Alexander}, title = {Graph-Based Matching of Points-of-Interest from Collaborative Geo-Datasets}, journal = {ISPRS International Journal of Geo-Information}, year = {2018}, volume = {7}, number = {3}, url = {https://www.mdpi.com/2220-9964/7/3/117}, doi = {https://doi.org/10.3390/ijgi7030117} }
Novikova, L.	Criminalized Liaisons: Soviet Women and Allied Sailors in Wartime Arkhangel’sk [Abstract] [BibTeX]	2020	Journal of Contemporary History Vol. 55(4), pp. 745-763	article	DOI
Abstract: From 1941 to 1945 thousands of British and American sailors came to the northern Soviet ports of Arkhangel’sk and Molotovsk with Lend-Lease convoys. On the shore they made many casual contacts with local residents, in particular with Soviet women. These contacts came under close scrutiny of the Soviet authorities who tried to limit the alleged subversive influence of foreign nationals on Soviet citizens. Local women who dated Allied personnel faced harassment and repression that ranged from administrative exile to imprisonment in the Gulag. Resentments against women who had intimate relationships with foreigners during the war were widespread throughout the European theater, and not limited to the USSR. Still the Soviet authorities’ treatment of Arkhangel’sk women who dated nationals of ‘friendly’ countries was particularly harsh. They faced not just moral condemnation, but legal prosecution and long prison terms. The severity of their repression is comparable to how the Soviet side treated civilian Nazi collaborators. Ultimately, Soviet reactions to such wartime contacts with Allied nationals shed light on the broader social history of the Soviet home front, inter-Allied relationships on a grassroots level, and Soviet wartime and postwar justice that was arbitrary in nature and largely defined by local initiatives.
BibTeX: @article{Novikova2020, author = {Liudmila Novikova}, title = {Criminalized Liaisons: Soviet Women and Allied Sailors in Wartime Arkhangel’sk}, journal = {Journal of Contemporary History}, publisher = {SAGE Publications}, year = {2020}, volume = {55}, number = {4}, pages = {745--763}, doi = {https://doi.org/10.1177/0022009419899149} }
Nüsser, M. and Schmidt, S.	Assessing glacier changes in the Nanga Parbat region using a multitemporal photographic dataset [BibTeX]	2021	Data in Brief Vol. 37, pp. 107178	article	DOI
BibTeX: @article{Nuesser2021, author = {Marcus Nüsser and Susanne Schmidt}, title = {Assessing glacier changes in the Nanga Parbat region using a multitemporal photographic dataset}, journal = {Data in Brief}, publisher = {Elsevier BV}, year = {2021}, volume = {37}, pages = {107178}, doi = {https://doi.org/10.1016/j.dib.2021.107178} }
Nüsser, M. and Schmidt, S.	Glacier changes on the Nanga Parbat 1856–2020: A multi-source retrospective analysis [BibTeX]	2021	Science of The Total Environment Vol. 785, pp. 147321	article	DOI
BibTeX: @article{Nuesser2021a, author = {Marcus Nüsser and Susanne Schmidt}, title = {Glacier changes on the Nanga Parbat 1856–2020: A multi-source retrospective analysis}, journal = {Science of The Total Environment}, publisher = {Elsevier BV}, year = {2021}, volume = {785}, pages = {147321}, doi = {https://doi.org/10.1016/j.scitotenv.2021.147321} }
Nůsková, H., Serebryakova, M.V., Ferrer-Caelles, A., Sachsenheimer, T., Lüchtenborg, C., Miller, A.K., Brügger, B., Kordyukova, L.V. and Teleman, A.A.	Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins [BibTeX]	2021	Nature Communications Vol. 12(1)	article	DOI
BibTeX: @article{Nuskova2021, author = {Hana Nůsková and Marina V. Serebryakova and Anna Ferrer-Caelles and Timo Sachsenheimer and Christian Lüchtenborg and Aubry K. Miller and Britta Brügger and Larisa V. Kordyukova and Aurelio A. Teleman}, title = {Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, doi = {https://doi.org/10.1038/s41467-021-24844-9} }
Nwaeburu, C.C., Abukiwan, A., Zhao, Z. and Herr, I.	Quercetin-induced miR-200b-3p regulates the mode of self-renewing divisions in pancreatic cancer [Abstract] [BibTeX]	2017	Molecular Cancer Vol. 16(1), pp. 23	article	DOI
Abstract: Cancer stem cells are suggested to contribute to the extremely poor prognosis of pancreatic ductal adenocarcinoma and dysregulation of symmetric and asymmetric stem cell division may be involved. Anticancer benefits of phytochemicals like the polyphenol quercetin, present in many fruits, nuts and vegetables, could be expedited by microRNAs, which orchestrate cell-fate decisions and tissue homeostasis. The mechanisms regulating the division mode of cancer stem cells in relation to phytochemical-induced microRNAs are poorly understood.
BibTeX: @article{Nwaeburu2017, author = {Nwaeburu, Clifford C. and Abukiwan, Alia and Zhao, Zhefu and Herr, Ingrid}, title = {Quercetin-induced miR-200b-3p regulates the mode of self-renewing divisions in pancreatic cancer}, journal = {Molecular Cancer}, year = {2017}, volume = {16}, number = {1}, pages = {23}, doi = {https://doi.org/10.1186/s12943-017-0589-8} }
Obermaier, B., Ananth, S., Tibroni, N., Pierini, V., Shytaj, I.L., Diaz, R.S., Lusic, M. and Fackler, O.T.	Patient-Derived HIV-1 Nef Alleles Reveal Uncoupling of CD4 Downregulation and SERINC5 Antagonism Functions of the Viral Pathogenesis Factor [BibTeX]	2020	JAIDS Journal of Acquired Immune Deficiency Syndromes Vol. 85(2), pp. e23-e26	article	DOI
BibTeX: @article{Obermaier2020, author = {Benedikt Obermaier and Swetha Ananth and Nadine Tibroni and Virginia Pierini and Iart L. Shytaj and Ricardo S. Diaz and Marina Lusic and Oliver T. Fackler}, title = {Patient-Derived HIV-1 Nef Alleles Reveal Uncoupling of CD4 Downregulation and SERINC5 Antagonism Functions of the Viral Pathogenesis Factor}, journal = {JAIDS Journal of Acquired Immune Deficiency Syndromes}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, year = {2020}, volume = {85}, number = {2}, pages = {e23--e26}, doi = {https://doi.org/10.1097/qai.0000000000002418} }
Oettl, L.-L., Ravi, N., Schneider, M., Scheller, M.F., Schneider, P., Mitre, M., da Silva Gouveia, M., Froemke, R.C., Chao, M.V., Young, W.S., Meyer-Lindenberg, A., Grinevich, V., Shusterman, R. and Kelsch, W.	Oxytocin Enhances Social Recognition by Modulating Cortical Control of Early Olfactory Processing [Abstract] [BibTeX]	2016	Neuron Vol. 90(3), pp. 609-621	article	DOI URL
Abstract: Summary Oxytocin promotes social interactions and recognition of conspecifics that rely on olfaction in most species. The circuit mechanisms through which oxytocin modifies olfactory processing are incompletely understood. Here, we observed that optogenetically induced oxytocin release enhanced olfactory exploration and same-sex recognition of adult rats. Consistent with oxytocin's function in the anterior olfactory cortex, particularly in social cue processing, region-selective receptor deletion impaired social recognition but left odor discrimination and recognition intact outside a social context. Oxytocin transiently increased the drive of the anterior olfactory cortex projecting to olfactory bulb interneurons. Cortical top-down recruitment of interneurons dynamically enhanced the inhibitory input to olfactory bulb projection neurons and increased the signal-to-noise of their output. In summary, oxytocin generates states for optimized information extraction in an early cortical top-down network that is required for social interactions with potential implications for sensory processing deficits in autism spectrum disorders.
BibTeX: @article{Oettl2016, author = {Oettl, Lars-Lennart and Ravi, Namasivayam and Schneider, Miriam and Scheller, Max F. and Schneider, Peggy and Mitre, Mariela and da Silva Gouveia, Miriam and Froemke, Robert C. and Chao, Moses V. and Young, W. Scott and Meyer-Lindenberg, Andreas and Grinevich, Valery and Shusterman, Roman and Kelsch, Wolfgang}, title = {Oxytocin Enhances Social Recognition by Modulating Cortical Control of Early Olfactory Processing}, journal = {Neuron}, year = {2016}, volume = {90}, number = {3}, pages = {609--621}, url = {http://www.sciencedirect.com/science/article/pii/S0896627316300241}, doi = {https://doi.org/10.1016/j.neuron.2016.03.033} }
Olsavszky, V., Sticht, C., Schmid, C.D., Winkler, M., Wohlfeil, S.A., Olsavszky, A., Schledzewski, K., Géraud, C., Goerdt, S., Leibing, T. and Koch, P.-S.	Exploring the transcriptomic network of multi-ligand scavenger receptor Stabilin-1- and Stabilin-2-deficient liver sinusoidal endothelial cells [BibTeX]	2021	Vol. 768, pp. 145284	article	DOI
BibTeX: @article{Olsavszky2021, author = {Victor Olsavszky and Carsten Sticht and Christian D. Schmid and Manuel Winkler and Sebastian A. Wohlfeil and Ana Olsavszky and Kai Schledzewski and Cyrill Géraud and Sergij Goerdt and Thomas Leibing and Philipp-Sebastian Koch}, title = {Exploring the transcriptomic network of multi-ligand scavenger receptor Stabilin-1- and Stabilin-2-deficient liver sinusoidal endothelial cells}, publisher = {Elsevier BV}, year = {2021}, volume = {768}, pages = {145284}, doi = {https://doi.org/10.1016/j.gene.2020.145284} }
Opdenhoff, F.	Die Stadt als beschriebener Raum [BibTeX]	2021		book	DOI
BibTeX: @book{Opdenhoff2021, author = {Fanny Opdenhoff}, title = {Die Stadt als beschriebener Raum}, publisher = {De Gruyter}, year = {2021}, doi = {https://doi.org/10.1515/9783110722758} }
Orr, A., Ahmad, B., Alam, U., Appadurai, A., Bharucha, Z.P., Biemans, H., Bolch, T., Chaulagain, N.P., Dhaubanjar, S., Dimri, A.P., Dixon, H., Fowler, H.J., Gioli, G., Halvorson, S.J., Hussain, A., Jeelani, G., Kamal, S., Khalid, I.S., Liu, S., Lutz, A., Mehra, M.K., Miles, E., Momblanch, A., Muccione, V., Mukherji, A., Mustafa, D., Najmuddin, O., Nasimi, M.N., Nüsser, M., Pandey, V.P., Parveen, S., Pellicciotti, F., Pollino, C., Potter, E., Qazizada, M.R., Ray, S., Romshoo, S., Sarkar, S.K., Sawas, A., Sen, S., Shah, A., Shah, M.A.A., Shea, J.M., Sheikh, A.T., Shrestha, A.B., Tayal, S., Tigala, S., Virk, Z.T., Wester, P. and Wescoat, J.L.	Knowledge Priorities on Climate Change and Water in the Upper Indus Basin: A Horizon Scanning Exercise to Identify the Top 100 Research Questions in Social and Natural Sciences [BibTeX]	2022	Earth's Future Vol. 10(4)	article	DOI
BibTeX: @article{Orr2022, author = {Andrew Orr, Bashir Ahmad, Undala Alam, ArivudaiNambi Appadurai, Zareen P. Bharucha, Hester Biemans, Tobias Bolch, Narayan P. Chaulagain, Sanita Dhaubanjar, A. P. Dimri, Harry Dixon, Hayley J. Fowler, Giovanna Gioli, Sarah J. Halvorson, Abid Hussain, Ghulam Jeelani, Simi Kamal, Imran S. Khalid, Shiyin Liu, Arthur Lutz, Meeta K. Mehra, Evan Miles, Andrea Momblanch, Veruska Muccione, Aditi Mukherji, Daanish Mustafa, Omaid Najmuddin, Mohammad N. Nasimi, Marcus Nüsser, Vishnu P. Pandey, Sitara Parveen, Francesca Pellicciotti, Carmel Pollino, Emily Potter, Mohammad R. Qazizada, Saon Ray, Shakil Romshoo, Syamal K. Sarkar, Amiera Sawas, Sumit Sen, Attaullah Shah, M. Azeem Ali Shah, Joseph M. Shea, Ali T. Sheikh, Arun B. Shrestha, Shresth Tayal, Snehlata Tigala, Zeeshan T. Virk, Philippus Wester, James L. Wescoat}, title = {Knowledge Priorities on Climate Change and Water in the Upper Indus Basin: A Horizon Scanning Exercise to Identify the Top 100 Research Questions in Social and Natural Sciences}, journal = {Earth's Future}, publisher = {American Geophysical Union (AGU)}, year = {2022}, volume = {10}, number = {4}, doi = {https://doi.org/10.1029/2021EF002619} }
Paech, D., Klopries, K., Nawrotzki, R., Schlemmer, H.-P., Giesel, F.L., Kirsch, J., Schultz, J.-H., Kuner, T. and Doll, S.	Strengths and Weaknesses of Non-enhanced and Contrast-enhanced Cadaver Computed Tomography Scans in the Teaching of Gross Anatomy in an Integrated Curriculum [BibTeX]	2021		article	DOI
BibTeX: @article{Paech2021, author = {Daniel Paech and Kerstin Klopries and Ralph Nawrotzki and Heinz-Peter Schlemmer and Frederik L. Giesel and Joachim Kirsch and Jobst-Hendrik Schultz and Thomas Kuner and Sara Doll}, title = {Strengths and Weaknesses of Non-enhanced and Contrast-enhanced Cadaver Computed Tomography Scans in the Teaching of Gross Anatomy in an Integrated Curriculum}, publisher = {Wiley}, year = {2021}, doi = {https://doi.org/10.1002/ase.2034} }
Panagiotopoulos, D.	The ‘Death of the Painter’Towards a Radical Archaeology of (Minoan) Images [BibTeX]	2020	Current Approaches and New Perspectives in Aegean Iconography Vol. 18, pp. 385	article
BibTeX: @article{Panagiotopoulos2020, author = {Panagiotopoulos, Diamantis}, title = {The ‘Death of the Painter’Towards a Radical Archaeology of (Minoan) Images}, journal = {Current Approaches and New Perspectives in Aegean Iconography}, publisher = {Presses universitaires de Louvain}, year = {2020}, volume = {18}, pages = {385} }
Panagiotopoulos, D.	Ambiguous data and (political?) territories [BibTeX]	2022	Political Geographies of the Bronze Age Aegean - Proceedings of the joint workshop by the Belgian School at Athens (EBSA) and the Netherlands Institute at Athens (NIA). May 28 to 31, 2019, pp. 159-170	inproceedings
BibTeX: @inproceedings{Panagiotopoulos2022, author = {D. Panagiotopoulos}, title = {Ambiguous data and (political?) territories}, booktitle = {Political Geographies of the Bronze Age Aegean - Proceedings of the joint workshop by the Belgian School at Athens (EBSA) and the Netherlands Institute at Athens (NIA). May 28 to 31, 2019}, publisher = {Leuven}, year = {2022}, pages = {159-170}, note = {978-9-0429-4732-0} }
Pande, S., Haeffner, M., Blöschl, G., Alam, M.F., Castro, C., Baldassarre, G.D., Frick-Trzebitzky, F., Hogeboom, R., Kreibich, H., Mukherjee, J., Mukherji, A., Nardi, F., Nüsser, M., Tian, F., van Oel, P. and Sivapalan, M.	Never Ask for a Lighter Rain but a Stronger Umbrella [Abstract] [BibTeX]	2022	Frontiers in Water Vol. 3	article	DOI
Abstract: In a recent editorial in the journal Nature Sustainability, the editors raised the concern that journal submissions on water studies appear too similar. The gist of the editorial: “too many publications and not enough ideas.” In this response, we contest this notion, and point to the numerous new ideas that result from taking a broader view of the water science field. Drawing inspiration from a recently hosted conference geared at transcending traditional disciplinary silos and forging new paradigms for water research, we are, in fact, enthusiastic and optimistic about the ways scientists are investigating political, economic, historical, and cultural intersections toward more just and sustainable human-water relations and ways of knowing.
BibTeX: @article{Pande2022, author = {Saket Pande, Melissa Haeffner, Günter Blöschl, Mohammad Faiz Alam, Cyndi Castro, Giuliano Di Baldassarre, Fanny Frick-Trzebitzky, Rick Hogeboom, Heidi Kreibich, Jenia Mukherjee, Aditi Mukherji, Fernando Nardi, Marcus Nüsser, Fuqiang Tian, Pieter van Oel, Murugesu Sivapalan}, title = {Never Ask for a Lighter Rain but a Stronger Umbrella}, journal = {Frontiers in Water}, publisher = {Frontiers Media SA}, year = {2022}, volume = {3}, doi = {https://doi.org/10.3389/frwa.2021.822334} }
Pape, C., Matskevych, A., Wolny, A., Hennies, J., Mizzon, G., Louveaux, M., Musser, J., Maizel, A., Arendt, D. and Kreshuk, A.	Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts [Abstract] [BibTeX]	2019	Frontiers in Computer Science Vol. 1, pp. 6	article	DOI
Abstract: The throughput of electron microscopes has increased significantly in recent years, enabling detailed analysis of cell morphology and ultrastructure in fairly large tissue volumes. Analysis of neural circuits at single-synapse resolution remains the flagship target of this technique, but applications to cell and developmental biology are also starting to emerge at scale. On the light microscopy side, continuous development of light-sheet microscopes has led to a rapid increase in imaged volume dimensions, making Terabyte-scale acquisitions routine in the field. The amount of data acquired in such studies makes manual instance segmentation, a fundamental step in many analysis pipelines, impossible. While automatic segmentation approaches have improved significantly thanks to the adoption of convolutional neural networks, their accuracy still lags behind human annotations and requires additional manual proof-reading. A major hindrance to further improvements is the limited field of view of the segmentation networks preventing them from learning to exploit the expected cell morphology or other prior biological knowledge which humans use to inform their segmentation decisions. In this contribution, we show how such domain-specific information can be leveraged by expressing it as long-range interactions in a graph partitioning problem known as the lifted multicut problem. Using this formulation, we demonstrate significant improvement in segmentation accuracy for four challenging boundary-based segmentation problems from neuroscience and developmental biology.
BibTeX: @article{Pape2019, author = {Pape, Constantin and Matskevych, Alex and Wolny, Adrian and Hennies, Julian and Mizzon, Giulia and Louveaux, Marion and Musser, Jacob and Maizel, Alexis and Arendt, Detlev and Kreshuk, Anna}, title = {Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts}, journal = {Frontiers in Computer Science}, publisher = {Frontiers Media SA}, year = {2019}, volume = {1}, pages = {6}, doi = {https://doi.org/10.3389/fcomp.2019.00006} }
Pape, C., Remme, R., Wolny, A., Olberg, S., Wolf, S., Cerrone, L., Cortese, M., Klaus, S., Lucic, B., Ullrich, S., Anders-Össwein, M., Wolf, S., Cerikan, B., Neufeldt, C.J., Ganter, M., Schnitzler, P., Merle, U., Lusic, M., Boulant, S., Stanifer, M., Bartenschlager, R., Hamprecht, F.A., Kreshuk, A., Tischer, C., Kräusslich, H.-G., Müller, B. and Laketa, V.	Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera [BibTeX]	2020	BioEssays Vol. 43(3), pp. 2000257	article	DOI
BibTeX: @article{Pape2020, author = {Constantin Pape and Roman Remme and Adrian Wolny and Sylvia Olberg and Steffen Wolf and Lorenzo Cerrone and Mirko Cortese and Severina Klaus and Bojana Lucic and Stephanie Ullrich and Maria Anders-Össwein and Stefanie Wolf and Berati Cerikan and Christopher J. Neufeldt and Markus Ganter and Paul Schnitzler and Uta Merle and Marina Lusic and Steeve Boulant and Megan Stanifer and Ralf Bartenschlager and Fred A. Hamprecht and Anna Kreshuk and Christian Tischer and Hans-Georg Kräusslich and Barbara Müller and Vibor Laketa}, title = {Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera}, journal = {BioEssays}, publisher = {Wiley}, year = {2020}, volume = {43}, number = {3}, pages = {2000257}, doi = {https://doi.org/10.1002/bies.202000257} }
Passang, S., Schmidt, S. and Nüsser, M.	Topographical Impact on Snow Cover Distribution in the Trans-Himalayan Region of Ladakh, India [Abstract] [BibTeX]	2022	Geosciences Vol. 12(8), pp. 311	article	DOI URL
Abstract: This article presents the distribution of seasonal snow cover in the Trans-Himalayan region of Ladakh over the observation period of 2000–2019. Seasonal snow cover area and duration have been monitored and mapped based on the MODIS Normalised Difference Snow Index (NDSI). Using different MODIS cloud removal algorithms, monthly mean cloud-covered areas have been reduced to 3%. Pixel-wise approaches using Mann–Kendall (MK) and Sen’s slope trend tests allow to assess seasonal and annual trends of snow cover days (SCD) and snow cover area (SCA) across seven delineated subregions of Ladakh. Analyses include the impact of topographical parameters (elevation, slope, aspect). Overall, the mean annual SCA amounts to 42%, varying from 15% in August to 71% in February. However, large differences of SCA have been detected between and within subregions. The trend analysis of SCA shows a non-significant, slight increase for summer as well as for the entire year and a decrease for spring and winter seasons. The SCD trend analysis indicates more pixels with a significant increase than a decrease. In total, 12% of all pixels show an increasing trend in summer, 6% over the entire year, 3% in autumn, and 2% in spring and winter, whereas less than 2% of all pixels show a decreasing trend in all seasons. The results are important for regional irrigated agricultural production and freshwater supply in the context of climate change.
BibTeX: @article{Passang2022, author = {Stanzin Passang, Susanne Schmidt, Marcus Nüsser}, title = {Topographical Impact on Snow Cover Distribution in the Trans-Himalayan Region of Ladakh, India}, journal = {Geosciences}, publisher = {MDPI AG}, year = {2022}, volume = {12}, number = {8}, pages = {311}, url = {https://www.mdpi.com/2076-3263/12/8/311/pdf}, doi = {https://doi.org/10.3390/geosciences12080311} }
Paternoga, H., Früh, A., Kunze, R., Bradatsch, B., Baßler, J. and Hurt, E.	Mutational Analysis of the Nsa2 N-Terminus Reveals Its Essential Role in Ribosomal 60S Subunit Assembly [BibTeX]	2020	International Journal of Molecular Sciences Vol. 21(23), pp. 9108	article	DOI
BibTeX: @article{Paternoga2020, author = {Helge Paternoga and Alexander Früh and Ruth Kunze and Bettina Bradatsch and Jochen Baßler and Ed Hurt}, title = {Mutational Analysis of the Nsa2 N-Terminus Reveals Its Essential Role in Ribosomal 60S Subunit Assembly}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2020}, volume = {21}, number = {23}, pages = {9108}, doi = {https://doi.org/10.3390/ijms21239108} }
Patzke, C., Brockmann, M.M., Dai, J., Gan, K.J., Grauel, M.K., Fenske, P., Liu, Y., Acuna, C., Rosenmund, C. and Südhof, T.C.	Neuromodulator Signaling Bidirectionally Controls Vesicle Numbers in Human Synapses [BibTeX]	2019	Cell Vol. 179(2), pp. 498-513.e22	article	DOI
BibTeX: @article{Patzke2019, author = {Christopher Patzke and Marisa M. Brockmann and Jinye Dai and Kathlyn J. Gan and M. Katharina Grauel and Pascal Fenske and Yu Liu and Claudio Acuna and Christian Rosenmund and Thomas C. Südhof}, title = {Neuromodulator Signaling Bidirectionally Controls Vesicle Numbers in Human Synapses}, journal = {Cell}, publisher = {Elsevier BV}, year = {2019}, volume = {179}, number = {2}, pages = {498--513.e22}, doi = {https://doi.org/10.1016/j.cell.2019.09.011} }
Pauli, C., Liu, Y., Rohde, C., Cui, C., Fijalkowska, D., Gerloff, D., Walter, C., Krijgsveld, J., Dugas, M., Edemir, B., Pabst, C., Müller, L.P., Zhou, F. and Müller-Tidow, C.	Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for acute myeloid leukemia cell proliferation [BibTeX]	2020	Blood Vol. 135(23), pp. 2059-2070	article	DOI
BibTeX: @article{Pauli2020, author = {Cornelius Pauli and Yi Liu and Christian Rohde and Chunhong Cui and Daria Fijalkowska and Dennis Gerloff and Carolin Walter and Jeroen Krijgsveld and Martin Dugas and Bayram Edemir and Caroline Pabst and Lutz P. Müller and Fengbiao Zhou and Carsten Müller-Tidow}, title = {Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for acute myeloid leukemia cell proliferation}, journal = {Blood}, publisher = {American Society of Hematology}, year = {2020}, volume = {135}, number = {23}, pages = {2059--2070}, doi = {https://doi.org/10.1182/blood.2019004121} }
Pekovic, F., Rammelt, C., Kubíková, J., Metz, J., Jeske, M. and Wahle, E.	RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: ABSTRACTPosttranscriptional regulation of the maternal nanos mRNA is essential for the development of the anterior – posterior axis of the Drosophila embryo. The nanos RNA is regulated by the protein Smaug. Binding to Smaug recognition elements (SREs) in the nanos 3’-UTR, Smaug nucleates the assembly of a larger repressor complex including the eIF4E-T paralog Cup and five additional proteins. The Smaug-dependent complex represses translation of nanos and induces its deadenylation by the CCR4-NOT deadenylase. Here we report an in vitro reconstitution of the Drosophila CCR4-NOT complex and Smaug-dependent deadenylation. We find that Smaug by itself is sufficient to cause deadenylation by the Drosophila or human CCR4-NOT complexes in an SRE-dependent manner. CCR4-NOT subunits NOT10 and NOT11 are dispensable, but the NOT module, consisting of NOT2, NOT3 and the C-terminal part of NOT1, is required. Smaug interacts with the C-terminal domain of NOT3. Both catalytic subunits of CCR4-NOT contribute to Smaug-dependent deadenylation. Whereas the CCR4-NOT complex itself acts distributively, Smaug induces a processive behavior. The cytoplasmic poly(A) binding protein (PABPC) has but a minor effect on Smaug-dependent deadenylation. Among the additional constituents of the Smaug-dependent repressor complex, Cup also facilitates CCR4-NOT-dependent deadenylation, both independently and in cooperation with Smaug.
BibTeX: @article{Pekovic2022, author = {Filip Pekovic, Christiane Rammelt, Jana Kubíková, Jutta Metz, Mandy Jeske, Elmar Wahle}, title = {RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.05.11.491288} }
Pekovic, F., Rammelt, C., Kub\iková, J., Metz, J., Jeske, M. and Wahle, E.	RNA binding proteins Smaug and Cup induce CCR4–NOT-dependent deadenylation of the lessigreaternanosless/igreater mRNA in a reconstituted system [BibTeX]	2023	Nucleic Acids Research Vol. 51(8), pp. 3950-3970	article	DOI
BibTeX: @article{Pekovic2023, author = {Filip Pekovic and Christiane Rammelt and Jana Kub\iková and Jutta Metz and Mandy Jeske and Elmar Wahle}, title = {RNA binding proteins Smaug and Cup induce CCR4–NOT-dependent deadenylation of the lessigreaternanosless/igreater mRNA in a reconstituted system}, journal = {Nucleic Acids Research}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {51}, number = {8}, pages = {3950--3970}, doi = {https://doi.org/10.1093/nar/gkad159} }
Pellegrini, E.W., Reissl, S., Rahner, D., Klessen, R.S., Glover, S.C.O., Pakmor, R., Herrera-Camus, R. and Grand, R.J.J.	[BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 498(3), pp. 3193-3214	article	DOI
BibTeX: @article{Pellegrini2020, author = {Eric W Pellegrini and Stefan Reissl and Daniel Rahner and Ralf S Klessen and Simon C O Glover and Rüdiger Pakmor and Rodrigo Herrera-Camus and Robert J J Grand}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {498}, number = {3}, pages = {3193--3214}, doi = {https://doi.org/10.1093/mnras/staa2555} }
Pelzer, P., Horstmann, H. and Kuner, T.	Ultrastructural and Functional Properties of a Giant Synapse Driving the Piriform Cortex to Mediodorsal Thalamus Projection [Abstract] [BibTeX]	2017	Frontiers in Synaptic Neuroscience Vol. 9, pp. 3	article	DOI
Abstract: Neocortico-thalamo-cortical loops represent a common, yet poorly understood, circuit employing giant synapses also referred to as ``class I'', giant, or driver synapses. Here, we characterize a giant synapse formed by projection neurons of the paleocortical piriform cortex (PIR) onto neurons of the mediodorsal thalamus (MD). Three-dimensional (3D) ultrastructure of labeled PIR-MD terminals, obtained by using serial-section scanning electron microscopy (EM) combined with photooxidation-based detection of labeled terminals, revealed a large terminal engulfing multiple postsynaptic dendritic excrescences. The terminal contained multiple synaptic contacts, a high density of synaptic vesicles and several central mitochondria. Using targeted stimulations of single identified PIR-MD terminals in combination with patch-clamp recordings from the connected MD neuron, we found large postsynaptic currents with fast kinetics and strong short-term depression, yet fast recovery upon repetitive stimulation. We conclude that the phylogenetically old paleocortex already developed giant synaptic connections exhibiting similar functional properties as connections formed by giant neocortico-thalamic projections.
BibTeX: @article{Pelzer2017, author = {Pelzer, Patric and Horstmann, Heinz and Kuner, Thomas}, title = {Ultrastructural and Functional Properties of a Giant Synapse Driving the Piriform Cortex to Mediodorsal Thalamus Projection}, journal = {Frontiers in Synaptic Neuroscience}, publisher = {Frontiers}, year = {2017}, volume = {9}, pages = {3}, doi = {https://doi.org/10.3389/fnsyn.2017.00003} }
Peñaloza, C.H., Clark, P.C., Glover, S.C.O. and Klessen, R.S.	CO line ratios in molecular clouds: the impact of environment [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 475(2), pp. 1508-1520	article	DOI
BibTeX: @article{Penaloza2018, author = {Peñaloza, Camilo H. and Clark, Paul C. and Glover, Simon C. O. and Klessen, Ralf S.}, title = {CO line ratios in molecular clouds: the impact of environment}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {475}, number = {2}, pages = {1508--1520}, doi = {https://doi.org/10.1093/mnras/stx3263} }
Penter, T.	Vergessene Opfer von Mord und Missbrauch: Behindertenmorde unter deutscher Besatzungsherrschaft in der Ukraine (1941-1943) und ihre juristische Aufarbeitung in der Sowjetunion [BibTeX]	2019	Journal of Modern European History Vol. 17(3), pp. 353-376	article	DOI
BibTeX: @article{Penter2019, author = {Tanja Penter}, title = {Vergessene Opfer von Mord und Missbrauch: Behindertenmorde unter deutscher Besatzungsherrschaft in der Ukraine (1941-1943) und ihre juristische Aufarbeitung in der Sowjetunion}, journal = {Journal of Modern European History}, publisher = {SAGE Publications}, year = {2019}, volume = {17}, number = {3}, pages = {353--376}, doi = {https://doi.org/10.1177/1611894419857526} }
Penter, T.	Vernichtungskrieg, Besatzung und juristische Aufarbeitung: Opferperspektiven [BibTeX]	2020	Jahrbücher für Geschichte Osteuropas Vol. 68(3-4), pp. 368	article	DOI
BibTeX: @article{Penter2020, author = {Tanja Penter}, title = {Vernichtungskrieg, Besatzung und juristische Aufarbeitung: Opferperspektiven}, journal = {Jahrbücher für Geschichte Osteuropas}, publisher = {Wissenschaftliche Verlagsgesellschaft mbH}, year = {2020}, volume = {68}, number = {3-4}, pages = {368}, doi = {https://doi.org/10.25162/jgo-2020-0011} }
Perkhun, P., Köntges, W., Pourcin, F., Esteoulle, D., Barulina, E., Yoshimoto, N., Pierron, P., Margeat, O., Videlot-Ackermann, C., Bharwal, A.K., Duché, D., Herrero, C.R., Gonzales, C., Guerrero, A., Bisquert, J., Schröder, R.R., Pfannmöller, M., Dkhil, S.B., Simon, J.-J. and Ackermann, J.	High-Efficiency Digital Inkjet-Printed Non-Fullerene Polymer Blends Using Non-Halogenated Solvents [BibTeX]	2021	Advanced Energy and Sustainability Research Vol. 2(4)	article	DOI
BibTeX: @article{Perkhun2021, author = {Pavlo Perkhun and Wolfgang Köntges and Florent Pourcin and Daniel Esteoulle and Elena Barulina and Noriyuki Yoshimoto and Pascal Pierron and Olivier Margeat and Christine Videlot-Ackermann and Anil Kumar Bharwal and David Duché and Carmen Ruiz Herrero and Cedric Gonzales and Antonio Guerrero and Juan Bisquert and Rasmus R. Schröder and Martin Pfannmöller and Sadok Ben Dkhil and Jean-Jacques Simon and Jörg Ackermann}, title = {High-Efficiency Digital Inkjet-Printed Non-Fullerene Polymer Blends Using Non-Halogenated Solvents}, journal = {Advanced Energy and Sustainability Research}, publisher = {Wiley}, year = {2021}, volume = {2}, number = {4}, doi = {https://doi.org/10.1002/aesr.202000086} }
Petersen, M., Kamurio, C.N., Kortom, C.D. and Nüsser, M.	Charcoal producers and the pandemic: effects of COVID-19 in Pokot Central, Kenya [BibTeX]	2021	Erdkunde Vol. 75(2), pp. 121-137	article	DOI
BibTeX: @article{Petersen2021, author = {Maike Petersen and Chebet N. Kamurio and Chepkemoi D. Kortom and Marcus Nüsser}, title = {Charcoal producers and the pandemic: effects of COVID-19 in Pokot Central, Kenya}, journal = {Erdkunde}, publisher = {Erdkunde}, year = {2021}, volume = {75}, number = {2}, pages = {121--137}, doi = {https://doi.org/10.3112/erdkunde.2021.02.04} }
Petersen, M., Bergmann, C., Roden, P. and Nüsser, M.	Contextualizing land-use and land-cover change with local knowledge: A case study from Pokot Central, Kenya [BibTeX]	2021	Land Degradation & Development Vol. 32(10), pp. 2992-3007	article	DOI
BibTeX: @article{Petersen2021a, author = {Maike Petersen and Christoph Bergmann and Paul Roden and Marcus Nüsser}, title = {Contextualizing land-use and land-cover change with local knowledge: A case study from Pokot Central, Kenya}, journal = {Land Degradation & Development}, publisher = {Wiley}, year = {2021}, volume = {32}, number = {10}, pages = {2992--3007}, doi = {https://doi.org/10.1002/ldr.3961} }
Petzold, K.J.	Masora und Exegese [BibTeX]	2019		book	DOI
BibTeX: @book{Petzold2019, author = {Kay Joe Petzold}, title = {Masora und Exegese}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110627121} }
Pfanmöller, M.	Understanding the Photophysical Processes within Organic Photovoltaic Blends by Functional Imaging in an Analytical Electron Microscope [BibTeX]	2019		inproceedings	DOI
BibTeX: @inproceedings{Pfanmoeller2019, author = {Pfanmöller, Martin}, title = {Understanding the Photophysical Processes within Organic Photovoltaic Blends by Functional Imaging in an Analytical Electron Microscope}, year = {2019}, doi = {https://doi.org/10.29363/nanoge.ngfm.2019.135} }
Pfannmöller, M., Kammerer, J., Schröder, R., Wacker, I., Alkarsifi, R., Perkhun, P., Videlot-Ackermann, C., Margeat, O. and Ackermann, J.	Visualizing the surface morphology of non-fullerene acceptor blends by automated segmentation of spatially resolved electron spectra from ultra-low voltage scanning electron microscopy [BibTeX]	2019		inproceedings	DOI
BibTeX: @inproceedings{Pfannmoeller2019, author = {Pfannmöller, Martin and Kammerer, Jochen and Schröder, Rasmus and Wacker, Irene and Alkarsifi, Riva and Perkhun, Pavlo and Videlot-Ackermann, Christine and Margeat, Olivier and Ackermann, Jörg}, title = {Visualizing the surface morphology of non-fullerene acceptor blends by automated segmentation of spatially resolved electron spectra from ultra-low voltage scanning electron microscopy}, year = {2019}, doi = {https://doi.org/10.29363/nanoge.hopv.2019.107} }
Pfeiffer, P., Egorov, A.V., Lorenz, F., Schleimer, J.-H., Draguhn, A. and Schreiber, S.	Clusters of cooperative ion channels enable a membrane-potential-based mechanism for short-term memory [BibTeX]	2020	eLife Vol. 9	article	DOI
BibTeX: @article{Pfeiffer2020, author = {Paul Pfeiffer and Alexei V Egorov and Franziska Lorenz and Jan-Hendrik Schleimer and Andreas Draguhn and Susanne Schreiber}, title = {Clusters of cooperative ion channels enable a membrane-potential-based mechanism for short-term memory}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2020}, volume = {9}, doi = {https://doi.org/10.7554/elife.49974} }
Pflug, H.	Vom Antiquarium Creuzerianum zum Archäologischen Museum der Universität Heidelberg [BibTeX]	2020	Archäologie und Kunstgeschichte im 19. Jahrhundert, Akten einer Tagung in Heidelberg 10.-11. Februar 2017, pp. 131-149	incollection
BibTeX: @incollection{Pflug2020, author = {Hermann Pflug}, title = {Vom Antiquarium Creuzerianum zum Archäologischen Museum der Universität Heidelberg}, booktitle = {Archäologie und Kunstgeschichte im 19. Jahrhundert, Akten einer Tagung in Heidelberg 10.-11. Februar 2017}, year = {2020}, pages = {131-149} }
Pfuderer, P.L., Ballhausen, A., Seidler, F., Stark, H.-J., Grabe, N., Frayling, I.M., Ager, A., von Knebel Doeberitz, M., Kloor, M. and Ahadova, A.	High endothelial venules are associated with microsatellite instability, hereditary background and immune evasion in colorectal cancer [BibTeX]	2019	British Journal of Cancer Vol. 121(5), pp. 395-404	article	DOI
BibTeX: @article{Pfuderer2019, author = {Pauline L. Pfuderer and Alexej Ballhausen and Florian Seidler and Hans-Jürgen Stark and Niels Grabe and Ian M. Frayling and Ann Ager and Magnus von Knebel Doeberitz and Matthias Kloor and Aysel Ahadova}, title = {High endothelial venules are associated with microsatellite instability, hereditary background and immune evasion in colorectal cancer}, journal = {British Journal of Cancer}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {121}, number = {5}, pages = {395--404}, doi = {https://doi.org/10.1038/s41416-019-0514-6} }
Pineda, J.L., Fischer, C., Kapala, M., Stutzki, J., Buchbender, C., Goldsmith, P.F., Ziebart, M., Glover, S.C.O., Klessen, R.S., Koda, J., Kramer, C., Mookerjea, B., Sandstrom, K., Scoville, N. and Smith, R.	A SOFIA Survey of [C II] in the Galaxy M51. I. [C II] as a Tracer of Star Formation [BibTeX]	2018	The Astrophysical Journal Vol. 869(2), pp. L30	article	DOI
BibTeX: @article{Pineda2018, author = {Pineda, Jorge L. and Fischer, Christian and Kapala, Maria and Stutzki, Jürgen and Buchbender, Christof and Goldsmith, Paul F. and Ziebart, Monika and Glover, Simon C. O. and Klessen, Ralf S. and Koda, Jin and Kramer, Carsten and Mookerjea, Bhaswati and Sandstrom, Karin and Scoville, Nick and Smith, Rowan}, title = {A SOFIA Survey of [C II] in the Galaxy M51. I. [C II] as a Tracer of Star Formation}, journal = {The Astrophysical Journal}, year = {2018}, volume = {869}, number = {2}, pages = {L30}, doi = {https://doi.org/10.3847/2041-8213/aaf1ad} }
Pineda, J.L., Stutzki, J., Buchbender, C., Koda, J., Fischer, C., Goldsmith, P.F., Glover, S.C.O., Klessen, R.S., Kramer, C., Mookerjea, B., Smith, R., Treß, R. and Ziebart, M.	A SOFIA Survey of [C ii] in the Galaxy M51. II. [C ii] and CO Kinematics across the Spiral Arms [BibTeX]	2020	The Astrophysical Journal Vol. 900(2), pp. 132	article	DOI
BibTeX: @article{Pineda2020, author = {Jorge L. Pineda and Jürgen Stutzki and Christof Buchbender and Jin Koda and Christian Fischer and Paul F. Goldsmith and Simon C. O. Glover and Ralf S. Klessen and Carsten Kramer and Bhaswati Mookerjea and Rowan Smith and Robin Treß and Monika Ziebart}, title = {A SOFIA Survey of [C ii] in the Galaxy M51. II. [C ii] and CO Kinematics across the Spiral Arms}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2020}, volume = {900}, number = {2}, pages = {132}, doi = {https://doi.org/10.3847/1538-4357/abab0a} }
Platten, M., Bunse, L., Wick, A., Bunse, T., Cornet, L.L., Harting, I., Sahm, F., Sanghvi, K., Tan, C.L., Poschke, I., Green, E., Justesen, S., Behrens, G.A., Breckwoldt, M.O., Freitag, A., Rother, L.-M., Schmitt, A., Schnell, O., Hense, J., Misch, M., Krex, D., Stevanovic, S., Tabatabai, G., Steinbach, J.P., Bendszus, M., von Deimling, A., Schmitt, M. and Wick, W.	A vaccine targeting mutant IDH1 in newly diagnosed glioma [BibTeX]	2021	Nature Vol. 592(7854), pp. 463-468	article	DOI
BibTeX: @article{Platten2021, author = {Michael Platten and Lukas Bunse and Antje Wick and Theresa Bunse and Lucian Le Cornet and Inga Harting and Felix Sahm and Khwab Sanghvi and Chin Leng Tan and Isabel Poschke and Edward Green and Sune Justesen and Geoffrey A. Behrens and Michael O. Breckwoldt and Angelika Freitag and Lisa-Marie Rother and Anita Schmitt and Oliver Schnell and Jörg Hense and Martin Misch and Dietmar Krex and Stefan Stevanovic and Ghazaleh Tabatabai and Joachim P. Steinbach and Martin Bendszus and Andreas von Deimling and Michael Schmitt and Wolfgang Wick}, title = {A vaccine targeting mutant IDH1 in newly diagnosed glioma}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {592}, number = {7854}, pages = {463--468}, doi = {https://doi.org/10.1038/s41586-021-03363-z} }
Pocha, K., Mock, A., Rapp, C., Dettling, S., Warta, R., Geisenberger, C., Jungk, C., Martins, L.R., Grabe, N., Reuss, D., Debus, J., von Deimling, A., Abdollahi, A., Unterberg, A. and Herold-Mende, C.C.	Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases that Correlates with Prolonged Survival [BibTeX]	2020	Clinical Cancer Research Vol. 26(9), pp. 2231-2243	article	DOI
BibTeX: @article{Pocha2020, author = {Kolja Pocha and Andreas Mock and Carmen Rapp and Steffen Dettling and Rolf Warta and Christoph Geisenberger and Christine Jungk and Leila R. Martins and Niels Grabe and David Reuss and Juergen Debus and Andreas von Deimling and Amir Abdollahi and Andreas Unterberg and Christel C. Herold-Mende}, title = {Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases that Correlates with Prolonged Survival}, journal = {Clinical Cancer Research}, publisher = {American Association for Cancer Research (AACR)}, year = {2020}, volume = {26}, number = {9}, pages = {2231--2243}, doi = {https://doi.org/10.1158/1078-0432.ccr-19-2184} }
Porth, I., Hirsch, D., Ceribas, Y., Weidner, P., Weichert, W., Götze, T.O., Perner, S., Luley, K., Heyer, C.M., de la Torre, C., Hofheinz, R.-D., Lorenzen, S. and Gaiser, T.	Comprehensive biomarker analysis of long-term response to trastuzumab in patients with HER2-positive advanced gastric or gastroesophageal adenocarcinoma [BibTeX]	2023	European Journal of Cancer Vol. 183, pp. 119-130	article	DOI
BibTeX: @article{Porth2023, author = {Isabel Porth and Daniela Hirsch and Yonca Ceribas and Philip Weidner and Wilko Weichert and Thorsten Oliver Götze and Sven Perner and Kim Luley and Christian Moritz Heyer and Carolina de la Torre and Ralf-Dieter Hofheinz and Sylvie Lorenzen and Timo Gaiser}, title = {Comprehensive biomarker analysis of long-term response to trastuzumab in patients with HER2-positive advanced gastric or gastroesophageal adenocarcinoma}, journal = {European Journal of Cancer}, publisher = {Elsevier BV}, year = {2023}, volume = {183}, pages = {119--130}, doi = {https://doi.org/10.1016/j.ejca.2023.01.022} }
Prasad, V., Cerikan, B., Stahl, Y., Kopp, K., Magg, V., Acosta-Rivero, N., Kim, H., Klein, K., Funaya, C., Haselmann, U., Cortese, M., Heigwer, F., Bageritz, J., Bitto, D., Jargalsaikhan, S., Neufeldt, C., Pahmeier, F., Boutros, M., Yamauchi, Y., Ruggieri, A. and Bartenschlager, R.	Enhanced SARS-CoV-2 entry via UPR-dependent AMPK-related kinase NUAK2 [BibTeX]	2023	Molecular Cell Vol. 83(14), pp. 2559-2577.e8	article	DOI
BibTeX: @article{Prasad2023, author = {Vibhu Prasad and Berati Cerikan and Yannick Stahl and Katja Kopp and Vera Magg and Nelson Acosta-Rivero and Heeyoung Kim and Katja Klein and Charlotta Funaya and Uta Haselmann and Mirko Cortese and Florian Heigwer and Josephine Bageritz and David Bitto and Saruul Jargalsaikhan and Christopher Neufeldt and Felix Pahmeier and Michael Boutros and Yohei Yamauchi and Alessia Ruggieri and Ralf Bartenschlager}, title = {Enhanced SARS-CoV-2 entry via UPR-dependent AMPK-related kinase NUAK2}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2023}, volume = {83}, number = {14}, pages = {2559--2577.e8}, doi = {https://doi.org/10.1016/j.molcel.2023.06.020} }
Priestley, F.D., Clark, P.C., Glover, S.C.O., Ragan, S.E., Fehér, O., Prole, L.R. and Klessen, R.S.	Non-Equilibrium Abundances Treated Holistically (NEATH): the molecular composition of star-forming clouds [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 524(4), pp. 5971-5983	article	DOI
BibTeX: @article{Priestley2023, author = {F D Priestley and P C Clark and S C O Glover and S E Ragan and O Fehér and L R Prole and R S Klessen}, title = {Non-Equilibrium Abundances Treated Holistically (NEATH): the molecular composition of star-forming clouds}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {524}, number = {4}, pages = {5971--5983}, doi = {https://doi.org/10.1093/mnras/stad2278} }
Prole, L.R., Clark, P.C., Klessen, R.S. and Glover, S.C.O.	Fragmentation-induced starvation in Population III star formation: a resolution study [Abstract] [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 510(3), pp. 4019-4030	article	DOI
Abstract: ABSTRACT The Population III initial mass function (IMF) is currently unknown, but recent studies agree that fragmentation of primordial gas gives a broader IMF than the initially suggested singular star per halo. In this study, we introduce sink particle mergers into arepo, to perform the first resolution study for primordial star formation simulations and present the first Population III simulations to run up to densities of 10−6 g cm−3 for hundreds of years after the formation of sink particles. The total number of sinks formed increases with increasing sink particle creation density, without achieving numerical convergence. The total mass in sinks remains invariant to the maximum resolution and is safe to estimate using low-resolution studies. This results in an IMF that shifts towards lower masses with increasing resolution. Greater numbers of sinks cause increased fragmentation-induced starvation of the most massive sink, yielding lower accretion rates, masses, and ionizing photons emitted per second. The lack of convergence up to densities two orders of magnitudes higher than all relevant chemical reactions suggests that the number of sinks will continue to grow with increasing resolution until H2 is fully dissociated and the collapse becomes almost adiabatic at 10−4 g cm−3. These results imply that many Population III studies utilising sink particles have produced IMFs that have overestimated the masses of primordial stars, and underestimated the number of stars formed. In the highest resolution runs, sinks with masses capable of surviving until the present day had an ejection fraction of 0.21.
BibTeX: @article{Prole2021, author = {Lewis R Prole, Paul C Clark, Ralf S Klessen, Simon C O Glover}, title = {Fragmentation-induced starvation in Population III star formation: a resolution study}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {510}, number = {3}, pages = {4019--4030}, doi = {https://doi.org/10.1093/mnras/stab3697} }
Prole, L.R., Clark, P.C., Klessen, R.S., Glover, S.C.O. and Pakmor, R.	Primordial magnetic fields in Population III star formation: a magnetized resolution study [Abstract] [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 516(2), pp. 2223-2234	article	DOI
Abstract: ABSTRACT Population III (Pop III) stars form in groups due to the fragmentation of primordial gas. While uniform magnetic fields have been shown to support against fragmentation in present-day star formation, it is unclear whether realistic k3/2 primordial fields can have the same effect. We bypass the issues associated with simulating the turbulent dynamo by introducing a saturated magnetic field at equipartition with the velocity field when the central densities reach 10−13 g cm−3. We test a range of sink particle creation densities from 10−10 to 10−8 g cm−3. Within the range tested, the fields did not suppress fragmentation of the gas and hence could not prevent the degree of fragmentation from increasing with increased resolution. The number of sink particles formed and total mass in sink particles was unaffected by the magnetic field across all seed fields and resolutions. The magnetic pressure remained sub-dominant to the gas pressure except in the highest density regions of the simulation box, where it became equal to but never exceeded gas pressure. Our results suggest that the inclusion of magnetic fields in numerical simulations of Pop III star formation is largely unimportant.
BibTeX: @article{Prole2022, author = {Lewis R Prole, Paul C Clark, Ralf S Klessen, Simon C O Glover, Rüdiger Pakmor}, title = {Primordial magnetic fields in Population III star formation: a magnetized resolution study}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {516}, number = {2}, pages = {2223--2234}, doi = {https://doi.org/10.1093/mnras/stac2327} }
Püffel, F., Pouget, A., Liu, X., Zuber, M., van de Kamp, T., Roces, F. and Labonte, D.	Morphological determinants of bite force capacity in insects: a biomechanical analysis of polymorphic leaf-cutter ants [BibTeX]	2021	Journal of The Royal Society Interface Vol. 18(182), pp. 20210424	article	DOI
BibTeX: @article{Pueffel2021, author = {Frederik Püffel and Anaya Pouget and Xinyue Liu and Marcus Zuber and Thomas van de Kamp and Flavio Roces and David Labonte}, title = {Morphological determinants of bite force capacity in insects: a biomechanical analysis of polymorphic leaf-cutter ants}, journal = {Journal of The Royal Society Interface}, publisher = {The Royal Society}, year = {2021}, volume = {18}, number = {182}, pages = {20210424}, doi = {https://doi.org/10.1098/rsif.2021.0424} }
Qian, L. and Radich, M.	Computer-assisted Analysis of Zhu Fonian's Original Mahayana Sutras [BibTeX]	2021	Buddhist Studies Review Vol. 38(2)	article	DOI
BibTeX: @article{Qian2021, author = {Lin Qian and Michael Radich}, title = {Computer-assisted Analysis of Zhu Fonian's Original Mahayana Sutras}, journal = {Buddhist Studies Review}, publisher = {Equinox Publishing}, year = {2021}, volume = {38}, number = {2}, doi = {https://doi.org/10.1558/bsrv.21194} }
Qu, Z., Fujita-Becker, S., Ballweber, E., Ince, S., Herrmann, C., Schröder, R.R. and Mannherz, H.G.	Interaction of isolated cross-linked short actin oligomers with the skeletal muscle myosin motor domain [Abstract] [BibTeX]	2018	The FEBS Journal Vol. 285(9), pp. 1715-1729	article	DOI
Abstract: The cyclical interaction between F-actin and myosin in muscle cells generates contractile force. The myosin motor domain hydrolyses ATP, resulting in conformational changes that are amplified by the myosin lever arm that links the motor domain to the rod domain. Recent cryo-electron microscopic data have provided a clear picture of the myosin-ATP--F-actin complex, but structural insights into other stages of the myosin-actin interaction have been less forthcoming. To address this issue, we cross-linked F-actin subunits between Cys374 and Lys191, and separated them by gel filtration. Purified actin-dimers, -trimers and -tetramers retained the ability to polymerize and to stimulate myosin-subfragment 1 (myosin-S1) ATPase activity. To generate stable actin oligomer:myosin-S1 complexes, we blocked actin polymerization with gelsolin and Clostridium botulinum iota toxin-mediated ADP-ribosylation. After polymerization inhibition, actin-trimers and -tetramers retained the ability to stimulate the myosin-S1-ATPase, whereas the actin-dimer showed very little ATPase stimulation. We then analysed the stoichiometry and binding affinity of myosin-S1 to actin oligomers. Actin-trimers and -tetramers bound myosin-S1 in the absence of nucleotide; the trimer contains one myosin-S1 binding site. We calculated a dissociation constant (Kd) of 1.1 texttimes 10−10 m and 1.9 texttimes 10−10 m for binding of native F-actin and the actin-trimer to myosin-S1, respectively. EM of the actin-trimer:myosin-S1 complex demonstrated the presence of single particles of uniform size. Image reconstruction allowed a reasonable fit of the actin-trimer and myosin-S1 into the obtained density clearly showing binding of one myosin-S1 molecule to the two long-pitch actins of the trimer, supporting the kinetic data.
BibTeX: @article{Qu2018, author = {Qu, Zheng and Fujita-Becker, Setsuko and Ballweber, Edda and Ince, Semra and Herrmann, Christian and Schröder, Rasmus R. and Mannherz, Hans Georg}, title = {Interaction of isolated cross-linked short actin oligomers with the skeletal muscle myosin motor domain}, journal = {The FEBS Journal}, year = {2018}, volume = {285}, number = {9}, pages = {1715--1729}, doi = {https://doi.org/10.1111/febs.14442} }
Quemin, E.R.J., Chlanda, P., Sachse, M., Forterre, P., Prangishvili, D. and Krupovic, M.	Eukaryotic-Like Virus Budding in Archaea [Abstract] [BibTeX]	2016	mBio Vol. 7(5)	article	DOI URL
Abstract: Similar to many eukaryotic viruses (and unlike bacteriophages), viruses infecting archaea are often encased in lipid-containing envelopes. However, the mechanisms of their morphogenesis and egress remain unexplored. Here, we used dual-axis electron tomography (ET) to characterize the morphogenesis of Sulfolobus spindle-shaped virus 1 (SSV1), the prototype of the family Fuselloviridae and representative of the most abundant archaea-specific group of viruses. Our results show that SSV1 assembly and egress are concomitant and occur at the cellular cytoplasmic membrane via a process highly reminiscent of the budding of enveloped viruses that infect eukaryotes. The viral nucleoprotein complexes are extruded in the form of previously unknown rod-shaped intermediate structures which have an envelope continuous with the host membrane. Further maturation into characteristic spindle-shaped virions takes place while virions remain attached to the cell surface. Our data also revealed the formation of constricted ring-like structures which resemble the budding necks observed prior to the ESCRT machinery-mediated membrane scission during egress of various enveloped viruses of eukaryotes. Collectively, we provide evidence that archaeal spindle-shaped viruses contain a lipid envelope acquired upon budding of the viral nucleoprotein complex through the host cytoplasmic membrane. The proposed model bears a clear resemblance to the egress strategy employed by enveloped eukaryotic viruses and raises important questions as to how the archaeal single-layered membrane composed of tetraether lipids can undergo scission.IMPORTANCE The replication of enveloped viruses has been extensively studied in eukaryotes but has remained unexplored for enveloped viruses infecting Archaea. Here, we provide a sequential view on the assembly and egress of SSV1, a prototypic archaeal virus. The observed process is highly similar to the budding of eukaryotic enveloped viruses, including human immunodeficiency virus, influenza virus, and Ebola virus. The present study is the first to characterize such a phenomenon in archeal cells, showing that membrane budding is not an exclusive feature of eukaryotic viruses. Our results provide significant insights into the biogenesis and architecture of unique, spindle-shaped virions that infect archaea. Furthermore, our findings open doors for future inquiries into (i) the evolution of the virus budding process, (ii) mechanistic details of virus-mediated membrane scission in Archaea, and (iii) elucidation of virus- and host-encoded molecular players responsible for archaeal membrane and surface remodeling.
BibTeX: @article{Quemin2016, author = {Quemin, Emmanuelle R. J. and Chlanda, Petr and Sachse, Martin and Forterre, Patrick and Prangishvili, David and Krupovic, Mart}, title = {Eukaryotic-Like Virus Budding in Archaea}, journal = {mBio}, publisher = {American Society for Microbiology}, year = {2016}, volume = {7}, number = {5}, url = {https://mbio.asm.org/content/7/5/e01439-16}, doi = {https://doi.org/10.1128/mBio.01439-16} }
Rademacher, A., Erdel, F., Weinmann, R. and Rippe, K.	Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation [BibTeX]	2022	Methods in Molecular Biology	incollection	DOI
BibTeX: @incollection{Rademacher2022, author = {Anne Rademacher, Fabian Erdel, Robin Weinmann, Karsten Rippe}, title = {Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation}, booktitle = {Methods in Molecular Biology}, publisher = {Springer US}, year = {2022}, doi = {https://doi.org/10.1007/978-1-0716-2663-4_20} }
Rahner, D., Pellegrini, E.W., Glover, S.C.O. and Klessen, R.S.	Forming clusters within clusters: how 30 Doradus recollapsed and gave birth again [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 473(1), pp. L11-L15	article	DOI
BibTeX: @article{Rahner2018a, author = {Rahner, Daniel and Pellegrini, Eric W. and Glover, Simon C. O. and Klessen, Ralf S.}, title = {Forming clusters within clusters: how 30 Doradus recollapsed and gave birth again}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {473}, number = {1}, pages = {L11--L15}, doi = {https://doi.org/10.1093/mnrasl/slx149} }
Rahner, D., Pellegrini, E.W., Glover, S.C.O. and Klessen, R.S.	WARPFIELD 2.0: feedback-regulated minimum star formation efficiencies of giant molecular clouds [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 483, pp. 2547-2560	article	DOI
BibTeX: @article{Rahner2019, author = {Daniel Rahner and Eric W Pellegrini and Simon C O Glover and Ralf S Klessen}, title = {WARPFIELD 2.0: feedback-regulated minimum star formation efficiencies of giant molecular clouds}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {483}, pages = {2547--2560}, doi = {https://doi.org/10.1093/mnras/sty3295} }
Raifer, M., Troilo, R., Kowatsch, F., Auer, M., Loos, L., Marx, S., Przybill, K., Fendrich, S., Mocnik, F.-B. and Zipf, A.	OSHDB: a framework for spatio-temporal analysis of OpenStreetMap history data [BibTeX]	2019	Open Geospatial Data, Software and Standards Vol. 4(1)	article	DOI
BibTeX: @article{Raifer2019, author = {Martin Raifer and Rafael Troilo and Fabian Kowatsch and Michael Auer and Lukas Loos and Sabrina Marx and Katharina Przybill and Sascha Fendrich and Franz-Benjamin Mocnik and Alexander Zipf}, title = {OSHDB: a framework for spatio-temporal analysis of OpenStreetMap history data}, journal = {Open Geospatial Data, Software and Standards}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {4}, number = {1}, doi = {https://doi.org/10.1186/s40965-019-0061-3} }
Ramakrishna, P., Ruiz Duarte, P., Rance, G.A., Schubert, M., Vordermaier, V., Vu, L.D., Murphy, E., Vilches Barro, A., Swarup, K., Moirangthem, K., Jørgensen, B., van de Cotte, B., Goh, T., Lin, Z., Voβ, U., Beeckman, T., Bennett, M.J., Gevaert, K., Maizel, A. and De Smet, I.	EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation [Abstract] [BibTeX]	2019	Proceedings of the National Academy of Sciences Vol. 116(17), pp. 8597-8602	article	DOI URL
Abstract: Organ formation is an essential process in plants and animals, driven by cell division and cell identity establishment. Root branching where lateral roots form along the primary root axis increases the root system and aids the capture of water and nutrients. We have discovered that tight control of the cell width is necessary to coordinate asymmetric cell divisions in cells that give rise to a new lateral root organ. Although biomechanical processes have been shown to play a role in plant organogenesis, including lateral root formation, our data give mechanistic insights into cell size control during lateral root initiation.In plants, postembryonic formation of new organs helps shape the adult organism. This requires the tight regulation of when and where a new organ is formed and a coordination of the underlying cell divisions. To build a root system, new lateral roots are continuously developing, and this process requires the tight coordination of asymmetric cell division in adjacent pericycle cells. We identified EXPANSIN A1 (EXPA1) as a cell wall modifying enzyme controlling the divisions marking lateral root initiation. Loss of EXPA1 leads to defects in the first asymmetric pericycle cell divisions and the radial swelling of the pericycle during auxin-driven lateral root formation. We conclude that a localized radial expansion of adjacent pericycle cells is required to position the asymmetric cell divisions and generate a core of small daughter cells, which is a prerequisite for lateral root organogenesis.
BibTeX: @article{Ramakrishna2019, author = {Ramakrishna, Priya and Ruiz Duarte, Paola and Rance, Graham A. and Schubert, Martin and Vordermaier, Vera and Vu, Lam Dai and Murphy, Evan and Vilches Barro, Amaya and Swarup, Kamal and Moirangthem, Kamaljit and Jørgensen, Bodil and van de Cotte, Brigitte and Goh, Tatsuaki and Lin, Zhefeng and Voβ, Ute and Beeckman, Tom and Bennett, Malcolm J. and Gevaert, Kris and Maizel, Alexis and De Smet, Ive}, title = {EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation}, journal = {Proceedings of the National Academy of Sciences}, publisher = {National Academy of Sciences}, year = {2019}, volume = {116}, number = {17}, pages = {8597--8602}, url = {https://www.pnas.org/content/116/17/8597}, doi = {https://doi.org/10.1073/pnas.1820882116} }
Ramos, J.R.D., Maizel, A. and Alim, K.	Tissue-wide integration of mechanical cues promotes efficient auxin patterning [Abstract] [BibTeX]	2019	bioRxiv	article	DOI URL
Abstract: New plants organs form by local accumulation of auxin, which is transported by PIN proteins that localize following mechanical stresses. As auxin itself modifies tissue mechanics, a feedback loop between tissue mechanics and auxin patterning unfolds -- yet the impact of tissue-wide mechanical coupling on auxin pattern emergence remains unclear. Here, we use a hybrid model composed of a vertex model for plant tissue mechanics, and a compartment model for auxin transport to explore the collective mechanical response of the tissue to auxin patterns and how it feeds back onto auxin transport. We compare a model accounting for a tissue-wide mechanical integration to a model where mechanical stresses are averaged out across the tissue. We show that only tissue-wide mechanical coupling leads to focused auxin spots, which we show to result from the formation of a circumferential stress field around these spots, self-reinforcing PIN polarity and auxin accumulation.
BibTeX: @article{Ramos2019, author = {Ramos, João R. D. and Maizel, Alexis and Alim, Karen}, title = {Tissue-wide integration of mechanical cues promotes efficient auxin patterning}, journal = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, year = {2019}, url = {https://www.biorxiv.org/content/early/2019/10/28/820837}, doi = {https://doi.org/10.1101/820837} }
Rathore, J.S., Konopczyŉski, T., Hesser, J., Lucchetta, G. and Carmignato, S.	Investigation on Tomographic-Based Nondestructive Characterization of Short Glass Fiber-Reinforced Composites as Obtained From Micro Injection Molding [BibTeX]	2020	Journal of Nondestructive Evaluation, Diagnostics and Prognostics of Engineering Systems Vol. 3(2)	article	DOI
BibTeX: @article{Rathore2020, author = {Jitendra Singh Rathore and Tomasz Konopczyŉski and Jürgen Hesser and Giovanni Lucchetta and Simone Carmignato}, title = {Investigation on Tomographic-Based Nondestructive Characterization of Short Glass Fiber-Reinforced Composites as Obtained From Micro Injection Molding}, journal = {Journal of Nondestructive Evaluation, Diagnostics and Prognostics of Engineering Systems}, publisher = {ASME International}, year = {2020}, volume = {3}, number = {2}, doi = {https://doi.org/10.1115/1.4046000} }
Rauer, L., Trost, S., Petrovic, A. and Gruber, O.	Cortical activation abnormalities in bipolar and schizophrenia patients in a combined oddball–incongruence paradigm [BibTeX]	2020	European Archives of Psychiatry and Clinical Neuroscience Vol. 271(8), pp. 1487-1499	article	DOI
BibTeX: @article{Rauer2020, author = {Lisa Rauer and Sarah Trost and Aleksandra Petrovic and Oliver Gruber}, title = {Cortical activation abnormalities in bipolar and schizophrenia patients in a combined oddball–incongruence paradigm}, journal = {European Archives of Psychiatry and Clinical Neuroscience}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {271}, number = {8}, pages = {1487--1499}, doi = {https://doi.org/10.1007/s00406-020-01168-1} }
Ravandi, F., Kreitman, R.J., Tiacci, E., Andritsos, L., Banerji, V., Barrientos, J.C., Bhat, S.A., Blachly, J.S., Broccoli, A., Call, T., Chihara, D., Dearden, C., Demeter, J., Dietrich, S., Else, M., Epperla, N., Falini, B., Forconi, F., Gladstone, D.E., Gozzetti, A., Iyengar, S., Johnston, J.B., Jorgensen, J., Juliusson, G., Lauria, F., Lozanski, G., Parikh, S.A., Park, J.H., Polliack, A., Quest, G., Robak, T., Rogers, K.A., Saven, A., Seymour, J.F., Tadmor, T., Tallman, M.S., Tam, C.S., Thompson, P.A., Troussard, X., Zent, C.S., Zenz, T., Zinzani, P.L., Wörmann, B., Rai, K. and Grever, M.	Consensus opinion from an international group of experts on measurable residual disease in hairy cell leukemia [BibTeX]	2022	Blood Cancer Journal Vol. 12(12)	article	DOI
BibTeX: @article{Ravandi2022, author = {Farhad Ravandi and Robert J. Kreitman and Enrico Tiacci and Leslie Andritsos and Versha Banerji and Jacqueline C. Barrientos and Seema A. Bhat and James S. Blachly and Alessandro Broccoli and Timothy Call and Dai Chihara and Claire Dearden and Judit Demeter and Sasha Dietrich and Monica Else and Narendranath Epperla and Brunangelo Falini and Francesco Forconi and Douglas E. Gladstone and Alessandro Gozzetti and Sunil Iyengar and James B. Johnston and Jeffrey Jorgensen and Gunnar Juliusson and Francesco Lauria and Gerard Lozanski and Sameer A. Parikh and Jae H. Park and Aaron Polliack and Graeme Quest and Tadeusz Robak and Kerry A. Rogers and Alan Saven and John F. Seymour and Tamar Tadmor and Martin S. Tallman and Constantine S. Tam and Philip A. Thompson and Xavier Troussard and Clive S. Zent and Thorsten Zenz and Pier Luigi Zinzani and Bernhard Wörmann and Kanti Rai and Michael Grever}, title = {Consensus opinion from an international group of experts on measurable residual disease in hairy cell leukemia}, journal = {Blood Cancer Journal}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {12}, number = {12}, doi = {https://doi.org/10.1038/s41408-022-00760-z} }
Re3data.Org	heidICON [BibTeX]	2013		misc	DOI
BibTeX: @misc{Re3data.Org2013, author = {Re3data.Org}, title = {heidICON}, publisher = {re3data.org - Registry of Research Data Repositories}, year = {2013}, doi = {https://doi.org/10.17616/R33W5K} }
Reif, T., Dyckhoff, G., Hohenberger, R., Kolbe, C.-C., Gruell, H., Klein, F., Latz, E., Stolp, B. and Fackler, O.T.	Contact-dependent inhibition of HIV-1 replication in ex vivo human tonsil cultures by polymorphonuclear neutrophils [BibTeX]	2021	Cell Reports Medicine Vol. 2(6), pp. 100317	article	DOI
BibTeX: @article{Reif2021, author = {Tatjana Reif and Gerhard Dyckhoff and Ralph Hohenberger and Carl-Christian Kolbe and Henning Gruell and Florian Klein and Eicke Latz and Bettina Stolp and Oliver T. Fackler}, title = {Contact-dependent inhibition of HIV-1 replication in ex vivo human tonsil cultures by polymorphonuclear neutrophils}, journal = {Cell Reports Medicine}, publisher = {Elsevier BV}, year = {2021}, volume = {2}, number = {6}, pages = {100317}, doi = {https://doi.org/10.1016/j.xcrm.2021.100317} }
Reinert, J.K., Schaefer, A.T. and Kuner, T.	High-Throughput Automated Olfactory Phenotyping of Group-Housed Mice [BibTeX]	2019	Frontiers in Behavioral Neuroscience Vol. 13	article	DOI
BibTeX: @article{Reinert2019, author = {Janine K. Reinert and Andreas T. Schaefer and Thomas Kuner}, title = {High-Throughput Automated Olfactory Phenotyping of Group-Housed Mice}, journal = {Frontiers in Behavioral Neuroscience}, publisher = {Frontiers Media SA}, year = {2019}, volume = {13}, doi = {https://doi.org/10.3389/fnbeh.2019.00267} }
Reinhardt, A.	Der schlaffe Thyrsos. Zur Plinthe des Farnesischen Stiers und zur Frage der expliziten künstlerischen Selbstreferenz in kaiserzeitlichen Marmorbildwerken [BibTeX]	2020	Archäologischer Anzeiger, pp. 1-30	article
BibTeX: @article{Reinhardt2020, author = {Reinhardt, Arne}, title = {Der schlaffe Thyrsos. Zur Plinthe des Farnesischen Stiers und zur Frage der expliziten künstlerischen Selbstreferenz in kaiserzeitlichen Marmorbildwerken}, journal = {Archäologischer Anzeiger}, year = {2020}, pages = {1--30} }
Reinhardt, A.	Alexandre Simon STEFAN, Die Trajanssäule. Dargestellt anhand der 1862 für Napoleon III. gefertigten Fotografien [BibTeX]	2021	Göttinger Forum für Altertumswissenschaft, pp. Bd. 24 Nr. 1 (2021): Göttinger Forum für Altertumswissenschaft	article	DOI
BibTeX: @article{Reinhardt2021, author = {Reinhardt, Arne}, title = {Alexandre Simon STEFAN, Die Trajanssäule. Dargestellt anhand der 1862 für Napoleon III. gefertigten Fotografien}, journal = {Göttinger Forum für Altertumswissenschaft}, publisher = {Göttinger Forum für Altertumswissenschaft}, year = {2021}, pages = {Bd. 24 Nr. 1 (2021): Göttinger Forum für Altertumswissenschaft}, doi = {https://doi.org/10.14628/GFA.2021.1.83872} }
Reinhardt, A.	Diverging Trends in the Visual Appearance of Fired Clay in Roman Architecture: ‘Campana Plaques’ and Terracotta Façades [BibTeX]	2021	Materiality in Roman Art and Architecture	incollection	DOI
BibTeX: @incollection{Reinhardt2021a, author = {Arne Reinhardt}, title = {Diverging Trends in the Visual Appearance of Fired Clay in Roman Architecture: ‘Campana Plaques’ and Terracotta Façades}, booktitle = {Materiality in Roman Art and Architecture}, publisher = {De Gruyter}, year = {2021}, doi = {https://doi.org/10.1515/9783110764734-008} }
Reinhardt, A.	Bekrönte Giebel. Zur Persistenz des etruskisch-italischen Architekturmotivs der ‚durchbrochenen Krönung‘ an kaiserzeitlichen Tempelbauten. Bildliche Zeugnisse und materielle Evidenz [BibTeX]	2022	Römische Mitteilungen 128	article
BibTeX: @article{Reinhardt2022, author = {A. Reinhardt}, title = {Bekrönte Giebel. Zur Persistenz des etruskisch-italischen Architekturmotivs der ‚durchbrochenen Krönung‘ an kaiserzeitlichen Tempelbauten. Bildliche Zeugnisse und materielle Evidenz}, journal = {Römische Mitteilungen 128}, year = {2022} }
Reinhardt, A.	Bilder einer intermedialen Inszenierung: Zur ara des M Cocceius Iulianus aus dem Theater von Itálica [BibTeX]	2022	Image, Text, Stone. Intermedial Perspectives on Graeco-Roman Sculpture, Materiale Textkulturen 36, pp. 237-256	incollection
BibTeX: @incollection{Reinhardt2022a, author = {A. Reinhardt}, title = {Bilder einer intermedialen Inszenierung: Zur ara des M Cocceius Iulianus aus dem Theater von Itálica}, booktitle = {Image, Text, Stone. Intermedial Perspectives on Graeco-Roman Sculpture, Materiale Textkulturen 36}, publisher = {DeGruyter}, year = {2022}, pages = {237-256} }
Reinoso, B., Schleicher, D.R.G., Fellhauer, M., Klessen, R.S. and Boekholt, T.C.N.	Collisions in primordial star clusters. Formation pathway for intermediate mass black holes [BibTeX]	2018	Astronomy & Astrophysics Vol. 614, pp. A14	article	DOI
BibTeX: @article{Reinoso2018, author = {Reinoso, B. and Schleicher, D. R. G. and Fellhauer, M. and Klessen, R. S. and Boekholt, T. C. N.}, title = {Collisions in primordial star clusters. Formation pathway for intermediate mass black holes}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {614}, pages = {A14}, doi = {https://doi.org/10.1051/0004-6361/201732224} }
Reinoso, B., Schleicher, D.R.G., Fellhauer, M., Klessen, R.S., Boekholt, T.C.N., Vergara, M.Z.C. and Alister Seguel, P.J.	Formation of massive black hole seeds in the early Universe: Runaway stellar collisions in the first star clusters [BibTeX]	2019	Boletin de la Asociacion Argentina de Astronomia La Plata Argentina Vol. 61, pp. 154-156	article
BibTeX: @article{Reinoso2019, author = {Reinoso, B. and Schleicher, D. R. G. and Fellhauer, M. and Klessen, R. S. and Boekholt, T. C. N. and Vergara, M. Z. C. and Alister Seguel, P. J.}, title = {Formation of massive black hole seeds in the early Universe: Runaway stellar collisions in the first star clusters}, journal = {Boletin de la Asociacion Argentina de Astronomia La Plata Argentina}, year = {2019}, volume = {61}, pages = {154--156} }
Reinoso, B., Leigh, N.W.C., Barrera-Retamal, C.M., Schleicher, D., Klessen, R.S. and Stutz, A.M.	The mean free path approximation and stellar collisions in star clusters: numerical exploration of the analytic rates and the role of perturbations on binary star mergers [Abstract] [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 509(3), pp. 3724-3736	article	DOI
Abstract: ABSTRACTIn this paper, we compute predictions for the number of stellar collisions derived from analytic models based on the mean free path (MFP) approximation and compare them to the results of N-body simulations. Our goal is to identify the cluster conditions under which the MFP approximation remains valid. Adopting a range of particle numbers (100 ≤ N ≤ 5000) and different combinations of particle masses and radii, we explore three different channels leading to stellar collisions, all of which are expected to occur in realistic stellar environments. At high densities, binaries form from isolated three-body interactions of single stars. Hence, we consider collisions between single stars and collisions involving binary stars, after they form in our simulations. For the latter, we consider two channels for mergers, namely direct stellar collisions during chaotic single–binary interactions and perturbation-driven mergers of binaries due to random walks in eccentricity approaching unity. In the densest systems considered here, a very massive object is formed at the cluster centre, causing local stellar orbits to become increasingly Keplerian and the assumptions going into our analytic model to break down. Before reaching this limit, we obtain excellent agreement between our theoretical predictions and the simulations: The analytic rates are typically accurate to within one standard deviation for the entire parameter space considered here, but the agreement is best for short integration times. Our results have direct implications for blue straggler formation in dense star clusters, and stellar mergers in galactic nuclei hosting massive black holes.
BibTeX: @article{Reinoso2021, author = {Bastián Reinoso, Nathan W C Leigh, Carlos M Barrera-Retamal, Dominik Schleicher, Ralf S Klessen, Amelia M Stutz}, title = {The mean free path approximation and stellar collisions in star clusters: numerical exploration of the analytic rates and the role of perturbations on binary star mergers}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {509}, number = {3}, pages = {3724--3736}, doi = {https://doi.org/10.1093/mnras/stab3254} }
Reissl, S., Stutz, A.M., Brauer, R., Pellegrini, E.W., Schleicher, D.R.G. and Klessen, R.S.	Magnetic fields in star-forming systems (I): idealized synthetic signatures of dust polarization and Zeeman splitting in filaments [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 481(2), pp. 2507-2522	article	DOI
BibTeX: @article{Reissl2018, author = {Stefan Reissl and Amelia M Stutz and Robert Brauer and Eric W Pellegrini and Dominik R G Schleicher and Ralf S Klessen}, title = {Magnetic fields in star-forming systems (I): idealized synthetic signatures of dust polarization and Zeeman splitting in filaments}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {481}, number = {2}, pages = {2507--2522}, doi = {https://doi.org/10.1093/mnras/sty2415} }
Reissl, S., Klessen, R.S., Mac Low, M.-M. and Pellegrini, E.W.	Spectral shifting strongly constrains molecular cloud disruption by radiation pressure on dust [BibTeX]	2018	Astronomy & Astrophysics Vol. 611, pp. A70	article	DOI
BibTeX: @article{Reissl2018b, author = {Reissl, Stefan and Klessen, Ralf S. and Mac Low, Mordecai-Mark and Pellegrini, Eric W.}, title = {Spectral shifting strongly constrains molecular cloud disruption by radiation pressure on dust}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {611}, pages = {A70}, doi = {https://doi.org/10.1051/0004-6361/201731698} }
Reissl, S., Brauer, R., Klessen, R.S. and Pellegrini, E.W.	Radiative Transfer with POLARIS. II. Modeling of Synthetic Galactic Synchrotron Observations [BibTeX]	2019	The Astrophysical Journal Vol. 885(1), pp. 15	article	DOI
BibTeX: @article{Reissl2019, author = {Stefan Reissl and Robert Brauer and Ralf S. Klessen and Eric W. Pellegrini}, title = {Radiative Transfer with POLARIS. II. Modeling of Synthetic Galactic Synchrotron Observations}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2019}, volume = {885}, number = {1}, pages = {15}, doi = {https://doi.org/10.3847/1538-4357/ab3664} }
Reissl, S., Stutz, A.M., Klessen, R.S., Seifried, D. and Walch, S.	Magnetic fields in star-forming systems – II: Examining dust polarization, the Zeeman effect, and the Faraday rotation measure as magnetic field tracers [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 500(1), pp. 153-176	article	DOI
BibTeX: @article{Reissl2020, author = {Stefan Reissl and Amelia M Stutz and Ralf S Klessen and Daniel Seifried and Stefanie Walch}, title = {Magnetic fields in star-forming systems – II: Examining dust polarization, the Zeeman effect, and the Faraday rotation measure as magnetic field tracers}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {500}, number = {1}, pages = {153--176}, doi = {https://doi.org/10.1093/mnras/staa3148} }
Reissl, S., Meehan, P. and Klessen, R.S.	The mechanical alignment of dust (MAD) [BibTeX]	2023	Astronomy &ampmathsemicolon Astrophysics Vol. 674, pp. A47	article	DOI
BibTeX: @article{Reissl2023, author = {Stefan Reissl and Paul Meehan and Ralf S. Klessen}, title = {The mechanical alignment of dust (MAD)}, journal = {Astronomy &ampmathsemicolon Astrophysics}, publisher = {EDP Sciences}, year = {2023}, volume = {674}, pages = {A47}, doi = {https://doi.org/10.1051/0004-6361/202142528} }
Rheinberger, M., Costa, A.L., Kampmann, M., Glavas, D., Shytaj, I.L., Penzo, C., Tibroni, N., Fackler, O.T., Vlahovicek, K., Lucic, B., Herrmann, C. and Lusic, M.	Genomic profiling of HIV-1 integration in microglia links viral insertions to TAD organization [BibTeX]	2022	bioRxiv	article	DOI
BibTeX: @article{Rheinberger2022, author = {Mona Rheinberger, Ana Luisa Costa, Martin Kampmann, Dunja Glavas, Iart Luca Shytaj, Carlotta Penzo, Nadine Tibroni, Oliver T. Fackler, Kristian Vlahovicek, Bojana Lucic, Carl Herrmann, Marina Lusic}, title = {Genomic profiling of HIV-1 integration in microglia links viral insertions to TAD organization}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.02.14.480322} }
Rhys Wardman, J.H.	See more with C-MORE: Addressing the need of robust cardiomyocyte morphological assessment [BibTeX]	2021	Cell Reports Medicine Vol. 2(11), pp. 100435	article	DOI URL
BibTeX: @article{RhysWardman2021, author = {Rhys Wardman, Joerg Heineke}, title = {See more with C-MORE: Addressing the need of robust cardiomyocyte morphological assessment}, journal = {Cell Reports Medicine}, publisher = {Elsevier BV}, year = {2021}, volume = {2}, number = {11}, pages = {100435}, url = {https://api.elsevier.com/content/article/PII:S2666379121002974?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.xcrm.2021.100435} }
Richter, A. and Gruber, O.	Influence of ventral tegmental area input on cortico-subcortical networks underlying action control and decision making [Abstract] [BibTeX]	2018	Human Brain Mapping Vol. 39(2), pp. 1004-1014	article	DOI
Abstract: Abstract It is argued that the mesolimbic system has a more general function in processing all salient events, including and extending beyond rewards. Saliency was defined as an event that is unexpected due to its frequency of occurrence and elicits an attentional-behavioral switch. Using functional magnetic resonance imaging (fMRI), signals were measured in response to the modulation of salience of rewarding and nonrewarding events during a reward-based decision making task, the so called desire-reason dilemma paradigm (DRD). Replicating previous findings, both frequent and infrequent, and therefore salient, reward stimuli elicited reliable activation of the ventral tegmental area (VTA) and ventral striatum (vStr). When immediate reward desiring contradicted the superordinate task-goal, we found an increased activation of the VTA and vStr when the salient reward stimuli were presented compared to the nonsalient reward stimuli, indicating a boosting of activation in these brain regions. Furthermore, we found a significantly increased functional connectivity between the VTA and vStr, confirming the boosting of vStr activation via VTA input. Moreover, saliency per se without a reward association led to an increased activation of brain regions in the mesolimbic reward system as well as the orbitofrontal cortex (OFC), inferior frontal gyrus (IFG), and anterior cingulate cortex (ACC). Finally, findings uncovered multiple increased functional interactions between cortical saliency-processing brain areas and the VTA and vStr underlying detection and processing of salient events and adaptive decision making.
BibTeX: @article{Richter2018, author = {Richter, Anja and Gruber, Oliver}, title = {Influence of ventral tegmental area input on cortico-subcortical networks underlying action control and decision making}, journal = {Human Brain Mapping}, year = {2018}, volume = {39}, number = {2}, pages = {1004--1014}, doi = {https://doi.org/10.1002/hbm.23899} }
Rikke Wulff Krabbenhøft, P.A.M.	Woolley‘s ‘Public Chapels’ at Ur and Other Small Shrines in the Isin-Larsa and Old Babylonian Periods [BibTeX]	2021	Altorientalische Variationen zum 90. Geburtstag von Eva Strommenger, Heidelberger Studien zum Alten Orient 17, pp. 111-138	incollection
BibTeX: @incollection{RikkeWulffKrabbenhoeft2021, author = {Rikke Wulff Krabbenhøft, Peter A. Miglus}, title = {Woolley‘s ‘Public Chapels’ at Ur and Other Small Shrines in the Isin-Larsa and Old Babylonian Periods}, booktitle = {Altorientalische Variationen zum 90. Geburtstag von Eva Strommenger, Heidelberger Studien zum Alten Orient 17}, year = {2021}, pages = {111--138} }
Rinnenthal, J., Dittmayer, C., Irlbacher, K., Hahn, K., Wacker, I., Stenzel, W. and Goebel, H.	P.263 - Vacuolar necklace muscle fibers -- a new variant? [BibTeX]	2017	Neuromuscular Disorders Vol. 27, pp. S174	article	DOI URL
BibTeX: @article{Rinnenthal2017, author = {Rinnenthal, J. and Dittmayer, C. and Irlbacher, K. and Hahn, K. and Wacker, I. and Stenzel, W. and Goebel, H.}, title = {P.263 - Vacuolar necklace muscle fibers -- a new variant?}, journal = {Neuromuscular Disorders}, year = {2017}, volume = {27}, pages = {S174}, note = {22nd International Congress of the World Muscle Society}, url = {http://www.sciencedirect.com/science/article/pii/S0960896617308660}, doi = {https://doi.org/10.1016/j.nmd.2017.06.293} }
	Antike Texte und ihre Materialität [BibTeX]	2019		book	DOI
BibTeX: @book{RitterSchmalz2019,, title = {Antike Texte und ihre Materialität}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110641042} }
Rodriguez-Niño, A., Pastene, D.O., Hettler, S.A., Qiu, J., Albrecht, T., Vajpayee, S., Perciaccante, R., Gretz, N., Bakker, S.J.L., Krämer, B.K., Yard, B.A. and van den Born, J.	Influence of carnosine and carnosinase-1 on diabetes-induced afferent arteriole vasodilation: implications for glomerular hemodynamics [BibTeX]	2022	American Journal of Physiology-Renal Physiology Vol. 323(1), pp. F69-F80	article	DOI
BibTeX: @article{RodriguezNino2022, author = {Angelica Rodriguez-Niño and Diego O. Pastene and Steffen A. Hettler and Jiedong Qiu and Thomas Albrecht and Srishti Vajpayee and Rossana Perciaccante and Norbert Gretz and Stephan J. L. Bakker and Bernhard K. Krämer and Benito A. Yard and Jacob van den Born}, title = {Influence of carnosine and carnosinase-1 on diabetes-induced afferent arteriole vasodilation: implications for glomerular hemodynamics}, journal = {American Journal of Physiology-Renal Physiology}, publisher = {American Physiological Society}, year = {2022}, volume = {323}, number = {1}, pages = {F69--F80}, doi = {https://doi.org/10.1152/ajprenal.00232.2021} }
Roider, T., Seufert, J., Uvarovskii, A., Frauhammer, F., Bordas, M., Abedpour, N., Stolarczyk, M., Mallm, J.-P., Herbst, S.A., Bruch, P.-M., Balke-Want, H., Hundemer, M., Rippe, K., Goeppert, B., Seiffert, M., Brors, B., Mechtersheimer, G., Zenz, T., Peifer, M., Chapuy, B., Schlesner, M., Müller-Tidow, C., Fröhling, S., Huber, W., Anders, S. and Dietrich, S.	Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels [BibTeX]	2020	Nature Cell Biology Vol. 22, pp. 896-906	article	DOI
BibTeX: @article{Roider2020, author = {Tobias Roider and Julian Seufert and Alexey Uvarovskii and Felix Frauhammer and Marie Bordas and Nima Abedpour and Marta Stolarczyk and Jan-Philipp Mallm and Sophie A. Herbst and Peter-Martin Bruch and Hyatt Balke-Want and Michael Hundemer and Karsten Rippe and Benjamin Goeppert and Martina Seiffert and Benedikt Brors and Gunhild Mechtersheimer and Thorsten Zenz and Martin Peifer and Björn Chapuy and Matthias Schlesner and Carsten Müller-Tidow and Stefan Fröhling and Wolfgang Huber and Simon Anders and Sascha Dietrich}, title = {Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels}, journal = {Nature Cell Biology}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {22}, pages = {896--906}, doi = {https://doi.org/10.1038/s41556-020-0532-x} }
Roider, T., Wang, X., Hüttl, K., Müller-Tidow, C., Klapper, W., Rosenwald, A., Stewart, J.P., Castro, D.G., Dreger, P., Hermine, O., Kluin-Nelemans, H.C., Grabe, N., Dreyling, M., Pott, C., Ott, G., Hoster, E. and Dietrich, S.	The impact of SAMHD1 expression and mutation status in mantle cell lymphoma: An analysis of the MCL Younger and Elderly trial [BibTeX]	2020	International Journal of Cancer Vol. 148(1), pp. 150-160	article	DOI
BibTeX: @article{Roider2020a, author = {Tobias Roider and Xi Wang and Katrin Hüttl and Carsten Müller-Tidow and Wolfram Klapper and Andreas Rosenwald and James Peter Stewart and David Gonzalez Castro and Peter Dreger and Olivier Hermine and Hanneke C. Kluin-Nelemans and Niels Grabe and Martin Dreyling and Christiane Pott and German Ott and Eva Hoster and Sascha Dietrich}, title = {The impact of SAMHD1 expression and mutation status in mantle cell lymphoma: An analysis of the MCL Younger and Elderly trial}, journal = {International Journal of Cancer}, publisher = {Wiley}, year = {2020}, volume = {148}, number = {1}, pages = {150--160}, doi = {https://doi.org/10.1002/ijc.33202} }
Rojas, D.R., Kuner, R. and Agarwal, N.	Metabolomic signature of type 1 diabetes-induced sensory loss and nerve damage in diabetic neuropathy [BibTeX]	2019	Journal of Molecular Medicine Vol. 97(6), pp. 845-854	article	DOI
BibTeX: @article{Rojas2019, author = {Daniel Rangel Rojas, Rohini Kuner, Nitin Agarwal}, title = {Metabolomic signature of type 1 diabetes-induced sensory loss and nerve damage in diabetic neuropathy}, journal = {Journal of Molecular Medicine}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {97}, number = {6}, pages = {845--854}, doi = {https://doi.org/10.1007/s00109-019-01781-1} }
Rousseau-Nepton, L., Martin, R.P., Robert, C., Drissen, L., Amram, P., Prunet, S., Martin, T., Moumen, I., Adamo, A., Alarie, A., Barmby, P., Boselli, A., Bresolin, F., Bureau, M., Chemin, L., Fernandes, R.C., Combes, F., Crowder, C., Della Bruna, L., Duarte Puertas, S., Egusa, F., Epinat, B., Ksoll, V.F., Girard, M., Gómez Llanos, V., Gouliermis, D., Grasha, K., Higgs, C., Hlavacek-Larrondo, J., Ho, I.-T., Iglesias-Páramo, J., Joncas, G., Kam, Z.S., Karera, P., Kennicutt, R.C., Klessen, R.S., Lianou, S., Liu, L., Liu, Q., de Amorim , A.L., Lyman, J.D., Martel, H., Mazzilli-Ciraulo, B., McLeod, A.F., Melchior, A.-L., Millan, I., Mollá, M., Momose, R., Morisset, C., Pan, H.-A., Pati, A.K., Pellerin, A., Pellegrini, E., Pérez, I., Petric, A., Plana, H., Rahner, D., Ruiz Lara, T., Sánchez-Menguiano, L., Spekkens, K., Stasiŉska, G., Takamiya, M., Vale Asari, N. and V\ilchez, J.M.	SIGNALS: I. Survey description [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 489(4), pp. 5530-5546	article	DOI
BibTeX: @article{RousseauNepton2019, author = {L Rousseau-Nepton and R P Martin and C Robert and L Drissen and P Amram and S Prunet and T Martin and I Moumen and A Adamo and A Alarie and P Barmby and A Boselli and F Bresolin and M Bureau and L Chemin and R C Fernandes and F Combes and C Crowder and L Della Bruna and S Duarte Puertas and F Egusa and B Epinat and V F Ksoll and M Girard and V Gómez Llanos and D Gouliermis and K Grasha and C Higgs and J Hlavacek-Larrondo and I-T Ho and J Iglesias-Páramo and G Joncas and Z S Kam and P Karera and R C Kennicutt and R S Klessen and S Lianou and L Liu and Q Liu and A Luiz de Amorim and J D Lyman and H Martel and B Mazzilli-Ciraulo and A F McLeod and A-L Melchior and I Millan and M Mollá and R Momose and C Morisset and H-A Pan and A K Pati and A Pellerin and E Pellegrini and I Pérez and A Petric and H Plana and D Rahner and T Ruiz Lara and L Sánchez-Menguiano and K Spekkens and G Stasiŉska and M Takamiya and N Vale Asari and J M V\ilchez}, title = {SIGNALS: I. Survey description}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {489}, number = {4}, pages = {5530--5546}, doi = {https://doi.org/10.1093/mnras/stz2455} }
Rubio, K., Singh, I., Dobersch, S., Sarvari, P., Günther, S., Cordero, J., Mehta, A., Wujak, L., Cabrera-Fuentes, H., Chao, C.-M., Braubach, P., Bellusci, S., Seeger, W., Günther, A., Preissner, K.T., Wygrecka, M., Savai, R., Papy-Garcia, D., Dobreva, G., Heikenwalder, M., Savai-Pullamsetti, S., Braun, T. and Barreto, G.	Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis [BibTeX]	2019	Vol. 10(1)	article	DOI
BibTeX: @article{Rubio2019, author = {Karla Rubio and Indrabahadur Singh and Stephanie Dobersch and Pouya Sarvari and Stefan Günther and Julio Cordero and Aditi Mehta and Lukasz Wujak and Hector Cabrera-Fuentes and Cho-Ming Chao and Peter Braubach and Saverio Bellusci and Werner Seeger and Andreas Günther and Klaus T. Preissner and Malgorzata Wygrecka and Rajkumar Savai and Dulce Papy-Garcia and Gergana Dobreva and Mathias Heikenwalder and Soni Savai-Pullamsetti and Thomas Braun and Guillermo Barreto}, title = {Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {10}, number = {1}, doi = {https://doi.org/10.1038/s41467-019-10066-7} }
Rubio, K., Romero-Olmedo, A.J., Sarvari, P., Swaminathan, G., Ranvir, V.P., Rogel-Ayala, D.G., Cordero, J., Günther, S., Mehta, A., Bassaly, B., Braubach, P., Wygrecka, M., Gattenlöhner, S., Tresch, A., Braun, T., Dobreva, G., Rivera, M.N., Singh, I., Graumann, J. and Barreto, G.	Non-canonical integrin signaling activates EGFR and RAS-MAPK-ERK signaling in small cell lung cancer [BibTeX]	2023	Theranostics Vol. 13(8), pp. 2384-2407	article	DOI
BibTeX: @article{Rubio2023, author = {Karla Rubio and Addi J. Romero-Olmedo and Pouya Sarvari and Guruprasadh Swaminathan and Vikas P. Ranvir and Diana G. Rogel-Ayala and Julio Cordero and Stefan Günther and Aditi Mehta and Birgit Bassaly and Peter Braubach and Malgorzata Wygrecka and Stefan Gattenlöhner and Achim Tresch and Thomas Braun and Gergana Dobreva and Miguel N. Rivera and Indrabahadur Singh and Johannes Graumann and Guillermo Barreto}, title = {Non-canonical integrin signaling activates EGFR and RAS-MAPK-ERK signaling in small cell lung cancer}, journal = {Theranostics}, publisher = {Ivyspring International Publisher}, year = {2023}, volume = {13}, number = {8}, pages = {2384--2407}, doi = {https://doi.org/10.7150/thno.79493} }
Rüthnick, D., Neuner, A., Dietrich, F., Kirrmaier, D., Engel, U., Knop, M. and Schiebel, E.	Characterization of spindle pole body duplication reveals a regulatory role for nuclear pore complexes [BibTeX]	2017	The Journal of cell biology Vol. 216(8), pp. 2425-2442	article	DOI URL
BibTeX: @article{Ruethnick2017, author = {Rüthnick, Diana and Neuner, Annett and Dietrich, Franziska and Kirrmaier, Daniel and Engel, Ulrike and Knop, Michael and Schiebel, Elmar}, title = {Characterization of spindle pole body duplication reveals a regulatory role for nuclear pore complexes}, journal = {The Journal of cell biology}, publisher = {The Rockefeller University Press}, year = {2017}, volume = {216}, number = {8}, pages = {2425--2442}, note = {28659328[pmid]}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28659328}, doi = {https://doi.org/10.1083/jcb.201612129} }
Rugel, M.R., Beuther, H., Bihr, S., Wang, Y., Ott, J., Brunthaler, A., Walsh, A., Glover, S.C.O., Goldsmith, P.F., Anderson, L.D., Schneider, N., Menten, K.M., Ragan, S.E., Urquhart, J.S., Klessen, R.S., Soler, J.D., Roy, N., Kainulainen, J., Henning, T., Bigiel, F., Smith, R.J., Wyrowski, F. and Longmore, S.N.	OH absorption in the first quadrant of the Milky Way as seen by THOR [BibTeX]	2018	Astronomy & Astrophysics Vol. 618, pp. A159	article	DOI
BibTeX: @article{Rugel2018, author = {Rugel, M. R. and Beuther, H. and Bihr, S. and Wang, Y. and Ott, J. and Brunthaler, A. and Walsh, A. and Glover, S. C. O. and Goldsmith, P. F. and Anderson, L. D. and Schneider, N. and Menten, K. M. and Ragan, S. E. and Urquhart, J. S. and Klessen, R. S. and Soler, J. D. and Roy, N. and Kainulainen, J. and Henning, T. and Bigiel, F. and Smith, R. J. and Wyrowski, F. and Longmore, S. N.}, title = {OH absorption in the first quadrant of the Milky Way as seen by THOR}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {618}, pages = {A159}, doi = {https://doi.org/10.1051/0004-6361/201731872} }
Rugel, M.R., Rahner, D., Beuther, H., Pellegrini, E.W., Wang, Y., Soler, J.D., Ott, J., Brunthaler, A., Anderson, L.D., Mottram, J.C., Henning, T., Goldsmith, P.F., Heyer, M., Klessen, R.S., Bihr, S., Menten, K.M., Smith, R.J., Urquhart, J.S., Ragan, S.E., Glover, S.C.O., McClure-Griffiths, N.M., Bigiel, F. and Roy, N.	Feedback in W49A diagnosed with radio recombination lines and models [BibTeX]	2019	Astronomy & Astrophysics Vol. 622	article	DOI
BibTeX: @article{Rugel2019, author = {M. R. Rugel and D. Rahner and H. Beuther and E. W. Pellegrini and Y. Wang and J. D. Soler and J. Ott and A. Brunthaler and L. D. Anderson and J. C. Mottram and T. Henning and P. F. Goldsmith and M. Heyer and R. S. Klessen and S. Bihr and K. M. Menten and R. J. Smith and J. S. Urquhart and S. E. Ragan and S. C. O. Glover and N. M. McClure-Griffiths and F. Bigiel and N. Roy}, title = {Feedback in W49A diagnosed with radio recombination lines and models}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2019}, volume = {622}, doi = {https://doi.org/10.1051/0004-6361/201834068} }
Rui Chen, T.S.	Tendon-Specific Activation of Tenogenic Transcription Factors Enables Keeping Tenocytes’ Identity In Vitro [Abstract] [BibTeX]	2022	International Journal of Molecular Sciences Vol. 23(22), pp. 14078	article	DOI URL
Abstract: We generated a novel tetracycline-inducible transgenic mouse line with the tendon-specific expression of a series of tendon-critical transcription factors. Primary tenocytes derived from this mouse line consistently expressed green fluorescent protein reporter transcription factors in response to doxycycline. The tenocytes maintained their tendon cell properties for a longer time after the transient induction in the absence of growth factors and mechanical stress. Four key transcription factors for tendon development and the green fluorescent protein reporter were linked with different viral 2A self-cleaving peptides. They were expressed under the control of the tet-responsive element. In combination with the expression of BFP, which reports on the tendon-specific collagen I, and mScarlet, which reports on the tendon-specific transcription factor Scleraxis (Scx), we observed the more extended maintenance of the tendon cell identity of in vitro cultured tendon cells and Achilles tendon explants. This means that the Scleraxis bHLH transcription factor (Scx), mohawk homeobox (Mkx), early growth response 1 (Egr1) and early growth response 2 (Egr2) contributed to the maintenance of tenocytes’ identity in vitro, providing a new model for studying extracellular matrix alterations and identifying alternative biomaterials in vitro.
BibTeX: @article{RuiChen2022, author = {Rui Chen, Thomas Skutella}, title = {Tendon-Specific Activation of Tenogenic Transcription Factors Enables Keeping Tenocytes’ Identity In Vitro}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2022}, volume = {23}, number = {22}, pages = {14078}, url = {https://www.mdpi.com/1422-0067/23/22/14078/pdf}, doi = {https://doi.org/10.3390/ijms232214078} }
Runz, M., Rusche, D., Schmidt, S., Weihrauch, M.R., Hesser, J. and Weis, C.-A.	Normalization of HE-stained histological images using cycle consistent generative adversarial networks [BibTeX]	2021	Vol. 16(1)	article	DOI
BibTeX: @article{Runz2021, author = {Marlen Runz and Daniel Rusche and Stefan Schmidt and Martin R. Weihrauch and Jürgen Hesser and Cleo-Aron Weis}, title = {Normalization of HE-stained histological images using cycle consistent generative adversarial networks}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {16}, number = {1}, doi = {https://doi.org/10.1186/s13000-021-01126-y} }
Ruppert, M., Korkmaz-Icöz, S., Li, S., Brlecic, P., Németh, B., Oláh, A., Horváth, E., Veres, G., Pleger, S., Grabe, N., Merkely, B., Karck, M., Radovits, T. and Szabó, G.	Comparison of the Reverse-Remodeling Effect of Pharmacological Soluble Guanylate Cyclase Activation With Pressure Unloading in Pathological Myocardial Left Ventricular Hypertrophy [BibTeX]	2019	Frontiers in Physiology Vol. 9	article	DOI
BibTeX: @article{Ruppert2019, author = {Ruppert, Mihály and Korkmaz-Icöz, Sevil and Li, Shiliang and Brlecic, Paige and Németh, Balázs and Oláh, Attila and Horváth, Eszter and Veres, Gábor and Pleger, Sven and Grabe, Niels and Merkely, Béla and Karck, Matthias and Radovits, Tamás and Szabó, Gábor}, title = {Comparison of the Reverse-Remodeling Effect of Pharmacological Soluble Guanylate Cyclase Activation With Pressure Unloading in Pathological Myocardial Left Ventricular Hypertrophy}, journal = {Frontiers in Physiology}, year = {2019}, volume = {9}, doi = {https://doi.org/10.3389/fphys.2018.01869} }
Rydberg, C.-E., Whalen, D.J., Maturi, M., Collett, T., Carrasco, M., Magg, M. and Klessen, R.S.	Detecting strongly lensed supernovae at z ∼ 5–7 with LSST [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 491(2), pp. 2447-2459	article	DOI
BibTeX: @article{Rydberg2019, author = {Claes-Erik Rydberg and Daniel J Whalen and Matteo Maturi and Thomas Collett and Mauricio Carrasco and Mattis Magg and Ralf S Klessen}, title = {Detecting strongly lensed supernovae at z ∼ 5–7 with LSST}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {491}, number = {2}, pages = {2447--2459}, doi = {https://doi.org/10.1093/mnras/stz3203} }
Salgania, H.K., Metz, J. and Jeske, M.	ReLo: a simple colocalization assay to identify and characterize physical protein-protein interactions [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: ABSTRACTCharacterizing protein-protein interactions (PPIs) is fundamental for understanding biochemical processes. Many methods have been established to identify and study direct PPIs; however, screening and investigating PPIs involving large and poorly soluble proteins remain challenges. As a result, we developed ReLo, a simple cell culture-based method to detect and investigate interactions in a cellular context. ReLo allows both the identification of protein domains that mediate the formation of complexes and screening of interfering point mutations. ReLo is sensitive to drugs that mediate or interfere with a specific interaction. Furthermore, protein conformation- and protein arginine methylation-dependent interactions can be studied. Importantly, ReLo can be used for specifically detecting direct but not indirect PPIs and can be applied for describing the binding topology of subunits within multiprotein complexes. Because of these attributes, ReLo is a simple, quick and versatile tool for identifying and studying binary PPIs, as well as for characterizing multisubunit complexes.
BibTeX: @article{Salgania2022, author = {Harpreet Kaur Salgania, Jutta Metz, Mandy Jeske}, title = {ReLo: a simple colocalization assay to identify and characterize physical protein-protein interactions}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.03.04.482790} }
Santoliquido, F., Mapelli, M., Iorio, G., Costa, G., Glover, S.C.O., Hartwig, T., Klessen, R.S. and Merli, L.	Binary black hole mergers from population III stars: uncertainties from star formation and binary star properties [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 524(1), pp. 307-324	article	DOI
BibTeX: @article{Santoliquido2023, author = {Filippo Santoliquido and Michela Mapelli and Giuliano Iorio and Guglielmo Costa and Simon C O Glover and Tilman Hartwig and Ralf S Klessen and Lorenzo Merli}, title = {Binary black hole mergers from population III stars: uncertainties from star formation and binary star properties}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {524}, number = {1}, pages = {307--324}, doi = {https://doi.org/10.1093/mnras/stad1860} }
Sarri, A.	Material Aspects of Letter Writing in the Graeco-Roman World [BibTeX]	2017		book	DOI
BibTeX: @book{Sarri2017, author = {Antonia Sarri}, title = {Material Aspects of Letter Writing in the Graeco-Roman World}, publisher = {De Gruyter}, year = {2017}, doi = {https://doi.org/10.1515/9783110426953} }
Sarropoulos, I., Marin, R., Cardoso-Moreira, M. and Kaessmann, H.	Developmental dynamics of lncRNAs across mammalian organs and species [Abstract] [BibTeX]	2019	Nature Vol. 571(7766), pp. 510-514	article	DOI
Abstract: Although many long noncoding RNAs (lncRNAs) have been identified in human and other mammalian genomes, there has been limited systematic functional characterization of these elements. In particular, the contribution of lncRNAs to organ development remains largely unexplored. Here we analyse the expression patterns of lncRNAs across developmental time points in seven major organs, from early organogenesis to adulthood, in seven species (human, rhesus macaque, mouse, rat, rabbit, opossum and chicken). Our analyses identified approximately 15,000 to 35,000 candidate lncRNAs in each species, most of which show species specificity. We characterized the expression patterns of lncRNAs across developmental stages, and found many with dynamic expression patterns across time that show signatures of enrichment for functionality. During development, there is a transition from broadly expressed and conserved lncRNAs towards an increasing number of lineage- and organ-specific lncRNAs. Our study provides a resource of candidate lncRNAs and their patterns of expression and evolutionary conservation across mammalian organ development.
BibTeX: @article{Sarropoulos2019, author = {Ioannis Sarropoulos and Ray Marin and Margarida Cardoso-Moreira and Henrik Kaessmann}, title = {Developmental dynamics of lncRNAs across mammalian organs and species}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {571}, number = {7766}, pages = {510--514}, doi = {https://doi.org/10.1038/s41586-019-1341-x} }
Sarropoulos, I., Sepp, M., Frömel, R., Leiss, K., Trost, N., Leushkin, E., Okonechnikov, K., Joshi, P., Giere, P., Kutscher, L.M., Cardoso-Moreira, M., Pfister, S.M. and Kaessmann, H.	Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells [BibTeX]	2021	Science Vol. 373(6558)	article	DOI
BibTeX: @article{Sarropoulos2021, author = {Ioannis Sarropoulos and Mari Sepp and Robert Frömel and Kevin Leiss and Nils Trost and Evgeny Leushkin and Konstantin Okonechnikov and Piyush Joshi and Peter Giere and Lena M. Kutscher and Margarida Cardoso-Moreira and Stefan M. Pfister and Henrik Kaessmann}, title = {Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells}, journal = {Science}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2021}, volume = {373}, number = {6558}, doi = {https://doi.org/10.1126/science.abg4696} }
Scharf, G.M., Kilian, K., Cordero, J., Wang, Y., Grund, A., Hofmann, M., Froese, N., Wang, X., Kispert, A., Kist, R., Conway, S.J., Geffers, R., Wollert, K.C., Dobreva, G., Bauersachs, J. and Heineke, J.	Inactivation of Sox9 in fibroblasts reduces cardiac fibrosis and inflammation [BibTeX]	2019	JCI Insight Vol. 4(15)	article	DOI
BibTeX: @article{Scharf2019, author = {Gesine M. Scharf and Katja Kilian and Julio Cordero and Yong Wang and Andrea Grund and Melanie Hofmann and Natali Froese and Xue Wang and Andreas Kispert and Ralf Kist and Simon J. Conway and Robert Geffers and Kai C. Wollert and Gergana Dobreva and Johann Bauersachs and Joerg Heineke}, title = {Inactivation of Sox9 in fibroblasts reduces cardiac fibrosis and inflammation}, journal = {JCI Insight}, publisher = {American Society for Clinical Investigation}, year = {2019}, volume = {4}, number = {15}, doi = {https://doi.org/10.1172/jci.insight.126721} }
Schauer, A.T.P., Glover, S.C.O., Klessen, R.S. and Ceverino, D.	The influence of streaming velocities on the formation of the first stars [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 484(3), pp. 3510-3521	article	DOI
BibTeX: @article{Schauer2019, author = {Anna T P Schauer and Simon C O Glover and Ralf S Klessen and Daniel Ceverino}, title = {The influence of streaming velocities on the formation of the first stars}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {484}, number = {3}, pages = {3510--3521}, doi = {https://doi.org/10.1093/mnras/stz013} }
Schauer, A.T.P., Glover, S.C.O., Klessen, R.S. and Clark, P.	The influence of streaming velocities and Lyman–Werner radiation on the formation of the first stars [Abstract] [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 507(2), pp. 1775-1787	article	DOI
Abstract: The first stars in the Universe, the so-called Population III stars, form in small dark matter minihaloes with virial temperatures Tvir < 104 K. Cooling in these minihaloes is dominated by molecular hydrogen (H2), and so Population III star formation is only possible in those minihaloes that form enough H2 to cool on a short timescale. As H2 cooling is more effective in more massive minihaloes, there is therefore a critical halo mass scale Mmin above which Population III star formation first becomes possible. Two important processes can alter this minimum mass scale: streaming of baryons relative to the dark matter and the photodissociation of H2 by a high redshift Lyman–Werner (LW) background. In this paper, we present results from a set of high resolution cosmological simulations that examine the impact of these processes on Mmin and on Mave (the average minihalo mass for star formation), both individually and in combination. We show that streaming has a bigger impact on Mmin than the LW background, but also that both effects are additive. We also provide a fitting functions quantifying the dependence of Mave and Mmin on the streaming velocity and the strength of the LW background.
BibTeX: @article{Schauer2021, author = {Schauer, Anna T P and Glover, Simon C O and Klessen, Ralf S and Clark, Paul}, title = {The influence of streaming velocities and Lyman–Werner radiation on the formation of the first stars}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {507}, number = {2}, pages = {1775--1787}, doi = {https://doi.org/10.1093/mnras/stab1953} }
Schauer, A.T.P., Bromm, V., Boylan-Kolchin, M., Glover, S.C.O. and Klessen, R.S.	Globular Clusters and Streaming Velocities: Testing the New Formation Channel in High-resolution Cosmological Simulations [Abstract] [BibTeX]	2021	The Astrophysical Journal Vol. 922(2), pp. 193	article	DOI
Abstract: Abstract The formation of globular clusters and their relation to the distribution of dark matter have long puzzled astronomers. One of the most recently proposed globular cluster formation channels ties ancient star clusters to the large-scale streaming velocity of baryons relative to dark matter in the early universe. These streaming velocities affect the global infall of baryons into dark matter halos, the high-redshift halo mass function, and the earliest generations of stars. In some cases, streaming velocities may result in dense regions of dark matter-free gas that becomes Jeans unstable, potentially leading to the formation of compact star clusters. We investigate this hypothesis using cosmological hydrodynamical simulations that include a full chemical network and the formation and destruction of H2, a process crucial for the formation of the first stars. We find that high-density gas in regions with significant streaming velocities is indeed somewhat offset from the centers of dark matter halos, but this offset is typically significantly smaller than the virial radius. Gas outside of dark matter halos never reaches Jeans-unstable densities in our simulations. We postulate that low-level (Z ≈ 10−3 Z ⊙) metal enrichment by Population III supernovae may enable cooling in the extra-virial regions, allowing gas outside of dark matter halos to cool to the cosmic microwave background temperature and become Jeans unstable. Follow-up simulations that include both streaming velocities and metal enrichment by Population III supernovae are needed to understand if streaming velocities provide one path for the formation of globular clusters in the early universe.
BibTeX: @article{Schauer2021a, author = {Anna T. P. Schauer, Volker Bromm, Michael Boylan-Kolchin, Simon C. O. Glover, Ralf S. Klessen}, title = {Globular Clusters and Streaming Velocities: Testing the New Formation Channel in High-resolution Cosmological Simulations}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2021}, volume = {922}, number = {2}, pages = {193}, doi = {https://doi.org/10.3847/1538-4357/ac27aa} }
Scheller, M., Ludwig, A.K., Göllner, S., Rohde, C., Krämer, S., Stäble, S., Janssen, M., Müller, J.-A., He, L., Bäumer, N., Arnold, C., Gerß, J., Schönung, M., Thiede, C., Niederwieser, C., Niederwieser, D., Serve, H., Berdel, W.E., Thiem, U., Hemmerling, I., Leuschner, F., Plass, C., Schlesner, M., Zaugg, J., Milsom, M.D., Trumpp, A., Pabst, C., Lipka, D.B. and Müller-Tidow, C.	Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response [BibTeX]	2021	Nature Cancer Vol. 2(5), pp. 527-544	article	DOI
BibTeX: @article{Scheller2021, author = {Marina Scheller and Anne Kathrin Ludwig and Stefanie Göllner and Christian Rohde and Stephen Krämer and Sina Stäble and Maike Janssen and James-Arne Müller and Lixiazi He and Nicole Bäumer and Christian Arnold and Joachim Gerß and Maximilian Schönung and Christian Thiede and Christian Niederwieser and Dietger Niederwieser and Hubert Serve and Wolfgang E. Berdel and Ulrich Thiem and Inga Hemmerling and Florian Leuschner and Christoph Plass and Matthias Schlesner and Judith Zaugg and Michael D. Milsom and Andreas Trumpp and Caroline Pabst and Daniel B. Lipka and Carsten Müller-Tidow}, title = {Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response}, journal = {Nature Cancer}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {2}, number = {5}, pages = {527--544}, doi = {https://doi.org/10.1038/s43018-021-00213-9} }
Schinke, C., Poos, A.M., Bauer, M., John, L., Johnson, S., Deshpande, S., Carrillo, L., Alapat, D., Rasche, L., Thanendrarajan, S., Zangari, M., Hadidi, S.A., van Rhee, F., Davies, F., Raab, M.S., Morgan, G. and Weinhold, N.	Characterizing the role of the immune microenvironment in multiple myeloma progression at a single-cell level [Abstract] [BibTeX]	2022	Blood Advances Vol. 6(22), pp. 5873-5883	article	DOI URL
Abstract: Abstract Early alterations within the bone marrow microenvironment that contribute to the progression of multiple myeloma (MM) from its precursor stages could be the key to identifying novel therapeutic approaches. However, the intrinsic variability in cellular populations between patients and the differences in sample processing and analysis methods have made it difficult to identify consistent changes between data sets. Here, we used single-cell RNA sequencing of bone marrow cells from precursor stages, monoclonal gammopathy of unknown significance, smoldering MM, and newly diagnosed MM and analyzed our data in combination with a previously published data set that used a similar patient population and sample processing. Despite the vast interpatient heterogeneity, some alterations were consistently observed in both data sets. We identified changes in immune cell populations as the disease progressed, which were characterized by a substantial decrease in memory and naïve CD4 T cells, and an increase in CD8+ effector T cells and T-regulatory cells. These alterations were further accompanied by an enrichment of nonclonal memory B cells and an increase in CD14 and CD16 monocytes in MM compared with its precursor stages. These results provide crucial information on the immune changes associated with the progression to clinical MM and can help to develop immune-based strategies for patient stratification and early therapeutic intervention.
BibTeX: @article{Schinke2022, author = {Carolina Schinke, Alexandra M. Poos, Michael Bauer, Lukas John, Sarah Johnson, Shayu Deshpande, Luis Carrillo, Daisy Alapat, Leo Rasche, Sharmilan Thanendrarajan, Maurizio Zangari, Samer Al Hadidi, Frits van Rhee, Faith Davies, Marc S. Raab, Gareth Morgan, Niels Weinhold}, title = {Characterizing the role of the immune microenvironment in multiple myeloma progression at a single-cell level}, journal = {Blood Advances}, publisher = {American Society of Hematology}, year = {2022}, volume = {6}, number = {22}, pages = {5873--5883}, url = {https://ashpublications.org/bloodadvances/article-pdf/6/22/5873/1929929/blooda_adv-2022-007217-main.pdf}, doi = {https://doi.org/10.1182/bloodadvances.2022007217} }
Schirra, A.P., Habouzit, M., Klessen, R.S., Fornasini, F., Nelson, D., Pillepich, A., Anglés-Alcázar, D., Davé, R. and Civano, F.	Bringing faint active galactic nuclei (AGNs) to light: a view from large-scale cosmological simulations [Abstract] [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 508(4), pp. 4816-4843	article	DOI
Abstract: ABSTRACT The sensitivity of X-ray facilities and our ability to detect fainter active galactic nuclei (AGNs) will increase with the upcoming Athena mission and the AXIS and Lynx concept missions, thus improving our understanding of supermassive black holes (BHs) in a luminosity regime that can be dominated by X-ray binaries. We analyse the population of faint AGNs (L_rm x, 2-10 , keV⩽ 10^42, rm erg,s^ -1) in the Illustris, TNG100, EAGLE, and SIMBA cosmological simulations, and find that the properties of their host galaxies vary from one simulation to another. In Illustris and EAGLE, faint AGNs are powered by low-mass BHs located in low-mass star-forming galaxies. In TNG100 and SIMBA, they are mostly associated with more massive BHs in quenched massive galaxies. We model the X-ray binary (XRB) populations of the simulated galaxies, and find that AGNs often dominate the galaxy AGN + XRB hard X-ray luminosity at z &gt; 2, while XRBs dominate in some simulations at z &lt; 2. Whether the AGN or XRB emission dominates in star-forming and quenched galaxies depends on the simulations. These differences in simulations can be used to discriminate between galaxy formation models with future high-resolution X-ray observations. We compare the luminosity of simulated faint AGN host galaxies to observations of stacked galaxies from Chandra. Our comparison indicates that the simulations post-processed with our X-ray modelling tend to overestimate the AGN + XRB X-ray luminosity; luminosity that can be strongly affected by AGN obscuration. Some simulations reveal clear AGN trends as a function of stellar mass (e.g. galaxy luminosity drop in massive galaxies), which are not apparent in the observations.
BibTeX: @article{Schirra2021, author = {Adrian P Schirra, Mélanie Habouzit, Ralf S Klessen, Francesca Fornasini, Dylan Nelson, Annalisa Pillepich, Daniel Anglés-Alcázar, Romeel Davé, Francesca Civano}, title = {Bringing faint active galactic nuclei (AGNs) to light: a view from large-scale cosmological simulations}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {508}, number = {4}, pages = {4816--4843}, doi = {https://doi.org/10.1093/mnras/stab2863} }
Schleicher, D.R.G., Fellhauer, M., Boekholt, T.C.N., Reinoso, B., Klessen, R.S., Vergara, M.Z.C., Alister Seguel, P.J., Bovino, S., Olave, C., Díaz, V.B., FFibla, P., Riaz, R., Band yopadhyay, B., San Martín-Pérez, R.I., Zamponi, J. and Haemmerle, L.	Formation of massive black holes via collisions and accretion [BibTeX]	2019	Boletin de la Asociacion Argentina de Astronomia La Plata Argentina Vol. 61, pp. 234-236	article
BibTeX: @article{Schleicher2019, author = {Schleicher, D. R. G. and Fellhauer, M. and Boekholt, T. C. N. and Reinoso, B. and Klessen, R. S. and Vergara, M. Z. C. and Alister Seguel, P. J. and Bovino, S. and Olave, C. and Díaz, V. B. and FFibla, P. and Riaz, R. and Band yopadhyay, B. and San Martín-Pérez, R. I. and Zamponi, J. and Haemmerle, L.}, title = {Formation of massive black holes via collisions and accretion}, journal = {Boletin de la Asociacion Argentina de Astronomia La Plata Argentina}, year = {2019}, volume = {61}, pages = {234--236} }
Schlüter, A., Aksan, B., Fioravanti, R., Valente, S., Mai, A. and Mauceri, D.	Histone Deacetylases Contribute to Excitotoxicity-Triggered Degeneration of Retinal Ganglion Cells In Vivo [BibTeX]	2019	Molecular Neurobiology Vol. 56(12), pp. 8018-8034	article	DOI
BibTeX: @article{Schlueter2019, author = {Annabelle Schlüter and Bahar Aksan and Rossella Fioravanti and Sergio Valente and Antonello Mai and Daniela Mauceri}, title = {Histone Deacetylases Contribute to Excitotoxicity-Triggered Degeneration of Retinal Ganglion Cells In Vivo}, journal = {Molecular Neurobiology}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {56}, number = {12}, pages = {8018--8034}, doi = {https://doi.org/10.1007/s12035-019-01658-x} }
Schmid, C.D., Olsavszky, V., Reinhart, M., Weyer, V., Trogisch, F.A., Sticht, C., Winkler, M., Kürschner, S.W., Hoffmann, J., Ola, R., Staniczek, T., Heineke, J., Straub, B.K., Mittler, J., Schledzewski, K., ten Dijke, P., Richter, K., Dooley, S., Géraud, C., Goerdt, S. and Koch, P.	ALK1 controls hepatic vessel formation, angiodiversity, and angiocrine functions in hereditary hemorrhagic telangiectasia of the liver [BibTeX]	2022	Hepatology Vol. 77(4), pp. 1211-1227	article	DOI
BibTeX: @article{Schmid2022, author = {Christian David Schmid, Victor Olsavszky, Manuel Reinhart, Vanessa Weyer, Felix A. Trogisch, Carsten Sticht, Manuel Winkler, Sina W. Kürschner, Johannes Hoffmann, Roxana Ola, Theresa Staniczek, Joerg Heineke, Beate K. Straub, Jens Mittler, Kai Schledzewski, Peter ten Dijke, Karsten Richter, Steven Dooley, Cyrill Géraud, Sergij Goerdt, Philipp‐Sebastian Koch}, title = {ALK1 controls hepatic vessel formation, angiodiversity, and angiocrine functions in hereditary hemorrhagic telangiectasia of the liver}, journal = {Hepatology}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, year = {2022}, volume = {77}, number = {4}, pages = {1211--1227}, doi = {https://doi.org/10.1002/hep.32641} }
Schmieder, C.	Bild und Text auf römischen Mosaiken [BibTeX]	2022		book	DOI
BibTeX: @book{Schmieder2022, author = {Claudia Schmieder}, title = {Bild und Text auf römischen Mosaiken}, publisher = {De Gruyter}, year = {2022}, doi = {https://doi.org/10.1515/9783110775730} }
Schneider, F.R.N., Ramírez-Agudelo, O.H., Tramper, F., Bestenlehner, J.M., Castro, N., Sana, H., Evans, C.J., Sabín-Sanjulián, C., Simón-Díaz, S., Langer, N., Fossati, L., Gräfener, G., Crowther, P.A., de Mink, S.E., de Koter, A., Gieles, M., Herrero, A., Izzard, R.G., Kalari, V., Klessen, R.S., Lennon, D.J., Mahy, L., Maíz Apellániz, J., Markova, N., van Loon, J.T., Vink, J.S. and Walborn, N.R.	The VLT-FLAMES Tarantula Survey. XXIX. Massive star formation in the local 30 Doradus starburst [BibTeX]	2018	Astronomy & Astrophysics Vol. 618, pp. A73	article	DOI
BibTeX: @article{Schneider2018, author = {Schneider, F. R. N. and Ramírez-Agudelo, O. H. and Tramper, F. and Bestenlehner, J. M. and Castro, N. and Sana, H. and Evans, C. J. and Sabín-Sanjulián, C. and Simón-Díaz, S. and Langer, N. and Fossati, L. and Gräfener, G. and Crowther, P. A. and de Mink, S. E. and de Koter, A. and Gieles, M. and Herrero, A. and Izzard, R. G. and Kalari, V. and Klessen, R. S. and Lennon, D. J. and Mahy, L. and Maíz Apellániz, J. and Markova, N. and van Loon, J. Th. and Vink, J. S. and Walborn, N. R.}, title = {The VLT-FLAMES Tarantula Survey. XXIX. Massive star formation in the local 30 Doradus starburst}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {618}, pages = {A73}, doi = {https://doi.org/10.1051/0004-6361/201833433} }
Schott, M., Grinberger, A.Y., Lautenbach, S. and Zipf, A.	The Impact of Community Happenings in OpenStreetMap—Establishing a Framework for Online Community Member Activity Analyses [BibTeX]	2021	ISPRS International Journal of Geo-Information Vol. 10(3), pp. 164	article	DOI
BibTeX: @article{Schott2021, author = {Moritz Schott and Asher Yair Grinberger and Sven Lautenbach and Alexander Zipf}, title = {The Impact of Community Happenings in OpenStreetMap—Establishing a Framework for Online Community Member Activity Analyses}, journal = {ISPRS International Journal of Geo-Information}, publisher = {MDPI AG}, year = {2021}, volume = {10}, number = {3}, pages = {164}, doi = {https://doi.org/10.3390/ijgi10030164} }
Schrenk-Siemens, K., Pohle, J., Rostock, C., Hay, M.A.E., Lam, R.M., Szczot, M., Lu, S., Chesler, A.T. and Siemens, J.	Human Stem Cell-Derived TRPV1-Positive Sensory Neurons: A New Tool to Study Mechanisms of Sensitization [Abstract] [BibTeX]	2022	Cells Vol. 11(18), pp. 2905	article	DOI URL
Abstract: Somatosensation, the detection and transduction of external and internal stimuli such as temperature or mechanical force, is vital to sustaining our bodily integrity. But still, some of the mechanisms of distinct stimuli detection and transduction are not entirely understood, especially when noxious perception turns into chronic pain. Over the past decade major progress has increased our understanding in areas such as mechanotransduction or sensory neuron classification. However, it is in particular the access to human pluripotent stem cells and the possibility of generating and studying human sensory neurons that has enriched the somatosensory research field. Based on our previous work, we describe here the generation of human stem cell-derived nociceptor-like cells. We show that by varying the differentiation strategy, we can produce different nociceptive subpopulations with different responsiveness to nociceptive stimuli such as capsaicin. Functional as well as deep sequencing analysis demonstrated that one protocol in particular allowed the generation of a mechano-nociceptive sensory neuron population, homogeneously expressing TRPV1. Accordingly, we find the cells to homogenously respond to capsaicin, to become sensitized upon inflammatory stimuli, and to respond to temperature stimulation. The efficient and homogenous generation of these neurons make them an ideal translational tool to study mechanisms of sensitization, also in the context of chronic pain.
BibTeX: @article{SchrenkSiemens2022, author = {Katrin Schrenk-Siemens, Jörg Pohle, Charlotte Rostock, Muad Abd El Hay, Ruby M. Lam, Marcin Szczot, Shiying Lu, Alexander T. Chesler, Jan Siemens}, title = {Human Stem Cell-Derived TRPV1-Positive Sensory Neurons: A New Tool to Study Mechanisms of Sensitization}, journal = {Cells}, publisher = {MDPI AG}, year = {2022}, volume = {11}, number = {18}, pages = {2905}, url = {https://www.mdpi.com/2073-4409/11/18/2905/pdf}, doi = {https://doi.org/10.3390/cells11182905} }
Schroder, R.R., Schindler, B., Schnell, M., Hendrich, C., Wensorra, J., Zhang, W.-S., Eisele, J., Veith, L., Kammerer, J., Pfannmoller, M. and et al.	DELTA - A Novel Ultra-Low Voltage SEM for Electron Spectroscopic Imaging [BibTeX]	2018	Microscopy and Microanalysis Vol. 24(S1), pp. 626-627	article	DOI
BibTeX: @article{Schroder2018, author = {Schroder, Rasmus R. and Schindler, Bernd and Schnell, Michael and Hendrich, Christian and Wensorra, Jakob and Zhang, Wen-Shan and Eisele, Jorg and Veith, Lisa and Kammerer, Jochen and Pfannmoller, Martin and et al.}, title = {DELTA - A Novel Ultra-Low Voltage SEM for Electron Spectroscopic Imaging}, journal = {Microscopy and Microanalysis}, publisher = {Cambridge University Press}, year = {2018}, volume = {24}, number = {S1}, pages = {626--627}, doi = {https://doi.org/10.1017/S1431927618003628} }
Schütz, L.M., Louveaux, M., Barro, A.V., Bouziri, S., Cerrone, L., Wolny, A., Kreshuk, A., Hamprecht, F.A. and Maizel, A.	Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana [BibTeX]	2021	Plant and Cell Physiology Vol. 62(8), pp. 1269-1279	article	DOI
BibTeX: @article{Schuetz2021, author = {Lilli Marie Schütz and Marion Louveaux and Amaya Vilches Barro and Sami Bouziri and Lorenzo Cerrone and Adrian Wolny and Anna Kreshuk and Fred A Hamprecht and Alexis Maizel}, title = {Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana}, journal = {Plant and Cell Physiology}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {62}, number = {8}, pages = {1269--1279}, doi = {https://doi.org/10.1093/pcp/pcab038} }
Schultz, S.	Papierherstellung im deutschen Südwesten [BibTeX]	2018		book	DOI
BibTeX: @book{Schultz2018, author = {Sandra Schultz}, title = {Papierherstellung im deutschen Südwesten}, publisher = {De Gruyter}, year = {2018}, doi = {https://doi.org/10.1515/9783110583717} }
Schweitzer-Martin, P.	Kooperation und Innovation im Speyerer Buchdruck des ausgehenden Mittelalters [BibTeX]	2022		book	DOI
BibTeX: @book{SchweitzerMartin2022, author = {Paul Schweitzer-Martin}, title = {Kooperation und Innovation im Speyerer Buchdruck des ausgehenden Mittelalters}, publisher = {De Gruyter}, year = {2022}, doi = {https://doi.org/10.1515/9783110796599} }
Sclip, A., Acuna, C., Luo, F. and Südhof, T.C.	RIM -binding proteins recruit BK-channels to presynaptic release sites adjacent to voltage-gated Ca 2mathplus -channels [BibTeX]	2018	The EMBO Journal Vol. 37(16)	article	DOI
BibTeX: @article{Sclip2018, author = {Alessandra Sclip and Claudio Acuna and Fujun Luo and Thomas C Südhof}, title = {RIM -binding proteins recruit BK-channels to presynaptic release sites adjacent to voltage-gated Ca 2mathplus -channels}, journal = {The EMBO Journal}, publisher = {EMBO}, year = {2018}, volume = {37}, number = {16}, doi = {https://doi.org/10.15252/embj.201798637} }
Shah, P.N., Stanifer, M.L., Höhn, K., Engel, U., Haselmann, U., Bartenschlager, R., Kräusslich, H.-G., Krijnse-Locker, J. and Boulant, S.	Genome packaging of reovirus is mediated by the scaffolding property of the microtubule network [Abstract] [BibTeX]	2017	Cellular Microbiology Vol. 19(12), pp. e12765	article	DOI
Abstract: Summary Reovirus replication occurs in the cytoplasm of the host cell, in virally induced mini-organelles called virus factories. On the basis of the serotype of the virus, the virus factories can manifest as filamentous (type 1 Lang strain) or globular structures (type 3 Dearing strain). The filamentous factories morphology is dependent on the microtubule cytoskeleton; however, the exact function of the microtubule network in virus replication remains unknown. Using a combination of fluorescent microscopy, electron microscopy, and tomography of high-pressure frozen and freeze-substituted cells, we determined the ultrastructural organisation of reovirus factories. Cells infected with the reovirus microtubule-dependent strain display paracrystalline arrays of progeny virions resulting from their tiered organisation around microtubule filaments. On the contrary, in cells infected with the microtubule-independent strain, progeny virions lacked organisation. Conversely to the microtubule-dependent strain, around half of the viral particles present in these viral factories did not contain genomes (genome-less particles). Complementarily, interference with the microtubule filaments in cells infected with the microtubule-dependent strain resulted in a significant increase of genome-less particle number. This decrease of genome packaging efficiency could be rescued by rerouting viral factories on the actin cytoskeleton. These findings demonstrate that the scaffolding properties of the microtubule, and not biochemical nature of tubulin, are critical determinants for reovirus efficient genome packaging. This work establishes, for the first time, a functional correlation between ultrastructural organisation of reovirus factories with genome packaging efficiency and provides novel information on how viruses coordinate assembly of progeny particles.
BibTeX: @article{Shah2017, author = {Shah, Pranav N.M. and Stanifer, Megan L. and Höhn, Katharina and Engel, Ulrike and Haselmann, Uta and Bartenschlager, Ralf and Kräusslich, Hans-Georg and Krijnse-Locker, Jacomine and Boulant, Steeve}, title = {Genome packaging of reovirus is mediated by the scaffolding property of the microtubule network}, journal = {Cellular Microbiology}, year = {2017}, volume = {19}, number = {12}, pages = {e12765}, note = {e12765 CMI-17-0090.R1}, doi = {https://doi.org/10.1111/cmi.12765} }
Shostak, A., Schermann, G., Diernfellner, A. and Brunner, M.	MXD/MIZ1 transcription regulatory complexes activate the expression of MYC-repressed genes [BibTeX]	2021	FEBS Letters Vol. 595(12), pp. 1639-1655	article	DOI
BibTeX: @article{Shostak2021, author = {Anton Shostak and Géza Schermann and Axel Diernfellner and Michael Brunner}, title = {MXD/MIZ1 transcription regulatory complexes activate the expression of MYC-repressed genes}, journal = {FEBS Letters}, publisher = {Wiley}, year = {2021}, volume = {595}, number = {12}, pages = {1639--1655}, doi = {https://doi.org/10.1002/1873-3468.14097} }
Shytaj, I.L., Lucic, B., Forcato, M., Penzo, C., Billingsley, J., Laketa, V., Bosinger, S., Stanic, M., Gregoretti, F., Antonelli, L., Oliva, G., Frese, C.K., Trifunovic, A., Galy, B., Eibl, C., Silvestri, G., Bicciato, S., Savarino, A. and Lusic, M.	Alterations of redox and iron metabolism accompany the development of HIV latency [BibTeX]	2020	The EMBO Journal Vol. 39(9)	article	DOI
BibTeX: @article{Shytaj2020, author = {Iart Luca Shytaj and Bojana Lucic and Mattia Forcato and Carlotta Penzo and James Billingsley and Vibor Laketa and Steven Bosinger and Mia Stanic and Francesco Gregoretti and Laura Antonelli and Gennaro Oliva and Christian K Frese and Aleksandra Trifunovic and Bruno Galy and Clarissa Eibl and Guido Silvestri and Silvio Bicciato and Andrea Savarino and Marina Lusic}, title = {Alterations of redox and iron metabolism accompany the development of HIV latency}, journal = {The EMBO Journal}, publisher = {EMBO}, year = {2020}, volume = {39}, number = {9}, doi = {https://doi.org/10.15252/embj.2019102209} }
Shytaj, I.L., Procopio, F.A., Tarek, M., Carlon-Andres, I., Tang, H.-Y., Goldman, A.R., Munshi, M., Pal, V.K., Forcato, M., Sreeram, S., Leskov, K., Ye, F., Lucic, B., Cruz, N., Ndhlovu, L.C., Bicciato, S., Padilla-Parra, S., Diaz, R.S., Singh, A., Lusic, M., Karn, J., Alvarez-Carbonell, D. and Savarino, A.	Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress [BibTeX]	2021	EMBO Molecular Medicine Vol. 13(8)	article	DOI
BibTeX: @article{Shytaj2021, author = {Iart Luca Shytaj and Francesco Andrea Procopio and Mohammad Tarek and Irene Carlon-Andres and Hsin-Yao Tang and Aaron R Goldman and MohamedHusen Munshi and Virender Kumar Pal and Mattia Forcato and Sheetal Sreeram and Konstantin Leskov and Fengchun Ye and Bojana Lucic and Nicolly Cruz and Lishomwa C Ndhlovu and Silvio Bicciato and Sergi Padilla-Parra and Ricardo Sobhie Diaz and Amit Singh and Marina Lusic and Jonathan Karn and David Alvarez-Carbonell and Andrea Savarino}, title = {Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress}, journal = {EMBO Molecular Medicine}, publisher = {EMBO}, year = {2021}, volume = {13}, number = {8}, doi = {https://doi.org/10.15252/emmm.202013901} }
Shytaj, I.L., Fares, M., Gallucci, L., Lucic, B., Tolba, M.M., Zimmermann, L., Adler, J.M., Xing, N., Bushe, J., Gruber, A.D., Ambiel, I., Ayoub, A.T., Cortese, M., Neufeldt, C.J., Stolp, B., Sobhy, M.H., Fathy, M., Zhao, M., Laketa, V., Diaz, R.S., Sutton, R.E., Chlanda, P., Boulant, S., Bartenschlager, R., Stanifer, M.L., Fackler, O.T., Trimpert, J., Savarino, A. and Lusic, M.	The FDA-Approved Drug Cobicistat Synergizes with Remdesivir To Inhibit SARS-CoV-2 Replication In Vitro and Decreases Viral Titers and Disease Progression in Syrian Hamsters [Abstract] [BibTeX]	2022	mBio Vol. 13(2)	article	DOI
Abstract: The lack of effective antiviral treatments against SARS-CoV-2 is a significant limitation in the fight against the COVID-19 pandemic. Single-drug regimens have so far yielded limited results, indicating that combinations of antivirals might be required, as previously seen for other RNA viruses.
BibTeX: @article{Shytaj2022, author = {Iart Luca Shytaj, Mohamed Fares, Lara Gallucci, Bojana Lucic, Mahmoud M. Tolba, Liv Zimmermann, Julia M. Adler, Na Xing, Judith Bushe, Achim D. Gruber, Ina Ambiel, Ahmed Taha Ayoub, Mirko Cortese, Christopher J. Neufeldt, Bettina Stolp, Mohamed Hossam Sobhy, Moustafa Fathy, Min Zhao, Vibor Laketa, Ricardo Sobhie Diaz, Richard E. Sutton, Petr Chlanda, Steeve Boulant, Ralf Bartenschlager, Megan L. Stanifer, Oliver T. Fackler, Jakob Trimpert, Andrea Savarino, Marina Lusic}, title = {The FDA-Approved Drug Cobicistat Synergizes with Remdesivir To Inhibit SARS-CoV-2 Replication In Vitro and Decreases Viral Titers and Disease Progression in Syrian Hamsters}, journal = {mBio}, publisher = {American Society for Microbiology}, year = {2022}, volume = {13}, number = {2}, doi = {https://doi.org/10.1128/mbio.03705-21} }
Sigmund, L.M., Maier, R. and Greb, L.	The inversion of tetrahedral p-block element compounds: general trends and the relation to the second-order Jahn–Teller effect [Abstract] [BibTeX]	2022	Chemical Science Vol. 13(2), pp. 510-521	article	DOI URL
Abstract: The tetrahedron is the primary structural motif among the p-block elements and determines the architecture of our bio- and geosphere. This study sheds light on its stereochemical inversion process.
BibTeX: @article{Sigmund2022, author = {Lukas M. Sigmund, Rouven Maier, Lutz Greb}, title = {The inversion of tetrahedral p-block element compounds: general trends and the relation to the second-order Jahn–Teller effect}, journal = {Chemical Science}, publisher = {Royal Society of Chemistry (RSC)}, year = {2022}, volume = {13}, number = {2}, pages = {510--521}, url = {http://pubs.rsc.org/en/content/articlepdf/2022/SC/D1SC05395G}, doi = {https://doi.org/10.1039/D1SC05395G} }
Silos, R.G., Fischer, C. and Bermejo, J.L.	NGS allele counts versus called genotypes for testing genetic association [BibTeX]	2022	Computational and Structural Biotechnology Journal Vol. 20, pp. 3729-3733	article	DOI URL
BibTeX: @article{Silos2022, author = {Rosa González Silos, Christine Fischer, Justo Lorenzo Bermejo}, title = {NGS allele counts versus called genotypes for testing genetic association}, journal = {Computational and Structural Biotechnology Journal}, publisher = {Elsevier BV}, year = {2022}, volume = {20}, pages = {3729--3733}, url = {https://api.elsevier.com/content/article/PII:S2001037022002951?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.csbj.2022.07.016} }
Simonetti, M., Paldy, E., Njoo, C., Bali, K.K., Worzfeld, T., Pitzer, C., Kuner, T., Offermanns, S., Mauceri, D. and Kuner, R.	The impact of Semaphorin 4C/Plexin-B2 signaling on fear memory via remodeling of neuronal and synaptic morphology [BibTeX]	2019	Molecular Psychiatry Vol. 26(4), pp. 1376-1398	article	DOI
BibTeX: @article{Simonetti2019, author = {Manuela Simonetti and Eszter Paldy and Christian Njoo and Kiran Kumar Bali and Thomas Worzfeld and Claudia Pitzer and Thomas Kuner and Stefan Offermanns and Daniela Mauceri and Rohini Kuner}, title = {The impact of Semaphorin 4C/Plexin-B2 signaling on fear memory via remodeling of neuronal and synaptic morphology}, journal = {Molecular Psychiatry}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {26}, number = {4}, pages = {1376--1398}, doi = {https://doi.org/10.1038/s41380-019-0491-4} }
Singh, A., Schermann, G., Reislöhner, S., Kellner, N., Hurt, E. and Brunner, M.	Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum [BibTeX]	2021	Genes Vol. 12(10), pp. 1549	article	DOI
BibTeX: @article{Singh2021, author = {Amit Singh and Géza Schermann and Sven Reislöhner and Nikola Kellner and Ed Hurt and Michael Brunner}, title = {Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum}, journal = {Genes}, publisher = {MDPI AG}, year = {2021}, volume = {12}, number = {10}, pages = {1549}, doi = {https://doi.org/10.3390/genes12101549} }
Siovitz, I., Lannig, S., Deller, Y., Strobel, H., Oberthaler, M.K. and Gasenzer, T.	Universal dynamics of rogue waves in a quenched spinor Bose condensate [BibTeX]	2023		misc	DOI
BibTeX: @misc{Siovitz2023, author = {Siovitz, Ido and Lannig, Stefan and Deller, Yannick and Strobel, Helmut and Oberthaler, Markus K. and Gasenzer, Thomas}, title = {Universal dynamics of rogue waves in a quenched spinor Bose condensate}, publisher = {arXiv}, year = {2023}, doi = {https://doi.org/10.48550/ARXIV.2304.09293} }
Siovitz, I., Heinen, P., Rasch, N., Lannig, S., Deller, Y., Strobel, H., Oberthaler, M. and Gasenzer, T.	Universal Dynamics at the Lowest Temperatures [BibTeX]	2023		misc	DOI
BibTeX: @misc{Siovitz2023a, author = {Siovitz, Ido and Heinen, Philipp and Rasch, Niklas and Lannig, Stefan and Deller, Yannick and Strobel, Helmut and Oberthaler, Markus and Gasenzer, Thomas}, title = {Universal Dynamics at the Lowest Temperatures}, publisher = {arXiv}, year = {2023}, doi = {https://doi.org/10.48550/ARXIV.2310.03636} }
Sloan, J., Hakenjos, J.P., Gebert, M., Ermakova, O., Gumiero, A., Stier, G., Wild, K., Sinning, I. and Lohmann, J.U.	Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Sloan2020, author = {Jeremy Sloan and Jana P. Hakenjos and Michael Gebert and Olga Ermakova and Andrea Gumiero and Gunter Stier and Klemens Wild and Irmgard Sinning and Jan U. Lohmann}, title = {Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-16024-y} }
Smirnova-Pinchukova, I., Husemann, B., Davis, T.A., Smith, C.M.A., Singha, M., Tremblay, G.R., Klessen, R.S., Powell, M., Connor, T., Baum, S.A., Combes, F., Croom, S.M., Gaspari, M., Neumann, J., O’Dea, C.P., Pérez-Torres, M., Rosario, D.J., Rose, T., Scharwächter, J. and Winkel, N.	The Close AGN Reference Survey (CARS) [Abstract] [BibTeX]	2022	Astronomy & Astrophysics Vol. 659, pp. A125	article	DOI
Abstract: Context. Active galactic nuclei (AGN) are thought to be responsible for the suppression of star formation in massive ∼1010 M⊙ galaxies. While this process is a key feature in numerical simulations of galaxy formation, it has not been unambiguously confirmed in observational studies yet. Aims. The characterization of the star formation rate (SFR) in AGN host galaxies is challenging as AGN light contaminates most SFR tracers. Furthermore, the various SFR tracers are sensitive to different timescales of star formation from approximately a few to 100 Myr. We aim to obtain and compare SFR estimates from different tracers for AGN host galaxies in the Close AGN Reference Survey (CARS) to provide new observational insights into the recent SFR history of those systems. Methods. We constructed integrated panchromatic spectral energy distributions to measure the far infrared (FIR) luminosity as a tracer for the recent (< 100 Myr) SFR. In addition we used the integral-field unit observation of the CARS targets to employ the Hα luminosity decontaminated by AGN excitation as a proxy for the current (< 5 Myr) SFR. Results. We find that significant differences in specific SFR of the AGN host galaxies as compared with the larger galaxy population disappear once cold gas mass, in addition to stellar mass, is used to predict the SFR for a specific AGN host. Only a tentative trend with the inclination of the host galaxy remains, such that SFR appears slightly lower than expected when the galaxies of unobscured AGN appear more edge-on along our line-of-sight, particular for dust-insensitive FIR-based SFRs. We identify individual galaxies with a significant difference in their SFR which can be related to a recent enhancement or decline in their SFR history that might be related to various processes including interactions, gas consumption, outflows, and AGN feedback. Conclusions. AGN can be present in various stages of galaxy evolution which makes it difficult to relate the SFR solely to the impact of the AGN. Our study shows that stellar mass alone is an insufficient parameter to estimate the expected SFR of an AGN host galaxy compared to the underlying non-AGN galaxy population. We do not find any strong evidence for a global positive or negative AGN feedback in the CARS sample. However, there is tentative evidence that (1) the relative orientation of the AGN engine with respect to the host galaxies might alter the efficiency of AGN feedback and that (2) the recent SFH is an additional tool to identify rapid changes in galaxy growth driven by the AGN or other processes.
BibTeX: @article{SmirnovaPinchukova2022, author = {I. Smirnova-Pinchukova, B. Husemann, T. A. Davis, C. M. A. Smith, M. Singha, G. R. Tremblay, R. S. Klessen, M. Powell, T. Connor, S. A. Baum, F. Combes, S. M. Croom, M. Gaspari, J. Neumann, C. P. O’Dea, M. Pérez-Torres, D. J. Rosario, T. Rose, J. Scharwächter, N. Winkel}, title = {The Close AGN Reference Survey (CARS)}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2022}, volume = {659}, pages = {A125}, doi = {https://doi.org/10.1051/0004-6361/202142011} }
Smith, R.J., Tress, R., Soler, J.D., Klessen, R.S., Glover, S.C.O., Hennebelle, P., Molinari, S., Mac Low, M.-M. and Whitworth, D.	On the distribution of the cold neutral medium in galaxy discs [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 524(1), pp. 873-885	article	DOI
BibTeX: @article{Smith2023, author = {Rowan J Smith and Robin Tress and Juan D Soler and Ralf S Klessen and Simon C O Glover and Patrick Hennebelle and Sergio Molinari and Mordecai-Mark Mac Low and David Whitworth}, title = {On the distribution of the cold neutral medium in galaxy discs}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {524}, number = {1}, pages = {873--885}, doi = {https://doi.org/10.1093/mnras/stad1537} }
Soler, J.D., Beuther, H., Rugel, M., Wang, Y., Clark, P.C., Glover, S.C.O., Goldsmith, P.F., Heyer, M., Anderson, L.D., Goodman, A., Henning, T., Kainulainen, J., Klessen, R.S., Longmore, S.N., McClure-Griffiths, N.M., Menten, K.M., Mottram, J.C., Ott, J., Ragan, S.E., Smith, R.J., Urquhart, J.S., Bigiel, F., Hennebelle, P., Roy, N. and Schilke, P.	Histogram of oriented gradients: a technique for the study of molecular cloud formation [BibTeX]	2019	Astronomy & Astrophysics Vol. 622, pp. A166	article	DOI
BibTeX: @article{Soler2019, author = {J. D. Soler and H. Beuther and M. Rugel and Y. Wang and P. C. Clark and S. C. O. Glover and P. F. Goldsmith and M. Heyer and L. D. Anderson and A. Goodman and Th. Henning and J. Kainulainen and R. S. Klessen and S. N. Longmore and N. M. McClure-Griffiths and K. M. Menten and J. C. Mottram and J. Ott and S. E. Ragan and R. J. Smith and J. S. Urquhart and F. Bigiel and P. Hennebelle and N. Roy and P. Schilke}, title = {Histogram of oriented gradients: a technique for the study of molecular cloud formation}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2019}, volume = {622}, pages = {A166}, doi = {https://doi.org/10.1051/0004-6361/201834300} }
Soler, J.D., Miville-Deschênes, M.-A., Molinari, S., Klessen, R.S., Hennebelle, P., Testi, L., McClure-Griffiths, N.M., Beuther, H., Elia, D., Schisano, E., Traficante, A., Girichidis, P., Glover, S.C.O., Smith, R.J., Sormani, M. and Treß, R.	The Galactic dynamics revealed by the filamentary structure in atomic hydrogen emission [BibTeX]	2022	Astronomy &ampmathsemicolon Astrophysics Vol. 662, pp. A96	article	DOI
BibTeX: @article{Soler2022, author = {J. D. Soler and M.-A. Miville-Deschênes and S. Molinari and R. S. Klessen and P. Hennebelle and L. Testi and N. M. McClure-Griffiths and H. Beuther and D. Elia and E. Schisano and A. Traficante and P. Girichidis and S. C. O. Glover and R. J. Smith and M. Sormani and R. Treß}, title = {The Galactic dynamics revealed by the filamentary structure in atomic hydrogen emission}, journal = {Astronomy &ampmathsemicolon Astrophysics}, publisher = {EDP Sciences}, year = {2022}, volume = {662}, pages = {A96}, doi = {https://doi.org/10.1051/0004-6361/202243334} }
Soni, K., Kempf, G., Manalastas-Cantos, K., Hendricks, A., Flemming, D., Guizetti, J., Simon, B., Frischknecht, F., Svergun, D.I., Wild, K. and Sinning, I.	Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation [BibTeX]	2021	Communications Biology Vol. 4(1)	article	DOI
BibTeX: @article{Soni2021, author = {Komal Soni and Georg Kempf and Karen Manalastas-Cantos and Astrid Hendricks and Dirk Flemming and Julien Guizetti and Bernd Simon and Friedrich Frischknecht and Dmitri I. Svergun and Klemens Wild and Irmgard Sinning}, title = {Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation}, journal = {Communications Biology}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {4}, number = {1}, doi = {https://doi.org/10.1038/s42003-021-02132-y} }
Soni, K., Sivadas, A., Horvath, A., Dobrev, N., Hayashi, R., Kiss, L., Simon, B., Wild, K., Sinning, I. and Fischer, T.	Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex [Abstract] [BibTeX]	2023	Nature Communications Vol. 14(1)	article	DOI URL
Abstract: AbstractThe S. pombe orthologue of the human PAXT connection, Mtl1-Red1 Core (MTREC), is an eleven-subunit complex that targets cryptic unstable transcripts (CUTs) to the nuclear RNA exosome for degradation. It encompasses the canonical poly(A) polymerase Pla1, responsible for polyadenylation of nascent RNA transcripts as part of the cleavage and polyadenylation factor (CPF/CPSF). In this study we identify and characterise the interaction between Pla1 and the MTREC complex core component Red1 and analyse the functional relevance of this interaction in vivo. Our crystal structure of the Pla1-Red1 complex shows that a 58-residue fragment in Red1 binds to the RNA recognition motif domain of Pla1 and tethers it to the MTREC complex. Structure-based Pla1-Red1 interaction mutations show that Pla1, as part of MTREC complex, hyper-adenylates CUTs for their efficient degradation. Interestingly, the Red1-Pla1 interaction is also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3’-end processing machineries.
BibTeX: @article{Soni2023, author = {Komal Soni, Anusree Sivadas, Attila Horvath, Nikolay Dobrev, Rippei Hayashi, Leo Kiss, Bernd Simon, Klemens Wild, Irmgard Sinning, Tamás Fischer}, title = {Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2023}, volume = {14}, number = {1}, url = {https://www.nature.com/articles/s41467-023-36402-6.pdf}, doi = {https://doi.org/10.1038/s41467-023-36402-6} }
Sormani, M.C., Sobacchi, E., Shore, S.N., Treß, R.G. and Klessen, R.S.	Periodicity makes galactic shocks unstable – I. Linear analysis [BibTeX]	2017	Monthly Notices of the Royal Astronomical Society Vol. 471(3), pp. 2932-2951	article	DOI URL
BibTeX: @article{Sormani2017, author = {Mattia C. Sormani, Emanuele Sobacchi, Steven N. Shore, Robin G. Treß, Ralf S. Klessen}, title = {Periodicity makes galactic shocks unstable – I. Linear analysis}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2017}, volume = {471}, number = {3}, pages = {2932--2951}, url = {http://academic.oup.com/mnras/article-pdf/471/3/2932/19510740/stx1678.pdf}, doi = {https://doi.org/10.1093/mnras/stx1678} }
Sormani, M.C., Sobacchi, E., Pezzulli, G., Binney, J. and Klessen, R.S.	Models of rotating coronae [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 481(3), pp. 3370-3381	article	DOI
BibTeX: @article{Sormani2018, author = {Mattia C Sormani and Emanuele Sobacchi and Gabriele Pezzulli and James Binney and Ralf S Klessen}, title = {Models of rotating coronae}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {481}, number = {3}, pages = {3370--3381}, doi = {https://doi.org/10.1093/mnras/sty2500} }
Sormani, M.C., Sobacchi, E., Fragkoudi, F., Ridley, M., Treß, R.G., Glover, S.C.O. and Klessen, R.S.	A dynamical mechanism for the origin of nuclear rings [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 481(1), pp. 2-19	article	DOI
BibTeX: @article{Sormani2018a, author = {Mattia C Sormani and Emanuele Sobacchi and Francesca Fragkoudi and Matthew Ridley and Robin G Treß and Simon C O Glover and Ralf S Klessen}, title = {A dynamical mechanism for the origin of nuclear rings}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2018}, volume = {481}, number = {1}, pages = {2--19}, doi = {https://doi.org/10.1093/mnras/sty2246} }
Sormani, M.C., Treß, R.G., Glover, S.C.O., Klessen, R.S., Barnes, A.T., Battersby, C.D., Clark, P.C., Hatchfield, H.P. and Smith, R.J.	The geometry of the gas surrounding the Central Molecular Zone: on the origin of localized molecular clouds with extreme velocity dispersions [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 488(4), pp. 4663-4673	article	DOI
BibTeX: @article{Sormani2019, author = {Mattia C Sormani and Robin G Treß and Simon C O Glover and Ralf S Klessen and Ashley T Barnes and Cara D Battersby and Paul C Clark and H Perry Hatchfield and Rowan J Smith}, title = {The geometry of the gas surrounding the Central Molecular Zone: on the origin of localized molecular clouds with extreme velocity dispersions}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {488}, number = {4}, pages = {4663--4673}, doi = {https://doi.org/10.1093/mnras/stz2054} }
Sormani, M.C., Magorrian, J., Nogueras-Lara, F., Neumayer, N., Schönrich, R., Klessen, R.S. and Mastrobuono-Battisti, A.	Jeans modelling of the Milky Way's nuclear stellar disc [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 499(1), pp. 7-24	article	DOI
BibTeX: @article{Sormani2020a, author = {Mattia C Sormani and John Magorrian and Francisco Nogueras-Lara and Nadine Neumayer and Ralph Schönrich and Ralf S Klessen and Alessandra Mastrobuono-Battisti}, title = {Jeans modelling of the Milky Way's nuclear stellar disc}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {499}, number = {1}, pages = {7--24}, doi = {https://doi.org/10.1093/mnras/staa2785} }
Sormani, M.C., Sanders, J.L., Fritz, T.K., Smith, L.C., Gerhard, O., Schödel, R., Magorrian, J., Neumayer, N., Nogueras-Lara, F., Feldmeier-Krause, A., Mastrobuono-Battisti, A., Schultheis, M., Shahzamanian, B., Vasiliev, E., Klessen, R.S., Lucas, P. and Minniti, D.	Self-consistent modelling of the Milky Way's nuclear stellar disc [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society Vol. 512(2), pp. 1857-1884	article	DOI
BibTeX: @article{Sormani2022, author = {Mattia C Sormani, Jason L Sanders, Tobias K Fritz, Leigh C Smith, Ortwin Gerhard, Rainer Schödel, John Magorrian, Nadine Neumayer, Francisco Nogueras-Lara, Anja Feldmeier-Krause, Alessandra Mastrobuono-Battisti, Mathias Schultheis, Banafsheh Shahzamanian, Eugene Vasiliev, Ralf S Klessen, Philip Lucas, Dante Minniti}, title = {Self-consistent modelling of the Milky Way's nuclear stellar disc}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {512}, number = {2}, pages = {1857--1884}, doi = {https://doi.org/10.1093/mnras/stac639} }
Sormani, M.C., Gerhard, O., Portail, M., Vasiliev, E. and Clarke, J.	The stellar mass distribution of the Milky Way’s bar: an analytical model [Abstract] [BibTeX]	2022	Monthly Notices of the Royal Astronomical Society: Letters Vol. 514(1), pp. L1-L5	article	DOI
Abstract: ABSTRACT We present an analytic model of the stellar mass distribution of the Milky Way bar. The model is obtained by fitting a multicomponent parametric density distribution to a made-to-measure N-body model of Portail et al., constructed to match a variety of density and kinematics observational data. The analytic model reproduces in detail the 3D density distribution of the N-body bar including the X-shape. The model and the gravitational potential it generates are available as part of the software package agama for galactic dynamics, and can be readily used for orbit integrations, hydrodynamical simulations, or other applications.
BibTeX: @article{Sormani2022a, author = {Mattia C Sormani, Ortwin Gerhard, Matthieu Portail, Eugene Vasiliev, Jonathan Clarke}, title = {The stellar mass distribution of the Milky Way’s bar: an analytical model}, journal = {Monthly Notices of the Royal Astronomical Society: Letters}, publisher = {Oxford University Press (OUP)}, year = {2022}, volume = {514}, number = {1}, pages = {L1--L5}, doi = {https://doi.org/10.1093/mnrasl/slac046} }
Sormani, M.C., Barnes, A.T., Sun, J., Stuber, S.K., Schinnerer, E., Emsellem, E., Leroy, A.K., Glover, S.C.O., Henshaw, J.D., Meidt, S.E., Neumann, J., Querejeta, M., Williams, T.G., Bigiel, F., Eibensteiner, C., Fragkoudi, F., Levy, R.C., Grasha, K., Klessen, R.S., Kruijssen, J.M.D., Neumayer, N., Pinna, F., Rosolowsky, E.W., Smith, R.J., Teng, Y.-H., Tress, R.G. and Watkins, E.J.	Fuelling the nuclear ring of NGC 1097 [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 523(2), pp. 2918-2927	article	DOI
BibTeX: @article{Sormani2023, author = {Mattia C Sormani and Ashley T Barnes and Jiayi Sun and Sophia K Stuber and Eva Schinnerer and Eric Emsellem and Adam K Leroy and Simon C O Glover and Jonathan D Henshaw and Sharon E Meidt and Justus Neumann and Miguel Querejeta and Thomas G Williams and Frank Bigiel and Cosima Eibensteiner and Francesca Fragkoudi and Rebecca C Levy and Kathryn Grasha and Ralf S Klessen and J M Diederik Kruijssen and Nadine Neumayer and Francesca Pinna and Erik W Rosolowsky and Rowan J Smith and Yu-Hsuan Teng and Robin G Tress and Elizabeth J Watkins}, title = {Fuelling the nuclear ring of NGC 1097}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {523}, number = {2}, pages = {2918--2927}, doi = {https://doi.org/10.1093/mnras/stad1554} }
Spahn, C., Herrmannsdörfer, F., Kuner, T. and Heilemann, M.	Temporal accumulation analysis provides simplified artifact-free analysis of membrane-protein nanoclusters [BibTeX]	2016	Nature Methods Vol. 13(12), pp. 963	article	DOI
BibTeX: @article{Spahn2016, author = {Spahn, Christoph and Herrmannsdörfer, Frank and Kuner, Thomas and Heilemann, Mike}, title = {Temporal accumulation analysis provides simplified artifact-free analysis of membrane-protein nanoclusters}, journal = {Nature Methods}, publisher = {Nature Publishing Group}, year = {2016}, volume = {13}, number = {12}, pages = {963}, doi = {https://doi.org/10.1038/nmeth.4065} }
Spanier, F., Schreiner, C. and Schlickeiser, R.	Determining pitch-angle diffusion coefficients for electrons in whistler turbulence [Abstract] [BibTeX]	2022	Physics Vol. 4(1), pp. 80-103	article	DOI URL
Abstract: Transport of energetic electrons in the heliosphere is governed by resonant interaction with plasma waves, for for electrons with sub-GeV kinetic energies specifically with dispersive modes in the whistler regime. We have performed Particle in Cell simulations of kinetic turbulence with test-particle electrons. The pitch-angle diffusions coefficients of these test-particles have been analyzed and compared to an analytical model for left- and right-handed polarized wavemodes.
BibTeX: @article{Spanier2022, author = {Felix Spanier and Cedric Schreiner and Reinhard Schlickeiser}, title = {Determining pitch-angle diffusion coefficients for electrons in whistler turbulence}, journal = {Physics}, publisher = {MDPI AG}, year = {2022}, volume = {4}, number = {1}, pages = {80--103}, url = {https://www.mdpi.com/2624-8174/4/1/8/pdf}, doi = {https://doi.org/10.3390/physics4010008} }
Steinbuss, G., Kriegsmann, M., Zgorzelski, C., Brobeil, A., Goeppert, B., Dietrich, S., Mechtersheimer, G. and Kriegsmann, K.	Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images [BibTeX]	2021	Cancers Vol. 13(10), pp. 2419	article	DOI
BibTeX: @article{Steinbuss2021, author = {Georg Steinbuss and Mark Kriegsmann and Christiane Zgorzelski and Alexander Brobeil and Benjamin Goeppert and Sascha Dietrich and Gunhild Mechtersheimer and Katharina Kriegsmann}, title = {Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images}, journal = {Cancers}, publisher = {MDPI AG}, year = {2021}, volume = {13}, number = {10}, pages = {2419}, doi = {https://doi.org/10.3390/cancers13102419} }
Sticht, C., Torre, C.D.L., Parveen, A. and Gretz, N.	miRWalk: An online resource for prediction of microRNA binding sites [BibTeX]	2018	PLOS ONE Vol. 13	article	DOI
BibTeX: @article{Sticht2018, author = {Carsten Sticht and Carolina De La Torre and Alisha Parveen and Norbert Gretz}, title = {miRWalk: An online resource for prediction of microRNA binding sites}, journal = {PLOS ONE}, publisher = {Public Library of Science (PLoS)}, year = {2018}, volume = {13}, doi = {https://doi.org/10.1371/journal.pone.0206239} }
Stitz, M., Kuster, D., Reinert, M., Schepetilnikov, M., Berthet, B., Janocha, D., Artins, A., Boix, M., Henriques, R., Pfeiffer, A., Lohmann, J., Gaquerel, E. and Maizel, A.	TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana [Abstract] [BibTeX]	2022	bioRxiv	article	DOI
Abstract: AbstractPlants post-embryonic organogenesis requires matching the available metabolic resources to the developmental programs. The root system is determined by the formation of lateral roots (LR), which in Arabidopsis thaliana entails the auxin-induced activation of founder cells located in the pericycle. While the allocation of sugars to roots influences root branching, how sugar availability is sensed for auxin-triggered formation of LRs remains unknown. Here, we combine metabolic profiling with cell-specific genetic interference to show that LR formation is an important sink for carbohydrate accompanied by a switch to glycolysis. We show that the target-of-rapamycin (TOR) kinase is locally activated in the pericycle and the founder cells and that both chemical and genetic inhibition of TOR kinase lead to a block of LR initiation. TOR marginally affects the auxin-induced transcriptional response of the pericycle but modulates the translation of ARF19, ARF7 and LBD16, three key targets of auxin signalling. These data place TOR as a gatekeeper for post-embryonic LR formation that integrates local auxin-dependent pathways with systemic metabolic signals, modulating the translation of auxin induced gene expression.
BibTeX: @article{Stitz2022, author = {Michael Stitz, David Kuster, Maximilian Reinert, Mikhail Schepetilnikov, Béatrice Berthet, Denis Janocha, Anthony Artins, Marc Boix, Rossana Henriques, Anne Pfeiffer, Jan Lohmann, Emmanuel Gaquerel, Alexis Maizel}, title = {TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana}, journal = {bioRxiv}, year = {2022}, doi = {https://doi.org/10.1101/2022.03.29.486207} }
Stöckle, D., Reyes-Hernández, B.J., Barro, A.V., Nenadic, M., Winter, Z., Marc-Martin, S., Bald, L., Ursache, R., Fujita, S., Maizel, A. and Vermeer, J.E.	Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis [BibTeX]	2021		article	DOI
BibTeX: @article{Stoeckle2021, author = {Dorothee Stöckle and Blanca Jazmin Reyes-Hernández and Amaya Vilches Barro and Milica Nenadic and Zsófia Winter and Sophie Marc-Martin and Lotte Bald and Robertas Ursache and Satoshi Fujita and Alexis Maizel and Joop EM Vermeer}, title = {Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis}, publisher = {Cold Spring Harbor Laboratory}, year = {2021}, doi = {https://doi.org/10.1101/2021.09.09.459674} }
Stöckle, D., Reyes-Hernández, B.J., Barro, A.V., Nenadić, M., Winter, Z., Marc-Martin, S., Bald, L., Ursache, R., Fujita, S., Maizel, A. and Vermeer, J.E.	Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis [Abstract] [BibTeX]	2022	Science Advances Vol. 8(6)	article	DOI
Abstract: Precise coordination between cells and tissues is essential for differential growth in plants. During lateral root formation in Arabidopsis thaliana , the endodermis is actively remodeled to allow outgrowth of the new organ. Here, we show that microtubule arrays facing lateral root founder cells display a higher order compared to arrays on the opposite side of the same cell, and this asymmetry is required for endodermal remodeling and lateral root initiation. We identify that MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is necessary for the establishment of this spatially defined microtubule organization and endodermis remodeling and thus contributes to lateral root morphogenesis. We propose that MAP70-5 and cortical microtubule arrays in the endodermis integrate the mechanical signals generated by lateral root outgrowth, facilitating the channeling of organogenesis.
BibTeX: @article{Stoeckle2022, author = {Dorothee Stöckle, Blanca Jazmin Reyes-Hernández, Amaya Vilches Barro, Milica Nenadić, Zsofiá Winter, Sophie Marc-Martin, Lotte Bald, Robertas Ursache, Satoshi Fujita, Alexis Maizel, Joop EM Vermeer}, title = {Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis}, journal = {Science Advances}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2022}, volume = {8}, number = {6}, doi = {https://doi.org/10.1126/sciadv.abm4974} }
Stolper, J., Ambrosio, E.M., Danciu, D.-P., Buono, L., Elliott, D.A., Naruse, K., Mart\inez-Morales, J.R., Marciniak-Czochra, A. and Centanin, L.	Stem cell topography splits growth and homeostatic functions in the fish gill [BibTeX]	2019	eLife Vol. 8	article	DOI
BibTeX: @article{Stolper2019, author = {Julian Stolper and Elizabeth Mayela Ambrosio and Diana-Patricia Danciu and Lorena Buono and David A Elliott and Kiyoshi Naruse and Juan R Mart\inez-Morales and Anna Marciniak-Czochra and Lazaro Centanin}, title = {Stem cell topography splits growth and homeostatic functions in the fish gill}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2019}, volume = {8}, doi = {https://doi.org/10.7554/elife.43747} }
Strobel, N., Droseros, N., Köntges, W., Seiberlich, M., Pietsch, M., Schlisske, S., Lindheimer, F., Schröder, R.R., Lemmer, U., Pfannmöller, M., Banerji, N. and Hernandez-Sosa, G.	Color-Selective Printed Organic Photodiodes for Filterless Multichannel Visible Light Communication [BibTeX]	2020	Advanced Materials Vol. 32(12), pp. 1908258	article	DOI
BibTeX: @article{Strobel2020, author = {Noah Strobel and Nikolaos Droseros and Wolfgang Köntges and Mervin Seiberlich and Manuel Pietsch and Stefan Schlisske and Felix Lindheimer and Rasmus R. Schröder and Uli Lemmer and Martin Pfannmöller and Natalie Banerji and Gerardo Hernandez-Sosa}, title = {Color-Selective Printed Organic Photodiodes for Filterless Multichannel Visible Light Communication}, journal = {Advanced Materials}, publisher = {Wiley}, year = {2020}, volume = {32}, number = {12}, pages = {1908258}, doi = {https://doi.org/10.1002/adma.201908258} }
Stuber, S.K., Schinnerer, E., Williams, T.G., Querejeta, M., Meidt, S., Emsellem, É., Barnes, A., Klessen, R.S., Leroy, A.K., Neumann, J., Sormani, M.C., Bigiel, F., Chevance, M., Dale, D., Faesi, C., Glover, S.C.O., Grasha, K., Kruijssen, J.M.D., Liu, D., Pan, H.-a., Pety, J., Pinna, F., Saito, T., Usero, A. and Watkins, E.J.	The gas morphology of nearby star-forming galaxies [BibTeX]	2023	Astronomy &ampmathsemicolon Astrophysics Vol. 676, pp. A113	article	DOI
BibTeX: @article{Stuber2023, author = {Sophia K. Stuber and Eva Schinnerer and Thomas G. Williams and Miguel Querejeta and Sharon Meidt and Éric Emsellem and Ashley Barnes and Ralf S. Klessen and Adam K. Leroy and Justus Neumann and Mattia C. Sormani and Frank Bigiel and Mélanie Chevance and Danny Dale and Christopher Faesi and Simon C. O. Glover and Kathryn Grasha and J. M. Diederik Kruijssen and Daizhong Liu and Hsi-an Pan and Jérôme Pety and Francesca Pinna and Toshiki Saito and Antonio Usero and Elizabeth J. Watkins}, title = {The gas morphology of nearby star-forming galaxies}, journal = {Astronomy &ampmathsemicolon Astrophysics}, publisher = {EDP Sciences}, year = {2023}, volume = {676}, pages = {A113}, doi = {https://doi.org/10.1051/0004-6361/202346318} }
Studier-Fischer, A., Seidlitz, S., Sellner, J., Wiesenfarth, M., Ayala, L., Özdemir, B., Odenthal, J., Knödler, S., Kowalewski, K., Haney, C., Camplisson, I., Dietrich, M., Schmidt, K., Salg, G., Kenngott, H., Adler, T., Schreck, N., Kopp-Schneider, A., Maier-Hein, K., Maier-Hein, L., Müller-Stich, B. and Nickel, F.	Spectral organ fingerprints for intraoperative tissue classification with hyperspectral imaging [BibTeX]	2021		article	DOI
BibTeX: @article{StudierFischer2021, author = {A. Studier-Fischer and S. Seidlitz and J. Sellner and M. Wiesenfarth and L. Ayala and B. Özdemir and J. Odenthal and S. Knödler and K.F. Kowalewski and C.M. Haney and I. Camplisson and M. Dietrich and K. Schmidt and G.A. Salg and H.G. Kenngott and T.J. Adler and N. Schreck and A. Kopp-Schneider and K. Maier-Hein and L. Maier-Hein and B.P. Müller-Stich and F. Nickel}, title = {Spectral organ fingerprints for intraoperative tissue classification with hyperspectral imaging}, publisher = {Cold Spring Harbor Laboratory}, year = {2021}, doi = {https://doi.org/10.1101/2021.11.24.469943} }
Studier-Fischer, A., Seidlitz, S., Sellner, J., Özdemir, B., Wiesenfarth, M., Ayala, L., Odenthal, J., Knödler, S., Kowalewski, K.F., Haney, C.M., Camplisson, I., Dietrich, M., Schmidt, K., Salg, G.A., Kenngott, H.G., Adler, T.J., Schreck, N., Kopp-Schneider, A., Maier-Hein, K., Maier-Hein, L., Müller-Stich, B.P. and Nickel, F.	Spectral organ fingerprints for machine learning-based intraoperative tissue classification with hyperspectral imaging in a porcine model [Abstract] [BibTeX]	2022	Scientific Reports Vol. 12(1)	article	DOI URL
Abstract: AbstractVisual discrimination of tissue during surgery can be challenging since different tissues appear similar to the human eye. Hyperspectral imaging (HSI) removes this limitation by associating each pixel with high-dimensional spectral information. While previous work has shown its general potential to discriminate tissue, clinical translation has been limited due to the method’s current lack of robustness and generalizability. Specifically, the scientific community is lacking a comprehensive spectral tissue atlas, and it is unknown whether variability in spectral reflectance is primarily explained by tissue type rather than the recorded individual or specific acquisition conditions. The contribution of this work is threefold: (1) Based on an annotated medical HSI data set (9059 images from 46 pigs), we present a tissue atlas featuring spectral fingerprints of 20 different porcine organs and tissue types. (2) Using the principle of mixed model analysis, we show that the greatest source of variability related to HSI images is the organ under observation. (3) We show that HSI-based fully-automatic tissue differentiation of 20 organ classes with deep neural networks is possible with high accuracy (> 95%). We conclude from our study that automatic tissue discrimination based on HSI data is feasible and could thus aid in intraoperative decisionmaking and pave the way for context-aware computer-assisted surgery systems and autonomous robotics.
BibTeX: @article{StudierFischer2022, author = {Alexander Studier-Fischer, Silvia Seidlitz, Jan Sellner, Berkin Özdemir, Manuel Wiesenfarth, Leonardo Ayala, Jan Odenthal, Samuel Knödler, Karl Friedrich Kowalewski, Caelan Max Haney, Isabella Camplisson, Maximilian Dietrich, Karsten Schmidt, Gabriel Alexander Salg, Hannes Götz Kenngott, Tim Julian Adler, Nicholas Schreck, Annette Kopp-Schneider, Klaus Maier-Hein, Lena Maier-Hein, Beat Peter Müller-Stich, Felix Nickel}, title = {Spectral organ fingerprints for machine learning-based intraoperative tissue classification with hyperspectral imaging in a porcine model}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {12}, number = {1}, url = {https://www.nature.com/articles/s41598-022-15040-w.pdf}, doi = {https://doi.org/10.1038/s41598-022-15040-w} }
Sun, Q., Picascia, T., ul Maula Khan, A., Brenna, C., Heuveline, V., Schmaus, A., Sleeman, J.P. and Gretz, N.	Application of ethyl cinnamate based optical tissue clearing and expansion microscopy combined with retrograde perfusion for 3D lung imaging [BibTeX]	2020	Experimental Lung Research Vol. 46(10), pp. 393-408	article	DOI
BibTeX: @article{Sun2020, author = {Quanchao Sun, Tiziana Picascia, Arif ul Maula Khan, Cinzia Brenna, Vincent Heuveline, Anja Schmaus, Jonathan P. Sleeman, Norbert Gretz}, title = {Application of ethyl cinnamate based optical tissue clearing and expansion microscopy combined with retrograde perfusion for 3D lung imaging}, journal = {Experimental Lung Research}, publisher = {Informa UK Limited}, year = {2020}, volume = {46}, number = {10}, pages = {393--408}, doi = {https://doi.org/10.1080/01902148.2020.1829183} }
Sun, Q., Tiziana, P., ul Maula Khan, A., Heuveline, V. and Gretz, N.	A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice [BibTeX]	2021	International Journal of Experimental Pathology Vol. 102(4-5), pp. 218-227	article	DOI
BibTeX: @article{Sun2021, author = {Quanchao Sun, Picascia Tiziana, Arif ul Maula Khan, Vincent Heuveline, Norbert Gretz}, title = {A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice}, journal = {International Journal of Experimental Pathology}, publisher = {Wiley}, year = {2021}, volume = {102}, number = {4-5}, pages = {218--227}, doi = {https://doi.org/10.1111/iep.12399} }
Sunbul, M., Lackner, J., Martin, A., Englert, D., Hacene, B., Grün, F., Nienhaus, K., Nienhaus, G.U. and Jäschke, A.	Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics [BibTeX]	2021	Nature Biotechnology Vol. 39(6), pp. 686-690	article	DOI
BibTeX: @article{Sunbul2021, author = {Murat Sunbul and Jens Lackner and Annabell Martin and Daniel Englert and Benjamin Hacene and Franziska Grün and Karin Nienhaus and G. Ulrich Nienhaus and Andres Jäschke}, title = {Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics}, journal = {Nature Biotechnology}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {39}, number = {6}, pages = {686--690}, doi = {https://doi.org/10.1038/s41587-020-00794-3} }
Suri, S., Sánchez-Monge, Á., Schilke, P., Clarke, S.D., Smith, R.J., Ossenkopf-Okada, V., Klessen, R., Padoan, P., Goldsmith, P., Arce, H.G., Bally, J., Carpenter, J.M., Ginsburg, A., Johnstone, D., Kauffmann, J., Kong, S., Lis, D.C., Mairs, S., Pillai, T., Pineda, J.E. and Duarte-Cabral, A.	The CARMA-NRO Orion Survey [BibTeX]	2019	Astronomy & Astrophysics Vol. 623	article	DOI
BibTeX: @article{Suri2019, author = {Sümeyye Suri and Álvaro Sánchez-Monge and Peter Schilke and Seamus D. Clarke and Rowan J. Smith and Volker Ossenkopf-Okada and Ralf Klessen and Paolo Padoan and Paul Goldsmith and Héctor G. Arce and John Bally and John M. Carpenter and Adam Ginsburg and Doug Johnstone and Jens Kauffmann and Shuo Kong and Dariusz C. Lis and Steve Mairs and Thushara Pillai and Jaime E. Pineda and Ana Duarte-Cabral}, title = {The CARMA-NRO Orion Survey}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, year = {2019}, volume = {623}, doi = {https://doi.org/10.1051/0004-6361/201834049} }
Szaroszyk, M., Kattih, B., Martin-Garrido, A., Trogisch, F.A., Dittrich, G.M., Grund, A., Abouissa, A., Derlin, K., Meier, M., Holler, T., Korf-Klingebiel, M., Völker, K., Macedo, T.G., Tortola, C.P., Boschmann, M., Huang, N., Froese, N., Zwadlo, C., Mohammadi, M.M., Luo, X., Wagner, M., Cordero, J., Geffers, R., Batkai, S., Thum, T., Bork, N., Nikolaev, V.O., Müller, O.J., Katus, H.A., El-Armouche, A., Kraft, T., Springer, J., Dobreva, G., Wollert, K.C., Fielitz, J., von Haehling, S., Kuhn, M., Bauersachs, J. and Heineke, J.	Skeletal muscle derived Musclin protects the heart during pathological overload [BibTeX]	2022	Nature Communications Vol. 13(1)	article	DOI URL
BibTeX: @article{Szaroszyk2022, author = {Malgorzata Szaroszyk, Badder Kattih, Abel Martin-Garrido, Felix A. Trogisch, Gesine M. Dittrich, Andrea Grund, Aya Abouissa, Katja Derlin, Martin Meier, Tim Holler, Mortimer Korf-Klingebiel, Katharina Völker, Tania Garfias Macedo, Cristina Pablo Tortola, Michael Boschmann, Nora Huang, Natali Froese, Carolin Zwadlo, Mona Malek Mohammadi, Xiaojing Luo, Michael Wagner, Julio Cordero, Robert Geffers, Sandor Batkai, Thomas Thum, Nadja Bork, Viacheslav O. Nikolaev, Oliver J. Müller, Hugo A. Katus, Ali El-Armouche, Theresia Kraft, Jochen Springer, Gergana Dobreva, Kai C. Wollert, Jens Fielitz, Stephan von Haehling, Michaela Kuhn, Johann Bauersachs, Joerg Heineke}, title = {Skeletal muscle derived Musclin protects the heart during pathological overload}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {13}, number = {1}, url = {https://www.nature.com/articles/s41467-021-27634-5.pdf}, doi = {https://doi.org/10.1038/s41467-021-27634-5} }
Tabar, A.N., Azizi, H., Karoii, D.H. and Skutella, T.	Testicular Localization and Potential Function of Vimentin Positive Cells during Spermatogonial Differentiation Stages [Abstract] [BibTeX]	2022	Animals Vol. 12(3), pp. 268	article	DOI URL
Abstract: Vimentin is a type of intermediate filament (IF) and one of the first filaments expressed in spermatogenesis. Vimentin plays numerous roles, consisting of the determination of cell shape, differentiation, cell motility, the maintenance of cell junctions, intracellular trafficking, and assisting in keeping normal differentiating germ cell morphology. This study investigated the vimentin expression in two populations of undifferentiated and differentiated spermatogonia. We examined vimentin expression in vivo and in vitro by immunocytochemistry (ICC), immunohistochemistry (IMH), and Fluidigm real-time polymerase chain reaction. IMH data showed that the high vimentin expression was localized in the middle of seminiferous tubules, and low expression was in the basal membrane. ICC analysis of the colonies by isolated differentiated spermatogonia indicated the positive expression for the vimentin antibody, but vimentin’s expression level in the undifferentiated population was negative under in vitro conditions. Fluidigm real-time PCR analysis showed significant vimentin expression in differentiated spermatogonia compared to undifferentiated spermatogonia (p < 0.05). Our results showed that vimentin is upregulated in the differentiation stages of spermatogenesis, proving that vimentin is an intermediate filament with crucial roles in the differentiation stages of testicular germ cells. These results support the advanced investigations of the spermatogenic process, both in vitro and in vivo.
BibTeX: @article{Tabar2022, author = {Amirreza Niazi Tabar, Hossein Azizi, Danial Hashemi Karoii, Thomas Skutella}, title = {Testicular Localization and Potential Function of Vimentin Positive Cells during Spermatogonial Differentiation Stages}, journal = {Animals}, publisher = {MDPI AG}, year = {2022}, volume = {12}, number = {3}, pages = {268}, url = {https://www.mdpi.com/2076-2615/12/3/268/pdf}, doi = {https://doi.org/10.3390/ani12030268} }
Tail, M., Zhang, H., Zheng, G., Hatami, M., Skutella, T., Unterberg, A., Zweckberger, K. and Younsi, A.	The Sonic Hedgehog Pathway Modulates Survival, Proliferation, and Differentiation of Neural Progenitor Cells under Inflammatory Stress In Vitro [Abstract] [BibTeX]	2022	Cells Vol. 11(4), pp. 736	article	DOI URL
Abstract: The Sonic Hedgehog protein (Shh) has been extensively researched since its discovery in 1980. Its crucial role in early neurogenesis and endogenous stem cells of mature brains, as well as its recently described neuroprotective features, implicate further important effects on neuronal homeostasis. Here, we investigate its potential role in the survival, proliferation, and differentiation of neural precursors cells (NPCs) under inflammatory stress as a potential adjunct for NPC-transplantation strategies in spinal cord injury (SCI) treatment. To this end, we simulated an inflammatory environment in vitro using lipopolysaccharide (LPS) and induced the Shh-pathway using recombinant Shh or blocked it using Cyclopamine, a potent Smo inhibitor. We found that Shh mediates the proliferation and neuronal differentiation potential of NPCs in vitro, even in an inflammatory stress environment mimicking the subacute phase after SCI. At the same time, our results indicate that a reduction of the Shh-pathway activation by blockage with Cyclopamine is associated with reduced NPC-survival, reduced neuronal differentiation and increased astroglial differentiation. Shh might thus, play a role in endogenous NPC-mediated neuroregeneration or even be a potent conjunct to NPC-based therapies in the inflammatory environment after SCI.
BibTeX: @article{Tail2022, author = {Mohamed Tail, Hao Zhang, Guoli Zheng, Maryam Hatami, Thomas Skutella, Andreas Unterberg, Klaus Zweckberger, Alexander Younsi}, title = {The Sonic Hedgehog Pathway Modulates Survival, Proliferation, and Differentiation of Neural Progenitor Cells under Inflammatory Stress In Vitro}, journal = {Cells}, publisher = {MDPI AG}, year = {2022}, volume = {11}, number = {4}, pages = {736}, url = {https://www.mdpi.com/2073-4409/11/4/736/pdf}, doi = {https://doi.org/10.3390/cells11040736} }
Tan, L.L., Pelzer, P., Heinl, C., Tang, W., Gangadharan, V., Flor, H., Sprengel, R., Kuner, T. and Kuner, R.	A pathway from midcingulate cortex to posterior insula gates nociceptive hypersensitivity [Abstract] [BibTeX]	2017	Nature neuroscience Vol. 20(11), pp. 1591	article	DOI
Abstract: The authors identify the midcingulate cortex as a region that gates nociceptive plasticity without modulating basal nociception or the affective component of acute pain in mice. They identify a novel pathway from the midcingulate cortex to the posterior insula that recruits descending serotonergic projections to facilitate nociception.
BibTeX: @article{Tan2017, author = {Tan, Linette Liqi and Pelzer, Patric and Heinl, Céline and Tang, Wannan and Gangadharan, Vijayan and Flor, Herta and Sprengel, Rolf and Kuner, Thomas and Kuner, Rohini}, title = {A pathway from midcingulate cortex to posterior insula gates nociceptive hypersensitivity}, journal = {Nature neuroscience}, publisher = {Nature Publishing Group}, year = {2017}, volume = {20}, number = {11}, pages = {1591}, doi = {https://doi.org/10.1038/nn.4645} }
Tan, L.L., Oswald, M.J., Heinl, C., Romero, O.A.R., Kaushalya, S.K., Monyer, H. and Kuner, R.	Gamma oscillations in somatosensory cortex recruit prefrontal and descending serotonergic pathways in aversion and nociception [Abstract] [BibTeX]	2019	Nature Communications Vol. 10(1)	article	DOI URL
Abstract: AbstractIn humans, gamma-band oscillations in the primary somatosensory cortex (S1) correlate with subjective pain perception. However, functional contributions to pain and the nature of underlying circuits are unclear. Here we report that gamma oscillations, but not other rhythms, are specifically strengthened independently of any motor component in the S1 cortex of mice during nociception. Moreover, mice with inflammatory pain show elevated resting gamma and alpha activity and increased gamma power in response to sub-threshold stimuli, in association with behavioral nociceptive hypersensitivity. Inducing gamma oscillations via optogenetic activation of parvalbumin-expressing inhibitory interneurons in the S1 cortex enhances nociceptive sensitivity and induces aversive avoidance behavior. Activity mapping identified a network of prefrontal cortical and subcortical centers whilst morphological tracing and pharmacological studies demonstrate the requirement of descending serotonergic facilitatory pathways in these pain-related behaviors. This study thus describes a mechanistic framework for modulation of pain by specific activity patterns in the S1 cortex.
BibTeX: @article{Tan2019, author = {Linette Liqi Tan, Manfred Josef Oswald, Céline Heinl, Oscar Andrés Retana Romero, Sanjeev Kumar Kaushalya, Hannah Monyer, Rohini Kuner}, title = {Gamma oscillations in somatosensory cortex recruit prefrontal and descending serotonergic pathways in aversion and nociception}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {10}, number = {1}, url = {https://www.nature.com/articles/s41467-019-08873-z.pdf}, doi = {https://doi.org/10.1038/s41467-019-08873-z} }
Teh, J.W., Grasha, K., Krumholz, M.R., Battisti, A.J., Calzetti, D., Rousseau-Nepton, L., Rhea, C., Adamo, A., Kennicutt, R.C., Grebel, E.K., Cook, D.O., Combes, F., Messa, M., Linden, S.T., Klessen, R.S., Vilchez, J.M., Fumagalli, M., McLeod, A., Smith, L.J., Chemin, L., Wang, J., Sabbi, E., Sacchi, E., Petric, A., Bruna, L.D. and Boselli, A.	Constraining the LyC escape fraction from LEGUS star clusters with SIGNALS H lessscpgreateriiless/scpgreater region observations: a pilot study of NGC 628 [BibTeX]	2023	Monthly Notices of the Royal Astronomical Society Vol. 524(1), pp. 1191-1210	article	DOI
BibTeX: @article{Teh2023, author = {Jia Wei Teh and Kathryn Grasha and Mark R Krumholz and Andrew J Battisti and Daniela Calzetti and Laurie Rousseau-Nepton and Carter Rhea and Angela Adamo and Robert C Kennicutt and Eva K Grebel and David O Cook and Francoise Combes and Matteo Messa and Sean T Linden and Ralf S Klessen and José M Vilchez and Michele Fumagalli and Anna McLeod and Linda J Smith and Laurent Chemin and Junfeng Wang and Elena Sabbi and Elena Sacchi and Andreea Petric and Lorenza Della Bruna and Alessandro Boselli}, title = {Constraining the LyC escape fraction from LEGUS star clusters with SIGNALS H lessscpgreateriiless/scpgreater region observations: a pilot study of NGC 628}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2023}, volume = {524}, number = {1}, pages = {1191--1210}, doi = {https://doi.org/10.1093/mnras/stad1780} }
Teng, Y.-H., Sandstrom, K.M., Sun, J., Gong, M., Bolatto, A.D., Chiang, I.-D., Leroy, A.K., Usero, A., Glover, S.C.O., Klessen, R.S., Liu, D., Querejeta, M., Schinnerer, E., Bigiel, F., Cao, Y., Chevance, M., Eibensteiner, C., Grasha, K., Israel, F.P., Murphy, E.J., Neumann, L., Pan, H.-A., Pinna, F., Sormani, M.C., Smith, J.D., Walter, F. and Williams, T.G.	The Physical Drivers and Observational Tracers of CO-to-Hlesssubgreater2less/subgreater Conversion Factor Variations in Nearby Barred Galaxy Centers [BibTeX]	2023	The Astrophysical Journal Vol. 950(2), pp. 119	article	DOI
BibTeX: @article{Teng2023, author = {Yu-Hsuan Teng and Karin M. Sandstrom and Jiayi Sun and Munan Gong and Alberto D. Bolatto and I-Da Chiang and Adam K. Leroy and Antonio Usero and Simon C. O. Glover and Ralf S. Klessen and Daizhong Liu and Miguel Querejeta and Eva Schinnerer and Frank Bigiel and Yixian Cao and Mélanie Chevance and Cosima Eibensteiner and Kathryn Grasha and Frank P. Israel and Eric J. Murphy and Lukas Neumann and Hsi-An Pan and Francesca Pinna and Mattia C. Sormani and J. D. Smith and Fabian Walter and Thomas G. Williams}, title = {The Physical Drivers and Observational Tracers of CO-to-Hlesssubgreater2less/subgreater Conversion Factor Variations in Nearby Barred Galaxy Centers}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2023}, volume = {950}, number = {2}, pages = {119}, doi = {https://doi.org/10.3847/1538-4357/accb86} }
Theilmann, M., Lemp, J.M., Winkler, V., Manne-Goehler, J., Marcus, M.E., Probst, C., Lopez-Arboleda, W.A., Ebert, C., Bommer, C., Mathur, M., Andall-Brereton, G., Bahendeka, S.K., Bovet, P., Farzadfar, F., Ghasemi, E., Mayige, M.T., Moghaddam, S.S., Mwangi, K.J., Naderimagham, S., Sturua, L., Atun, R., Davies, J.I., Bärnighausen, T., Vollmer, S. and Geldsetzer, P.	Patterns of tobacco use in low and middle income countries by tobacco product and sociodemographic characteristics: nationally representative survey data from 82 countries [BibTeX]	2022	BMJ, pp. e067582	article	DOI
BibTeX: @article{Theilmann2022, author = {Michaela Theilmann, Julia M Lemp, Volker Winkler, Jennifer Manne-Goehler, Maja E Marcus, Charlotte Probst, William A Lopez-Arboleda, Cara Ebert, Christian Bommer, Maya Mathur, Glennis Andall-Brereton, Silver K Bahendeka, Pascal Bovet, Farshad Farzadfar, Erfan Ghasemi, Mary T Mayige, Sahar Saeedi Moghaddam, Kibachio J Mwangi, Shohreh Naderimagham, Lela Sturua, Rifat Atun, Justine I Davies, Till Bärnighausen, Sebastian Vollmer, Pascal Geldsetzer}, title = {Patterns of tobacco use in low and middle income countries by tobacco product and sociodemographic characteristics: nationally representative survey data from 82 countries}, journal = {BMJ}, publisher = {BMJ}, year = {2022}, pages = {e067582}, doi = {https://doi.org/10.1136/bmj-2021-067582} }
Tijdeman, E. and Menzel, L.	Controls on the development and persistence of soil moisture drought across Southwestern Germany [BibTeX]	2020		article	DOI
BibTeX: @article{Tijdeman2020, author = {Erik Tijdeman and Lucas Menzel}, title = {Controls on the development and persistence of soil moisture drought across Southwestern Germany}, publisher = {Copernicus GmbH}, year = {2020}, doi = {https://doi.org/10.5194/hess-2020-307} }
Tirier, S.M., Park, J., Preußer, F., Amrhein, L., Gu, Z., Steiger, S., Mallm, J.-P., Waschow, M., Eismann, B., Gut, M., Gut, I.G., Rippe, K., Schlesner, M., Theis, F., Fuchs, C., Ball, C.R., Glimm, H., Eils, R. and Conrad, C.	pheno-seq -- linking morphological features to gene expression in 3D cell culture systems [Abstract] [BibTeX]	2018	bioRxiv	article	DOI URL
Abstract: 3D-culture systems have advanced cancer modeling by reflecting physiological characteristics of in-vivo tissues, but our understanding of functional intratumor heterogeneity including visual phenotypes and underlying gene expression is still limited. Single-cell RNA-sequencing is the method of choice to dissect transcriptional tumor cell heterogeneity in an unbiased way, but this approach is limited in correlating gene expression with contextual cellular phenotypes.To link morphological features and gene expression in 3D-culture systems, we present `pheno-seq' for integrated high-throughput imaging and transcriptomic profiling of clonal tumor spheroids. Specifically, we identify characteristic EMT expression signatures that are associated with invasive growth behavior in a 3D breast cancer model. Additionally, pheno-seq determined transcriptional programs containing lineage-specific markers that can be linked to heterogeneous proliferative capacity in a patient-derived 3D model of colorectal cancer. Finally, we provide evidence that pheno-seq identifies morphology-specific genes that are missed by scRNA-seq and inferred single-cell regulatory states without acquiring additional single cell expression profiles. We anticipate that directly linking molecular features with patho-phenotypes of cancer cells will improve the understanding of intratumor heterogeneity and consequently be useful for translational research.
BibTeX: @article{Tirier2018, author = {Tirier, Stephan M. and Park, Jeongbin and Preußer, Friedrich and Amrhein, Lisa and Gu, Zuguang and Steiger, Simon and Mallm, Jan-Philipp and Waschow, Marcel and Eismann, Björn and Gut, Marta and Gut, Ivo G. and Rippe, Karsten and Schlesner, Matthias and Theis, Fabian and Fuchs, Christiane and Ball, Claudia R. and Glimm, Hanno and Eils, Roland and Conrad, Christian}, title = {pheno-seq -- linking morphological features to gene expression in 3D cell culture systems}, journal = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, year = {2018}, url = {https://www.biorxiv.org/content/early/2018/09/12/311472}, doi = {https://doi.org/10.1101/311472} }
Tirier, S.M., Park, J., Preußer, F., Amrhein, L., Gu, Z., Steiger, S., Mallm, J.-P., Krieger, T., Waschow, M., Eismann, B., Gut, M., Gut, I.G., Rippe, K., Schlesner, M., Theis, F., Fuchs, C., Ball, C.R., Glimm, H., Eils, R. and Conrad, C.	Pheno-seq – linking visual features and gene expression in 3D cell culture systems [Abstract] [BibTeX]	2019	Scientific Reports Vol. 9(1)	article	DOI URL
Abstract: AbstractPatient-derived 3D cell culture systems are currently advancing cancer research since they potentiate the molecular analysis of tissue-like properties and drug response under well-defined conditions. However, our understanding of the relationship between the heterogeneity of morphological phenotypes and the underlying transcriptome is still limited. To address this issue, we here introduce “pheno-seq” to directly link visual features of 3D cell culture systems with profiling their transcriptome. As prototypic applications breast and colorectal cancer (CRC) spheroids were analyzed by pheno-seq. We identified characteristic gene expression signatures of epithelial-to-mesenchymal transition that are associated with invasive growth behavior of clonal breast cancer spheroids. Furthermore, we linked long-term proliferative capacity in a patient-derived model of CRC to a lowly abundant PROX1-positive cancer stem cell subtype. We anticipate that the ability to integrate transcriptome analysis and morphological patho-phenotypes of cancer cells will provide novel insight on the molecular origins of intratumor heterogeneity.
BibTeX: @article{Tirier2019, author = {Stephan M. Tirier, Jeongbin Park, Friedrich Preußer, Lisa Amrhein, Zuguang Gu, Simon Steiger, Jan-Philipp Mallm, Teresa Krieger, Marcel Waschow, Björn Eismann, Marta Gut, Ivo G. Gut, Karsten Rippe, Matthias Schlesner, Fabian Theis, Christiane Fuchs, Claudia R. Ball, Hanno Glimm, Roland Eils, Christian Conrad}, title = {Pheno-seq – linking visual features and gene expression in 3D cell culture systems}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {9}, number = {1}, url = {https://www.nature.com/articles/s41598-019-48771-4.pdf}, doi = {https://doi.org/10.1038/s41598-019-48771-4} }
Tirier, S.M., Mallm, J.-P., Steiger, S., Poos, A.M., Awwad, M.H.S., Giesen, N., Casiraghi, N., Susak, H., Bauer, K., Baumann, A., John, L., Seckinger, A., Hose, D., Müller-Tidow, C., Goldschmidt, H., Stegle, O., Hundemer, M., Weinhold, N., Raab, M.S. and Rippe, K.	Subclone-specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single‐cell transcriptomics [Abstract] [BibTeX]	2021	Nature Communications Vol. 12(1)	article	DOI URL
Abstract: AbstractVirtually all patients with multiple myeloma become unresponsive to treatment over time. Relapsed/refractory multiple myeloma (RRMM) is accompanied by the clonal evolution of myeloma cells with heterogeneous genomic aberrations and profound changes of the bone marrow microenvironment (BME). However, the molecular mechanisms that drive drug resistance remain elusive. Here, we analyze the heterogeneous tumor cell population and its complex interaction network with the BME of 20 RRMM patients by single cell RNA-sequencing before/after treatment. Subclones with chromosome 1q-gain express a specific transcriptomic signature and frequently expand during treatment. Furthermore, RRMM cells shape an immune suppressive BME by upregulation of inflammatory cytokines and close interaction with the myeloid compartment. It is characterized by the accumulation of PD1+ γδ T-cells and tumor-associated macrophages as well as the depletion of hematopoietic progenitors. Thus, our study resolves transcriptional features of subclones in RRMM and mechanisms of microenvironmental reprogramming with implications for clinical decision-making.
BibTeX: @article{Tirier2021, author = {Stephan M. Tirier, Jan-Philipp Mallm, Simon Steiger, Alexandra M. Poos, Mohamed H. S. Awwad, Nicola Giesen, Nicola Casiraghi, Hana Susak, Katharina Bauer, Anja Baumann, Lukas John, Anja Seckinger, Dirk Hose, Carsten Müller-Tidow, Hartmut Goldschmidt, Oliver Stegle, Michael Hundemer, Niels Weinhold, Marc S. Raab, Karsten Rippe}, title = {Subclone-specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single‐cell transcriptomics}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, url = {https://www.nature.com/articles/s41467-021-26951-z.pdf}, doi = {https://doi.org/10.1038/s41467-021-26951-z} }
Tisch, N., Freire-Valls, A., Yerbes, R., Paredes, I., Porta, S.L., Wang, X., Mart\in-Pérez, R., Castro, L., Wong, W.W.-L., Coultas, L., Strilic, B., Gröne, H.-J., Hielscher, T., Mogler, C., Adams, R.H., Heiduschka, P., Claesson-Welsh, L., Mazzone, M., López-Rivas, A., Schmidt, T., Augustin, H.G. and de Almodovar, C.R.	Caspase-8 modulates physiological and pathological angiogenesis during retina development [BibTeX]	2019	Journal of Clinical Investigation Vol. 129(12), pp. 5092-5107	article	DOI
BibTeX: @article{Tisch2019, author = {Nathalie Tisch and Aida Freire-Valls and Rosario Yerbes and Isidora Paredes and Silvia La Porta and Xiaohong Wang and Rosa Mart\in-Pérez and Laura Castro and Wendy Wei-Lynn Wong and Leigh Coultas and Boris Strilic and Hermann-Josef Gröne and Thomas Hielscher and Carolin Mogler and Ralf H. Adams and Peter Heiduschka and Lena Claesson-Welsh and Massimiliano Mazzone and Abelardo López-Rivas and Thomas Schmidt and Hellmut G. Augustin and Carmen Ruiz de Almodovar}, title = {Caspase-8 modulates physiological and pathological angiogenesis during retina development}, journal = {Journal of Clinical Investigation}, publisher = {American Society for Clinical Investigation}, year = {2019}, volume = {129}, number = {12}, pages = {5092--5107}, doi = {https://doi.org/10.1172/jci122767} }
Tölle, M., Köthe, U., André, F., Meder, B. and Engelhardt, S.	Content-Aware Differential Privacy with Conditional Invertible Neural Networks [BibTeX]	2022	arXiv.org	article	DOI
BibTeX: @article{Toelle2022, author = {Tölle, Malte and Köthe, Ullrich and André, Florian and Meder, Benjamin and Engelhardt, Sandy}, title = {Content-Aware Differential Privacy with Conditional Invertible Neural Networks}, journal = {arXiv.org}, publisher = {arXiv}, year = {2022}, doi = {https://doi.org/10.48550/arXiv.2207.14625} }
Tölle, M., Köthe, U., André, F., Meder, B. and Engelhardt, S.	Content-Aware Differential Privacy with Conditional Invertible Neural Networks [BibTeX]	2022	Lecture Notes in Computer Science	incollection	DOI
BibTeX: @incollection{Toelle2022a, author = {Malte Tölle, Ullrich Köthe, Florian André, Benjamin Meder, Sandy Engelhardt}, title = {Content-Aware Differential Privacy with Conditional Invertible Neural Networks}, booktitle = {Lecture Notes in Computer Science}, publisher = {Springer Nature Switzerland}, year = {2022}, doi = {https://doi.org/10.1007/978-3-031-18523-6_9} }
Tóth, M., Wehling, L., Thiess, L., Rose, F., Schmitt, J., Weiler, S.M.E., Sticht, C., Torre, C.D.L., Rausch, M., Albrecht, T., Grabe, N., Duwe, L., Andersen, J.B., Köhler, B.C., Springfeld, C., Mehrabi, A., Kulu, Y., Schirmacher, P., Roessler, S., Goeppert, B. and Breuhahn, K.	Co-expression of YAP and TAZ associates with chromosomal instability in human cholangiocarcinoma [BibTeX]	2021	BMC Cancer Vol. 21(1)	article	DOI
BibTeX: @article{Toth2021, author = {Marcell Tóth and Lilija Wehling and Lena Thiess and Fabian Rose and Jennifer Schmitt and Sofia M. E. Weiler and Carsten Sticht and Carolina De La Torre and Melina Rausch and Thomas Albrecht and Niels Grabe and Lea Duwe and Jesper B. Andersen and Bruno C. Köhler and Christoph Springfeld and Arianeb Mehrabi and Yakup Kulu and Peter Schirmacher and Stephanie Roessler and Benjamin Goeppert and Kai Breuhahn}, title = {Co-expression of YAP and TAZ associates with chromosomal instability in human cholangiocarcinoma}, journal = {BMC Cancer}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {21}, number = {1}, doi = {https://doi.org/10.1186/s12885-021-08794-5} }
Tress, R.G., Smith, R.J., Sormani, M.C., Glover, S.C.O., Klessen, R.S., Mac Low, M.-M. and Clark, P.C.	Simulations of the star-forming molecular gas in an interacting M51-like galaxy [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 492(2), pp. 2973-2995	article	DOI
BibTeX: @article{Tress2020, author = {Robin G Tress and Rowan J Smith and Mattia C Sormani and Simon C O Glover and Ralf S Klessen and Mordecai-Mark Mac Low and Paul C Clark}, title = {Simulations of the star-forming molecular gas in an interacting M51-like galaxy}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {492}, number = {2}, pages = {2973--2995}, doi = {https://doi.org/10.1093/mnras/stz3600} }
Tress, R.G., Sormani, M.C., Glover, S.C.O., Klessen, R.S., Battersby, C.D., Clark, P.C., Hatchfield, H.P. and Smith, R.J.	Simulations of the Milky Way's central molecular zone – I. Gas dynamics [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 499(3), pp. 4455-4478	article	DOI
BibTeX: @article{Tress2020, author = {Robin G Tress and Mattia C Sormani and Simon C O Glover and Ralf S Klessen and Cara D Battersby and Paul C Clark and H Perry Hatchfield and Rowan J Smith}, title = {Simulations of the Milky Way's central molecular zone – I. Gas dynamics}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {499}, number = {3}, pages = {4455--4478}, doi = {https://doi.org/10.1093/mnras/staa3120} }
Treß, R.G., Sormani, M.C., Smith, R.J., Glover, S.C.O., Klessen, R.S., Mac Low, M.-M., Clark, P. and Duarte-Cabral, A.	Simulations of the star-forming molecular gas in an interacting M51-like galaxy: cloud population statistics [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 505(4), pp. 5438-5459	article	DOI
BibTeX: @article{Tress2021, author = {Robin G Treß and Mattia C Sormani and Rowan J Smith and Simon C O Glover and Ralf S Klessen and Mordecai-Mark Mac Low and Paul Clark and Ana Duarte-Cabral}, title = {Simulations of the star-forming molecular gas in an interacting M51-like galaxy: cloud population statistics}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {505}, number = {4}, pages = {5438--5459}, doi = {https://doi.org/10.1093/mnras/stab1683} }
Trobisch, T., Zulji, A., Stevens, N.A., Schwarz, S., Wischnewski, S., Öztürk, M., Perales-Patón, J., Haeussler, M., Saez-Rodriguez, J., Velmeshev, D. and Schirmer, L.	Cross-regional homeostatic and reactive glial signatures in multiple sclerosis [Abstract] [BibTeX]	2022	Acta Neuropathologica Vol. 144(5), pp. 987-1003	article	DOI
Abstract: AbstractMultiple sclerosis (MS) is a multifocal and progressive inflammatory disease of the central nervous system (CNS). However, the compartmentalized pathology of the disease affecting various anatomical regions including gray and white matter and lack of appropriate disease models impede understanding of the disease. Utilizing single-nucleus RNA-sequencing and multiplex spatial RNA mapping, we generated an integrated transcriptomic map comprising leukocortical, cerebellar and spinal cord areas in normal and MS tissues that captures regional subtype diversity of various cell types with an emphasis on astrocytes and oligodendrocytes. While we found strong cross-regional diversity among glial subtypes in control tissue, regional signatures become more obscure in MS. This suggests that patterns of transcriptomic changes in MS are shared across regions and converge on specific pathways, especially those regulating cellular stress and immune activation. In addition, we found evidence that a subtype of white matter oligodendrocytes appearing across all three CNS regions adopt pro-remyelinating gene signatures in MS. In summary, our data suggest that cross-regional transcriptomic glial signatures overlap in MS, with different reactive glial cell types capable of either exacerbating or ameliorating pathology.
BibTeX: @article{Trobisch2022, author = {Tim Trobisch, Amel Zulji, Nikolas A. Stevens, Sophia Schwarz, Sven Wischnewski, Mikail Öztürk, Javier Perales-Patón, Maximilian Haeussler, Julio Saez-Rodriguez, Dmitry Velmeshev, Lucas Schirmer}, title = {Cross-regional homeostatic and reactive glial signatures in multiple sclerosis}, journal = {Acta Neuropathologica}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {144}, number = {5}, pages = {987--1003}, doi = {https://doi.org/10.1007/s00401-022-02497-2} }
Trojanowski, J., Frank, L., Rademacher, A., Mücke, N., Grigaitis, P. and Rippe, K.	Transcription activation is enhanced by multivalent interactions independent of phase separation [BibTeX]	2022	Molecular Cell Vol. 82(10), pp. 1878-1893.e10	article	DOI URL
BibTeX: @article{Trojanowski2022, author = {Jorge Trojanowski, Lukas Frank, Anne Rademacher, Norbert Mücke, Pranas Grigaitis, Karsten Rippe}, title = {Transcription activation is enhanced by multivalent interactions independent of phase separation}, journal = {Molecular Cell}, publisher = {Elsevier BV}, year = {2022}, volume = {82}, number = {10}, pages = {1878--1893.e10}, url = {https://api.elsevier.com/content/article/PII:S1097276522003288?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.molcel.2022.04.017} }
Tsingos, E., Höckendorf, B., Sütterlin, T., Kirchmaier, S., Grabe, N., Centanin, L. and Wittbrodt, J.	Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish [Abstract] [BibTeX]	2019	eLife Vol. 8, pp. e42646	article	DOI
Abstract: Combining clonal analysis with a computational agent based model, we investigate how tissue-specific stem cells for neural retina (NR) and retinal pigmented epithelium (RPE) of the teleost medaka (Oryzias latipes) coordinate their growth rates. NR cell division timing is less variable, consistent with an upstream role as growth inducer. RPE cells divide with greater variability, consistent with a downstream role responding to inductive signals. Strikingly, the arrangement of the retinal ciliary marginal zone niche results in a spatially biased random lineage loss, where stem- and progenitor cell domains emerge spontaneously. Further, our data indicate that NR cells orient division axes to regulate organ shape and retinal topology. We highlight an unappreciated mechanism for growth coordination, where one tissue integrates cues to synchronize growth of nearby tissues. This strategy may enable evolution to modulate cell proliferation parameters in one tissue to adapt whole-organ morphogenesis in a complex vertebrate organ.
BibTeX: @article{Tsingos2019, author = {Tsingos, Erika and Höckendorf, Burkhard and Sütterlin, Thomas and Kirchmaier, Stephan and Grabe, Niels and Centanin, Lazaro and Wittbrodt, Joachim}, title = {Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2019}, volume = {8}, pages = {e42646}, doi = {https://doi.org/10.7554/eLife.42646} }
Tytarenko, D. and Penter, T.	Die Ermordung von psychisch kranken Menschen in Poltava (1941–1943) [BibTeX]	2020	Jahrbücher für Geschichte Osteuropas Vol. 68(3-4), pp. 455	article	DOI
BibTeX: @article{Tytarenko2020, author = {Dmytro Tytarenko and Tanja Penter}, title = {Die Ermordung von psychisch kranken Menschen in Poltava (1941–1943)}, journal = {Jahrbücher für Geschichte Osteuropas}, publisher = {Wissenschaftliche Verlagsgesellschaft mbH}, year = {2020}, volume = {68}, number = {3-4}, pages = {455}, doi = {https://doi.org/10.25162/jgo-2020-0015} }
Uhl, P., Pantze, S., Storck, P., Parmentier, J., Witzigmann, D., Hofhaus, G., Huwyler, J., Mier, W. and Fricker, G.	Oral delivery of vancomycin by tetraether lipid liposomes [Abstract] [BibTeX]	2017	European Journal of Pharmaceutical Sciences Vol. 108, pp. 111-118	article	DOI URL
Abstract: Despite the outstanding progress in modern medicine, the oral delivery of peptide drugs is limited until today due to their instability in the gastrointestinal tract and low mucosa penetration. To overcome these hurdles, liposomes containing the specific tetraether lipid GCTE (glycerylcaldityltetraether lipid) were examined. For this purpose, the glycopeptide antibiotic vancomycin was used as model substance and liposomes were prepared by DAC (dual assymetric centrifugation). These liposomes showed a size and polydispersity index comparable to standard liposomes. A high encapsulation efficiency of 58.53textpm1.76% of the peptide drug vancomycin could be obtained as detected by HPLC. FCS analysis showed that in average each liposome contains 30 molecules of vancomycin. TEM and Cryo-EM micrographs verified the size and lamellarity of the liposomal formulations. Cytotoxicity tests in Caco-2 cells showed no significant cytotoxicity for all liposomal concentrations tested, indicating the good tolerability of these formulations. Furthermore, the use of sucrose as lyoprotector enabled the long term storage of the liposomal formulation for at least three months. The potency of this drug delivery system could be proven in an animal model using Wistar rats. One hour after oral application, 4.82textpm0.56% of the administered dose of vancomycin could be found in the blood as detected by immunoassay measurements. This transport did also not affect the integrity of the peptide as verified by immunoassay measurements. In combination with long term storage stability, this formulation appears to be a promising delivery system for oral application of peptide drugs.
BibTeX: @article{Uhl2017, author = {Uhl, Philipp and Pantze, Silvia and Storck, Philip and Parmentier, Johannes and Witzigmann, Dominik and Hofhaus, Götz and Huwyler, Jörg and Mier, Walter and Fricker, Gert}, title = {Oral delivery of vancomycin by tetraether lipid liposomes}, journal = {European Journal of Pharmaceutical Sciences}, year = {2017}, volume = {108}, pages = {111--118}, note = {Use of phospholipids in oral drug delivery}, url = {http://www.sciencedirect.com/science/article/pii/S0928098717304128}, doi = {https://doi.org/10.1016/j.ejps.2017.07.013} }
Upadhyay, A., Marzoll, D., Diernfellner, A., Brunner, M. and Herzel, H.	Multiple random phosphorylations in clock proteins provide long delays and switches [BibTeX]	2020	Scientific Reports Vol. 10(1)	article	DOI
BibTeX: @article{Upadhyay2020, author = {Abhishek Upadhyay and Daniela Marzoll and Axel Diernfellner and Michael Brunner and Hanspeter Herzel}, title = {Multiple random phosphorylations in clock proteins provide long delays and switches}, journal = {Scientific Reports}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {10}, number = {1}, doi = {https://doi.org/10.1038/s41598-020-79277-z} }
Vale Asari, N., Wild, V., de Amorim , A.L., Werle, A., Zheng, Y., Kennicutt, R., Johnson, B.D., Galametz, M., Pellegrini, E.W., Klessen, R.S., Reissl, S., Glover, S.C.O. and Rahner, D.	Less than the sum of its parts: the dust-corrected H upalpha luminosity of star-forming galaxies explored at different spatial resolutions with MaNGA and MUSE [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 498(3), pp. 4205-4221	article	DOI
BibTeX: @article{ValeAsari2020, author = {N Vale Asari and V Wild and A L de Amorim and A Werle and Y Zheng and R Kennicutt and B D Johnson and M Galametz and E W Pellegrini and R S Klessen and S Reissl and S C O Glover and D Rahner}, title = {Less than the sum of its parts: the dust-corrected H upalpha luminosity of star-forming galaxies explored at different spatial resolutions with MaNGA and MUSE}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {498}, number = {3}, pages = {4205--4221}, doi = {https://doi.org/10.1093/mnras/staa2557} }
Veltchev, T.V., Ossenkopf-Okada, V., Stanchev, O., Schneider, N., Donkov, S. and Klessen, R.S.	Spatially associated clump populations in Rosette from CO and dust maps [BibTeX]	2018	Monthly Notices of the Royal Astronomical Society Vol. 475(2), pp. 2215-2235	article	DOI
BibTeX: @article{Veltchev2018, author = {Veltchev, Todor V. and Ossenkopf-Okada, Volker and Stanchev, Orlin and Schneider, Nicola and Donkov, Sava and Klessen, Ralf S.}, title = {Spatially associated clump populations in Rosette from CO and dust maps}, journal = {Monthly Notices of the Royal Astronomical Society}, year = {2018}, volume = {475}, number = {2}, pages = {2215--2235}, doi = {https://doi.org/10.1093/mnras/stx3267} }
Veltchev, T.V., Girichidis, P., Donkov, S., Schneider, N., Stanchev, O., Marinkova, L., Seifried, D. and Klessen, R.S.	On the extraction of the power-law parts of probability density functions in star-forming clouds [BibTeX]	2019	Monthly Notices of the Royal Astronomical Society Vol. 489(1), pp. 788-801	article	DOI
BibTeX: @article{Veltchev2019, author = {Todor V Veltchev and Philipp Girichidis and Sava Donkov and Nicola Schneider and Orlin Stanchev and Lyubov Marinkova and Daniel Seifried and Ralf S Klessen}, title = {On the extraction of the power-law parts of probability density functions in star-forming clouds}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2019}, volume = {489}, number = {1}, pages = {788--801}, doi = {https://doi.org/10.1093/mnras/stz2151} }
Venkataramani, V., Herrmannsdörfer, F., Heilemann, M. and Kuner, T.	SuReSim: simulating localization microscopy experiments from ground truth models [Abstract] [BibTeX]	2016	Nature Methods Vol. 13(4), pp. 319	article	DOI
Abstract: SuReSim software simulates single-molecule localization microscopy data for structures with known ground truth models to facilitate proper design, interpretation and validation of super-resolution imaging experiments.
BibTeX: @article{Venkataramani2016, author = {Venkataramani, Varun and Herrmannsdörfer, Frank and Heilemann, Mike and Kuner, Thomas}, title = {SuReSim: simulating localization microscopy experiments from ground truth models}, journal = {Nature Methods}, publisher = {Nature Publishing Group}, year = {2016}, volume = {13}, number = {4}, pages = {319}, doi = {https://doi.org/10.1038/nmeth.3775} }
Venkataramani, V., Kardorff, M., Herrmannsdörfer, F., Wieneke, R., Klein, A., Tampé, R., Heilemann, M. and Kuner, T.	Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins [Abstract] [BibTeX]	2018	Scientific Reports Vol. 8(1), pp. 5507	article	DOI
Abstract: With continuing advances in the resolving power of super-resolution microscopy, the inefficient labeling of proteins with suitable fluorophores becomes a limiting factor. For example, the low labeling density achieved with antibodies or small molecule tags limits attempts to reveal local protein nano-architecture of cellular compartments. On the other hand, high laser intensities cause photobleaching within and nearby an imaged region, thereby further reducing labeling density and impairing multi-plane whole-cell 3D super-resolution imaging. Here, we show that both labeling density and photobleaching can be addressed by repetitive application of trisNTA-fluorophore conjugates reversibly binding to a histidine-tagged protein by a novel approach called single-epitope repetitive imaging (SERI). For single-plane super-resolution microscopy, we demonstrate that, after multiple rounds of labeling and imaging, the signal density is increased. Using the same approach of repetitive imaging, washing and re-labeling, we demonstrate whole-cell 3D super-resolution imaging compensated for photobleaching above or below the imaging plane. This proof-of-principle study demonstrates that repetitive labeling of histidine-tagged proteins provides a versatile solution to break the `labeling barrier' and to bypass photobleaching in multi-plane, whole-cell 3D experiments.
BibTeX: @article{Venkataramani2018, author = {Venkataramani, Varun and Kardorff, Markus and Herrmannsdörfer, Frank and Wieneke, Ralph and Klein, Alina and Tampé, Robert and Heilemann, Mike and Kuner, Thomas}, title = {Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins}, journal = {Scientific Reports}, year = {2018}, volume = {8}, number = {1}, pages = {5507}, doi = {https://doi.org/10.1038/s41598-018-23818-0} }
Venkataramani, V., Tanev, D.I., Strahle, C., Studier-Fischer, A., Fankhauser, L., Kessler, T., Körber, C., Kardorff, M., Ratliff, M., Xie, R., Horstmann, H., Messer, M., Paik, S.P., Knabbe, J., Sahm, F., Kurz, F.T., Acikgöz, A.A., Herrmannsdörfer, F., Agarwal, A., Bergles, D.E., Chalmers, A., Miletic, H., Turcan, S., Mawrin, C., Hänggi, D., Liu, H.-K., Wick, W., Winkler, F. and Kuner, T.	Glutamatergic synaptic input to glioma cells drives brain tumour progression [BibTeX]	2019	Nature Vol. 573(7775), pp. 532-538	article	DOI
BibTeX: @article{Venkataramani2019, author = {Varun Venkataramani and Dimitar Ivanov Tanev and Christopher Strahle and Alexander Studier-Fischer and Laura Fankhauser and Tobias Kessler and Christoph Körber and Markus Kardorff and Miriam Ratliff and Ruifan Xie and Heinz Horstmann and Mirko Messer and Sang Peter Paik and Johannes Knabbe and Felix Sahm and Felix T. Kurz and Azer Aylin Acikgöz and Frank Herrmannsdörfer and Amit Agarwal and Dwight E. Bergles and Anthony Chalmers and Hrvoje Miletic and Sevin Turcan and Christian Mawrin and Daniel Hänggi and Hai-Kun Liu and Wolfgang Wick and Frank Winkler and Thomas Kuner}, title = {Glutamatergic synaptic input to glioma cells drives brain tumour progression}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2019}, volume = {573}, number = {7775}, pages = {532--538}, doi = {https://doi.org/10.1038/s41586-019-1564-x} }
Venkataramani, V., Yang, Y., Schubert, M.C., Reyhan, E., Tetzlaff, S.K., Wißmann, N., Botz, M., Soyka, S.J., Beretta, C.A., Pramatarov, R.L., Fankhauser, L., Garofano, L., Freudenberg, A., Wagner, J., Tanev, D.I., Ratliff, M., Xie, R., Kessler, T., Hoffmann, D.C., Hai, L., Dörflinger, Y., Hoppe, S., Yabo, Y.A., Golebiewska, A., Niclou, S.P., Sahm, F., Lasorella, A., Slowik, M., Döring, L., Iavarone, A., Wick, W., Kuner, T. and Winkler, F.	Glioblastoma hijacks neuronal mechanisms for brain invasion [BibTeX]	2022	Cell Vol. 185(16), pp. 2899-2917.e31	article	DOI URL
BibTeX: @article{Venkataramani2022, author = {Varun Venkataramani, Yvonne Yang, Marc Cicero Schubert, Ekin Reyhan, Svenja Kristin Tetzlaff, Niklas Wißmann, Michael Botz, Stella Judith Soyka, Carlo Antonio Beretta, Rangel Lyubomirov Pramatarov, Laura Fankhauser, Luciano Garofano, Alexander Freudenberg, Julia Wagner, Dimitar Ivanov Tanev, Miriam Ratliff, Ruifan Xie, Tobias Kessler, Dirk C. Hoffmann, Ling Hai, Yvette Dörflinger, Simone Hoppe, Yahaya A. Yabo, Anna Golebiewska, Simone P. Niclou, Felix Sahm, Anna Lasorella, Martin Slowik, Leif Döring, Antonio Iavarone, Wolfgang Wick, Thomas Kuner, Frank Winkler}, title = {Glioblastoma hijacks neuronal mechanisms for brain invasion}, journal = {Cell}, publisher = {Elsevier BV}, year = {2022}, volume = {185}, number = {16}, pages = {2899--2917.e31}, url = {https://api.elsevier.com/content/article/PII:S0092867422008479?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.cell.2022.06.054} }
Wacker, I., Schröder, R.R. and Schroeder, J.A.	Pathology goes 3D: Exploring the potential of array tomography versus FIB nanotomography for a CADASIL sample [BibTeX]	2017	Ultrastructural Pathology Vol. 41(1), pp. 114-115	article	DOI
BibTeX: @article{Wacker2017, author = {Wacker, Irene and Schröder, Rasmus R. and Schroeder, Josef A.}, title = {Pathology goes 3D: Exploring the potential of array tomography versus FIB nanotomography for a CADASIL sample}, journal = {Ultrastructural Pathology}, publisher = {Taylor & Francis}, year = {2017}, volume = {41}, number = {1}, pages = {114--115}, note = {PMID: 28230487}, doi = {https://doi.org/10.1080/01913123.2016.1272157} }
Wacker, I., Dittmayer, C., Schroeder, J.A. and Schröder, R.R.	Volume EM of Pathological Deposits -- Array Tomography and FIBSEM Nanotomography on Weakly Metalized Routine Samples [BibTeX]	2018	Microscopy and Microanalysis Vol. 24(S1), pp. 1272-1273	article	DOI
BibTeX: @article{Wacker2018, author = {Wacker, Irene and Dittmayer, Carsten and Schroeder, Joseph A. and Schröder, Rasmus R.}, title = {Volume EM of Pathological Deposits -- Array Tomography and FIBSEM Nanotomography on Weakly Metalized Routine Samples}, journal = {Microscopy and Microanalysis}, publisher = {Cambridge University Press}, year = {2018}, volume = {24}, number = {S1}, pages = {1272--1273}, doi = {https://doi.org/10.1017/S1431927618006840} }
Wacker, I.U., Veith, L., Spomer, W., Hofmann, A., Thaler, M., Hillmer, S., Gengenbach, U. and Schröder, R.R.	Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes [Abstract] [BibTeX]	2018	JoVE(133), pp. e57059	article	DOI URL
Abstract: Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a combination of light and electron microscopy. Samples embedded in resin are sectioned into arrays consisting of ribbons of hundreds of ultrathin sections and deposited on pieces of silicon wafer or conductively coated coverslips. Arrays are imaged at low resolution using a digital consumer like smartphone camera or light microscope (LM) for a rapid large area overview, or a wide field fluorescence microscope (fluorescence light microscopy (FLM)) after labeling with fluorophores. After post-staining with heavy metals, arrays are imaged in a scanning electron microscope (SEM). Selection of targets is possible from 3D reconstructions generated by FLM or from 3D reconstructions made from the SEM image stacks at intermediate resolution if no fluorescent markers are available. For ultrastructural analysis, selected targets are finally recorded in the SEM at high-resolution (a few nanometer image pixels). A ribbon-handling tool that can be retrofitted to any ultramicrotome is demonstrated. It helps with array production and substrate removal from the sectioning knife boat. A software platform that allows automated imaging of arrays in the SEM is discussed. Compared to other methods generating large volume EM data, such as serial block-face SEM (SBF-SEM) or focused ion beam SEM (FIB-SEM), this approach has two major advantages: (1) The resin-embedded sample is conserved, albeit in a sliced-up version. It can be stained in different ways and imaged with different resolutions. (2) As the sections can be post-stained, it is not necessary to use samples strongly block-stained with heavy metals to introduce contrast for SEM imaging or render the tissue blocks conductive. This makes the method applicable to a wide variety of materials and biological questions. Particularly prefixed materials e.g., from biopsy banks and pathology labs, can directly be embedded and reconstructed in 3D.
BibTeX: @article{Wacker2018a, author = {Wacker, Irene U. and Veith, Lisa and Spomer, Waldemar and Hofmann, Andreas and Thaler, Marlene and Hillmer, Stefan and Gengenbach, Ulrich and Schröder, Rasmus R.}, title = {Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes}, journal = {JoVE}, publisher = {MyJoVE Corp}, year = {2018}, number = {133}, pages = {e57059}, url = {https://www.jove.com/video/57059}, doi = {https://doi.org/10.3791/57059} }
Wacker, I., Curticean, R., Ryklin, D., Weidinger, B., Mayer, F., Huang, L.-Y., Hoffmann, J., Islam, M., von Coelln, N., Schmitt, T., Huck, C., Tegeder, P., Feist, F., Kammerer, J.A., Barner-Kowollik, C., Wegener, M., Blasco, E., Gengenbach, U. and Schröder, R.R.	Deconstructing 3D Structured Materials by Modern Ultramicrotomy for Multimodal Imaging and Volume Analysis across Length Scales [BibTeX]	2023	Advanced Functional Materials	article	DOI
BibTeX: @article{Wacker2023, author = {Irene Wacker and Ronald Curticean and Daniel Ryklin and Britta Weidinger and Frederik Mayer and Li-Yu Huang and Julian Hoffmann and Monsur Islam and Nadine von Coelln and Tanja Schmitt and Christian Huck and Petra Tegeder and Florian Feist and Jochen A. Kammerer and Christopher Barner-Kowollik and Martin Wegener and Eva Blasco and Ulrich Gengenbach and Rasmus R. Schröder}, title = {Deconstructing 3D Structured Materials by Modern Ultramicrotomy for Multimodal Imaging and Volume Analysis across Length Scales}, journal = {Advanced Functional Materials}, publisher = {Wiley}, year = {2023}, doi = {https://doi.org/10.1002/adfm.202302025} }
	Writing Beyond Pen and Parchment [BibTeX]	2019		book	DOI
BibTeX: @book{Wagner2019,, title = {Writing Beyond Pen and Parchment}, publisher = {De Gruyter}, year = {2019}, doi = {https://doi.org/10.1515/9783110645446} }
Wahis, J., Baudon, A., Althammer, F., Kerspern, D., Goyon, S., Hagiwara, D., Lefevre, A., Barteczko, L., Boury-Jamot, B., Bellanger, B., Abatis, M., Gouveia, M.D.S., Benusiglio, D., Eliava, M., Rozov, A., Weinsanto, I., Knobloch-Bollmann, H.S., Kirchner, M.K., Roy, R.K., Wang, H., Pertin, M., Inquimbert, P., Pitzer, C., Siemens, J., Goumon, Y., Boutrel, B., Lamy, C.M., Decosterd, I., Chatton, J.-Y., Rouach, N., Young, W.S., Stern, J.E., Poisbeau, P., Stoop, R., Darbon, P., Grinevich, V. and Charlet, A.	Astrocytes mediate the effect of oxytocin in the central amygdala on neuronal activity and affective states in rodents [BibTeX]	2021	Nature Neuroscience Vol. 24(4), pp. 529-541	article	DOI
BibTeX: @article{Wahis2021, author = {Jérôme Wahis and Angel Baudon and Ferdinand Althammer and Damien Kerspern and Stéphanie Goyon and Daisuke Hagiwara and Arthur Lefevre and Lara Barteczko and Benjamin Boury-Jamot and Benjamin Bellanger and Marios Abatis and Miriam Da Silva Gouveia and Diego Benusiglio and Marina Eliava and Andrei Rozov and Ivan Weinsanto and Hanna Sophie Knobloch-Bollmann and Matthew K. Kirchner and Ranjan K. Roy and Hong Wang and Marie Pertin and Perrine Inquimbert and Claudia Pitzer and Jan Siemens and Yannick Goumon and Benjamin Boutrel and Christophe Maurice Lamy and Isabelle Decosterd and Jean-Yves Chatton and Nathalie Rouach and W. Scott Young and Javier E. Stern and Pierrick Poisbeau and Ron Stoop and Pascal Darbon and Valery Grinevich and Alexandre Charlet}, title = {Astrocytes mediate the effect of oxytocin in the central amygdala on neuronal activity and affective states in rodents}, journal = {Nature Neuroscience}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {24}, number = {4}, pages = {529--541}, doi = {https://doi.org/10.1038/s41593-021-00800-0} }
Wallenwein, C.M., Weigel, V., Hofhaus, G., Dhakal, N., Schatton, W., Gelperina, S., Groeber-Becker, F.K., Dressman, J. and Wacker, M.G.	Pharmaceutical Development of Nanostructured Vesicular Hydrogel Formulations of Rifampicin for Wound Healing [Abstract] [BibTeX]	2022	International Journal of Molecular Sciences Vol. 23(24), pp. 16207	article	DOI URL
Abstract: Chronic wounds exhibit elevated levels of inflammatory cytokines, resulting in the release of proteolytic enzymes which delay wound-healing processes. In recent years, rifampicin has gained significant attention in the treatment of chronic wounds due to an interesting combination of antibacterial and anti-inflammatory effects. Unfortunately, rifampicin is sensitive to hydrolysis and oxidation. As a result, no topical drug product for wound-healing applications has been approved. To address this medical need two nanostructured hydrogel formulations of rifampicin were developed. The liposomal vesicles were embedded into hydroxypropyl methylcellulose (HPMC) gel or a combination of hyaluronic acid and marine collagen. To protect rifampicin from degradation in aqueous environments, a freeze-drying method was developed. Before freeze-drying, two well-defined hydrogel preparations were obtained. After freeze-drying, the visual appearance, chemical stability, residual moisture content, and redispersion time of both preparations were within acceptable limits. However, the morphological characterization revealed an increase in the vesicle size for collagen–hyaluronic acid hydrogel. This was confirmed by subsequent release studies. Interactions of marine collagen with phosphatidylcholine were held responsible for this effect. The HPMC hydrogel formulation remained stable over 6 months of storage. Moving forward, this product fulfills all criteria to be evaluated in preclinical and clinical studies.
BibTeX: @article{Wallenwein2022, author = {Chantal M. Wallenwein, Verena Weigel, Götz Hofhaus, Namrata Dhakal, Wolfgang Schatton, Svetlana Gelperina, Florian K. Groeber-Becker, Jennifer Dressman, Matthias G. Wacker}, title = {Pharmaceutical Development of Nanostructured Vesicular Hydrogel Formulations of Rifampicin for Wound Healing}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2022}, volume = {23}, number = {24}, pages = {16207}, url = {https://www.mdpi.com/1422-0067/23/24/16207/pdf}, doi = {https://doi.org/10.3390/ijms232416207} }
Wallenwein, C.M., Ashtikar, M., Hofhaus, G., Haferland, I., Thurn, M., König, A., Pinter, A., Dressman, J. and Wacker, M.G.	How wound environments trigger the release from Rifampicin-loaded liposomes [BibTeX]	2023	International Journal of Pharmaceutics Vol. 633, pp. 122606	article	DOI URL
BibTeX: @article{Wallenwein2023, author = {Chantal M. Wallenwein, Mukul Ashtikar, Götz Hofhaus, Isabel Haferland, Manuela Thurn, Anke König, Andreas Pinter, Jennifer Dressman, Matthias G. Wacker}, title = {How wound environments trigger the release from Rifampicin-loaded liposomes}, journal = {International Journal of Pharmaceutics}, publisher = {Elsevier BV}, year = {2023}, volume = {633}, pages = {122606}, url = {https://api.elsevier.com/content/article/PII:S0378517323000261?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.ijpharm.2023.122606} }
Walton, E., Hibar, D.P., van Erp, T.G.M., Potkin, S.G., Roiz-Santiañez, R., Crespo-Facorro, B., Suarez-Pinilla, P., van Haren, N.E.M., de Zwarte, S.M.C., Kahn, R.S. and et al.	Prefrontal cortical thinning links to negative symptoms in schizophrenia via the ENIGMA consortium [BibTeX]	2017	Psychological Medicine Vol. 48(1), pp. 82-94	article	DOI
BibTeX: @article{Walton2017, author = {Walton, E. and Hibar, D. P. and van Erp, T. G. M. and Potkin, S. G. and Roiz-Santiañez, R. and Crespo-Facorro, B. and Suarez-Pinilla, P. and van Haren, N. E. M. and de Zwarte, S. M. C. and Kahn, R. S. and et al.}, title = {Prefrontal cortical thinning links to negative symptoms in schizophrenia via the ENIGMA consortium}, journal = {Psychological Medicine}, publisher = {Cambridge University Press (CUP)}, year = {2017}, volume = {48}, number = {1}, pages = {82--94}, doi = {https://doi.org/10.1017/s0033291717001283} }
Wang, X., Freire Valls, A., Schermann, G., Shen, Y., Moya, I.M., Castro, L., Urban, S., Solecki, G.M., Winkler, F., Riedemann, L., Jain, R.K., Mazzone, M., Schmidt, T., Fischer, T., Halder, G. and Ruiz de Almodóvar, C.	YAP/TAZ Orchestrate VEGF Signaling during Developmental Angiogenesis [BibTeX]	2017	Developmental Cell Vol. 42(5), pp. 462-478.e7	article	DOI
BibTeX: @article{Wang2017, author = {Wang, Xiaohong and Freire Valls, Aida and Schermann, Géza and Shen, Ying and Moya, Ivan M. and Castro, Laura and Urban, Severino and Solecki, Gergely M. and Winkler, Frank and Riedemann, Lars and Jain, Rakesh K. and Mazzone, Massimilano and Schmidt, Thomas and Fischer, Tamás and Halder, Georg and Ruiz de Almodóvar, Carmen}, title = {YAP/TAZ Orchestrate VEGF Signaling during Developmental Angiogenesis}, journal = {Developmental Cell}, publisher = {Elsevier}, year = {2017}, volume = {42}, number = {5}, pages = {462--478.e7}, doi = {https://doi.org/10.1016/j.devcel.2017.08.002} }
Wang, Y., Bihr, S., Rugel, M., Beuther, H., Johnston, K.G., Ott, J., Soler, J.D., Brunthaler, A., Anderson, L.D., Urquhart, J.S., Klessen, R.S., Linz, H., McClure-Griffiths, N.M., Glover, S.C.O., Menten, K.M., Bigiel, F., Hoare, M. and Longmore, S.N.	Radio continuum emission in the northern Galactic plane: Sources and spectral indices from the THOR survey [BibTeX]	2018	Astronomy & Astrophysics Vol. 619, pp. A124	article	DOI
BibTeX: @article{Wang2018, author = {Wang, Y. and Bihr, S. and Rugel, M. and Beuther, H. and Johnston, K. G. and Ott, J. and Soler, J. D. and Brunthaler, A. and Anderson, L. D. and Urquhart, J. S. and Klessen, R. S. and Linz, H. and McClure-Griffiths, N. M. and Glover, S. C. O. and Menten, K. M. and Bigiel, F. and Hoare, M. and Longmore, S. N.}, title = {Radio continuum emission in the northern Galactic plane: Sources and spectral indices from the THOR survey}, journal = {Astronomy & Astrophysics}, year = {2018}, volume = {619}, pages = {A124}, doi = {https://doi.org/10.1051/0004-6361/201833642} }
Wang, Z.-Y., Leushkin, E., Liechti, A., Ovchinnikova, S., Mößinger, K., Brüning, T., Rummel, C., Grützner, F., Cardoso-Moreira, M., Janich, P., Gatfield, D., Diagouraga, B., de Massy, B., Gill, M.E., Peters, A.H.F.M., Anders, S. and Kaessmann, H.	Transcriptome and translatome co-evolution in mammals [BibTeX]	2020	Nature Vol. 588(7839), pp. 642-647	article	DOI
BibTeX: @article{Wang2020, author = {Zhong-Yi Wang and Evgeny Leushkin and Angélica Liechti and Svetlana Ovchinnikova and Katharina Mößinger and Thoomke Brüning and Coralie Rummel and Frank Grützner and Margarida Cardoso-Moreira and Peggy Janich and David Gatfield and Boubou Diagouraga and Bernard de Massy and Mark E. Gill and Antoine H. F. M. Peters and Simon Anders and Henrik Kaessmann}, title = {Transcriptome and translatome co-evolution in mammals}, journal = {Nature}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {588}, number = {7839}, pages = {642--647}, doi = {https://doi.org/10.1038/s41586-020-2899-z} }
Wang, D., Gao, Q., Schaefer, I., Moerz, H., Hoheisel, U., Rohr, K., Greffrath, W. and Treede, R.-D.	TRPM3-mediated dynamic mitochondrial activity in nerve growth factor–induced latent sensitization of chronic low back pain [BibTeX]	2022	Pain Vol. 163(11), pp. e1115-e1128	article	DOI
BibTeX: @article{Wang2022, author = {Dan Wang, Qi Gao, Ina Schaefer, Handan Moerz, Ulrich Hoheisel, Karl Rohr, Wolfgang Greffrath, Rolf-Detlef Treede}, title = {TRPM3-mediated dynamic mitochondrial activity in nerve growth factor–induced latent sensitization of chronic low back pain}, journal = {Pain}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, year = {2022}, volume = {163}, number = {11}, pages = {e1115--e1128}, doi = {https://doi.org/10.1097/j.pain.0000000000002642} }
Wang, S., Feng, R., Wang, S.S., Liu, H., Shao, C., Li, Y., Link, F., Munker, S., Liebe, R., Meyer, C., Burgermeister, E., Ebert, M., Dooley, S., Ding, H. and Weng, H.	FOXA2 prevents hyperbilirubinaemia in acute liver failure by maintaining apical MRP2 expression [Abstract] [BibTeX]	2022	Gut Vol. 72(3), pp. 549-559	article	DOI
Abstract: ObjectiveMultidrug resistance protein 2 (MRP2) is a bottleneck in bilirubin excretion. Its loss is sufficient to induce hyperbilirubinaemia, a prevailing characteristic of acute liver failure (ALF) that is closely associated with clinical outcome. This study scrutinises the transcriptional regulation of MRP2 under different pathophysiological conditions.DesignHepatic MRP2, farnesoid X receptor (FXR) and Forkhead box A2 (FOXA2) expression and clinicopathologic associations were examined by immunohistochemistry in 14 patients with cirrhosis and 22 patients with ALF. MRP2 regulatory mechanisms were investigated in primary hepatocytes,Fxr−/−mice and lipopolysaccharide (LPS)-treated mice.ResultsPhysiologically, homeostatic MRP2 transcription is mediated by the nuclear receptor FXR/retinoid X receptor complex.Fxr−/−mice lack apical MRP2 expression and rapidly progress into hyperbilirubinaemia. In patients with ALF, hepatic FXR expression is undetectable, however, patients without infection maintain apical MRP2 expression and do not suffer from hyperbilirubinaemia. These patients express FOXA2 in hepatocytes. FOXA2 upregulates MRP2 transcription through binding to its promoter. Physiologically, nuclear FOXA2 translocation is inhibited by insulin. In ALF, high levels of glucagon and tumour necrosis factor α induce FOXA2 expression and nuclear translocation in hepatocytes. Impressively, ALF patients with sepsis express low levels of FOXA2, lose MRP2 expression and develop severe hyperbilirubinaemia. In this case, LPS inhibits FXR expression, induces FOXA2 nuclear exclusion and thus abrogates the compensatory MRP2 upregulation. In bothFxr−/−and LPS-treated mice, ectopic FOXA2 expression restored apical MRP2 expression and normalised serum bilirubin levels.ConclusionFOXA2 replaces FXR to maintain MRP2 expression in ALF without sepsis. Ectopic FOXA2 expression to maintain MRP2 represents a potential strategy to prevent hyperbilirubinaemia in septic ALF.
BibTeX: @article{Wang2022a, author = {Sai Wang, Rilu Feng, Shan Shan Wang, Hui Liu, Chen Shao, Yujia Li, Frederik Link, Stefan Munker, Roman Liebe, Christoph Meyer, Elke Burgermeister, Matthias Ebert, Steven Dooley, Huiguo Ding, Honglei Weng}, title = {FOXA2 prevents hyperbilirubinaemia in acute liver failure by maintaining apical MRP2 expression}, journal = {Gut}, publisher = {BMJ}, year = {2022}, volume = {72}, number = {3}, pages = {549--559}, doi = {https://doi.org/10.1136/gutjnl-2022-326987} }
Waschow, M.	siRNA high-content screening of 3D cultured MCF10A spheroids probing breast tumorigenesis [BibTeX]	2017		book
BibTeX: @book{Waschow2017, author = {Waschow, Marcel}, title = {siRNA high-content screening of 3D cultured MCF10A spheroids probing breast tumorigenesis}, year = {2017} }
Weidenhausen, J., Kopp, J., Armbruster, L., Wirtz, M., Lapouge, K. and Sinning, I.	Structural and functional characterization of the N-terminal acetyltransferase Naa50 [BibTeX]	2021	Structure	article	DOI
BibTeX: @article{Weidenhausen2021, author = {Jonas Weidenhausen and Jürgen Kopp and Laura Armbruster and Markus Wirtz and Karine Lapouge and Irmgard Sinning}, title = {Structural and functional characterization of the N-terminal acetyltransferase Naa50}, journal = {Structure}, publisher = {Elsevier BV}, year = {2021}, doi = {https://doi.org/10.1016/j.str.2020.12.004} }
Weidenhausen, J., Kopp, J., Ruger-Herreros, C., Stein, F., Haberkant, P., Lapouge, K. and Sinning, I.	Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity [Abstract] [BibTeX]	2022	International Journal of Molecular Sciences Vol. 23(18), pp. 10805	article	DOI URL
Abstract: Most eukaryotic proteins are N-terminally acetylated by a set of Nα acetyltransferases (NATs). This ancient and ubiquitous modification plays a fundamental role in protein homeostasis, while mutations are linked to human diseases and phenotypic defects. In particular, Naa50 features species-specific differences, as it is inactive in yeast but active in higher eukaryotes. Together with NatA, it engages in NatE complex formation for cotranslational acetylation. Here, we report Naa50 homologs from the filamentous fungi Chaetomium thermophilum and Neurospora crassa with significant N- and C-terminal extensions to the conserved GNAT domain. Structural and biochemical analyses show that CtNaa50 shares the GNAT structure and substrate specificity with other homologs. However, in contrast to previously analyzed Naa50 proteins, it does not form NatE. The elongated N-terminus increases Naa50 thermostability and binds to dynein light chain protein 1, while our data suggest that conserved positive patches in the C-terminus allow for ribosome binding independent of NatA. Our study provides new insights into the many facets of Naa50 and highlights the diversification of NATs during evolution.
BibTeX: @article{Weidenhausen2022, author = {Jonas Weidenhausen, Jürgen Kopp, Carmen Ruger-Herreros, Frank Stein, Per Haberkant, Karine Lapouge, Irmgard Sinning}, title = {Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity}, journal = {International Journal of Molecular Sciences}, publisher = {MDPI AG}, year = {2022}, volume = {23}, number = {18}, pages = {10805}, url = {https://www.mdpi.com/1422-0067/23/18/10805/pdf}, doi = {https://doi.org/10.3390/ijms231810805} }
Weidinger, B., Yang, G., von Coelln, N., Nirschl, H., Wacker, I., Tegeder, P., Schröder, R.R. and Blasco, E.	3D Printing Hierarchically Nano-Ordered Structures [BibTeX]	2023	Advanced Science Vol. 10(28)	article	DOI
BibTeX: @article{Weidinger2023, author = {Britta Weidinger and Guohui Yang and Nadine von Coelln and Hermann Nirschl and Irene Wacker and Petra Tegeder and Rasmus R. Schröder and Eva Blasco}, title = {3D Printing Hierarchically Nano-Ordered Structures}, journal = {Advanced Science}, publisher = {Wiley}, year = {2023}, volume = {10}, number = {28}, doi = {https://doi.org/10.1002/advs.202302756} }
Weidner, P., Söhn, M., Schroeder, T., Helm, L., Hauber, V., Gutting, T., Betge, J., Röcken, C., Rohrbacher, F.N., Pattabiraman, V.R., Bode, J.W., Seger, R., Saar, D., Nunes-Alves, A., Wade, R.C., Ebert, M.P.A. and Burgermeister, E.	Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma [BibTeX]	2020	Oncogenesis Vol. 9(6)	article	DOI
BibTeX: @article{Weidner2020, author = {Philip Weidner and Michaela Söhn and Torsten Schroeder and Laura Helm and Veronika Hauber and Tobias Gutting and Johannes Betge and Christoph Röcken and Florian N. Rohrbacher and Vijaya R. Pattabiraman and Jeffrey W. Bode and Rony Seger and Daniel Saar and Ariane Nunes-Alves and Rebecca C. Wade and Matthias P. A. Ebert and Elke Burgermeister}, title = {Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma}, journal = {Oncogenesis}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {9}, number = {6}, doi = {https://doi.org/10.1038/s41389-020-0238-8} }
von Weikersthal, F.F., Penter, T. and Redepenning, D.	Oktoberrevolution 1917: Ereignis, Rezeption, künstlerische Deutung [BibTeX]	2018		book
BibTeX: @book{Weikersthal2018, author = {von Weikersthal, Felicitas Fischer and Penter, Tanja and Redepenning, Dorothea}, title = {Oktoberrevolution 1917: Ereignis, Rezeption, künstlerische Deutung}, publisher = {Universitätsverlag Winter GmbH Heidelberg}, year = {2018} }
Weis, C.-A., Kather, J., Melchers, S., Al-ahmdi, H., Pollheimer, M., Langner, C. and Gaiser, T.	Automatic evaluation of tumor budding in immunohistochemically stained colorectal carcinomas and correlation to clinical outcome [BibTeX]	2018	Diagnostic Pathology Vol. 13	article	DOI
BibTeX: @article{Weis2018, author = {Weis, Cleo-Aron and Kather, Jakob and Melchers, Susanne and Al-ahmdi, Hanaa and Pollheimer, Marion and Langner, Cord and Gaiser, Timo}, title = {Automatic evaluation of tumor budding in immunohistochemically stained colorectal carcinomas and correlation to clinical outcome}, journal = {Diagnostic Pathology}, year = {2018}, volume = {13}, doi = {https://doi.org/10.1186/s13000-018-0739-3} }
Weis, C.-A., Bindzus, J.N., Voigt, J., Runz, M., Hertjens, S., Gaida, M.M., Popovic, Z.V. and Porubsky, S.	Assessment of glomerular morphological patterns by deep learning algorithms [BibTeX]	2022	Journal of Nephrology	article	DOI
BibTeX: @article{Weis2022, author = {Cleo-Aron Weis and Jan Niklas Bindzus and Jonas Voigt and Marlen Runz and Svetlana Hertjens and Matthias M. Gaida and Zoran V. Popovic and Stefan Porubsky}, title = {Assessment of glomerular morphological patterns by deep learning algorithms}, journal = {Journal of Nephrology}, publisher = {Springer Science and Business Media LLC}, year = {2022}, doi = {https://doi.org/10.1007/s40620-021-01221-9} }
Weis, C.-A., Weihrauch, K.R., Kriegsmann, K. and Kriegsmann, M.	Unsupervised Segmentation in NSCLC: How to Map the Output of Unsupervised Segmentation to Meaningful Histological Labels by Linear Combination? [BibTeX]	2022	Applied Sciences Vol. 12(8), pp. 3718	article	DOI URL
BibTeX: @article{Weis2022, author = {Cleo-Aron Weis, Kian R. Weihrauch, Katharina Kriegsmann, Mark Kriegsmann}, title = {Unsupervised Segmentation in NSCLC: How to Map the Output of Unsupervised Segmentation to Meaningful Histological Labels by Linear Combination?}, journal = {Applied Sciences}, publisher = {MDPI AG}, year = {2022}, volume = {12}, number = {8}, pages = {3718}, url = {https://www.mdpi.com/2076-3417/12/8/3718/pdf}, doi = {https://doi.org/10.3390/app12083718} }
Wentzensen, N., Lahrmann, B., Clarke, M.A., Kinney, W., Tokugawa, D., Poitras, N., Locke, A., Bartels, L., Krauthoff, A., Walker, J., Zuna, R., Grewal, K.K., Goldhoff, P.E., Kingery, J.D., Castle, P.E., Schiffman, M., Lorey, T.S. and Grabe, N.	Accuracy and Efficiency of Deep-Learning–Based Automation of Dual Stain Cytology in Cervical Cancer Screening [BibTeX]	2020	JNCI: Journal of the National Cancer Institute Vol. 113(1), pp. 72-79	article	DOI
BibTeX: @article{Wentzensen2020, author = {Nicolas Wentzensen and Bernd Lahrmann and Megan A Clarke and Walter Kinney and Diane Tokugawa and Nancy Poitras and Alex Locke and Liam Bartels and Alexandra Krauthoff and Joan Walker and Rosemary Zuna and Kiranjit K Grewal and Patricia E Goldhoff and Julie D Kingery and Philip E Castle and Mark Schiffman and Thomas S Lorey and Niels Grabe}, title = {Accuracy and Efficiency of Deep-Learning–Based Automation of Dual Stain Cytology in Cervical Cancer Screening}, journal = {JNCI: Journal of the National Cancer Institute}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {113}, number = {1}, pages = {72--79}, doi = {https://doi.org/10.1093/jnci/djaa066} }
Werhahn, S.M., Kreusser, J.S., Hagenmüller, M., Beckendorf, J., Diemert, N., Hoffmann, S., Schultz, J.-H., Backs, J. and Dewenter, M.	Adaptive versus maladaptive cardiac remodelling in response to sustained upbeta-adrenergic stimulation in a new `ISO on/off model' [BibTeX]	2021	PLOS ONE Vol. 16(6), pp. e0248933	article	DOI
BibTeX: @article{Werhahn2021, author = {Stefanie Maria Werhahn and Julia S. Kreusser and Marco Hagenmüller and Jan Beckendorf and Nathalie Diemert and Sophia Hoffmann and Jobst-Hendrik Schultz and Johannes Backs and Matthias Dewenter}, title = {Adaptive versus maladaptive cardiac remodelling in response to sustained upbeta-adrenergic stimulation in a new `ISO on/off model'}, journal = {PLOS ONE}, publisher = {Public Library of Science (PLoS)}, year = {2021}, volume = {16}, number = {6}, pages = {e0248933}, doi = {https://doi.org/10.1371/journal.pone.0248933} }
Wetzel, S., Geldsetzer, P., Mani, S.S., Gupta, A., Singh, K., Ali, M.K., Prabhakaran, D., Tandon, N. and Sudharsanan, N.	Changing socioeconomic and geographic gradients in cardiovascular disease risk factors among Indians aged 15–49 years – evidence from nationally representative household surveys [BibTeX]	2023	The Lancet Regional Health - Southeast Asia Vol. 12, pp. 100188	article	DOI URL
BibTeX: @article{Wetzel2023, author = {Sarah Wetzel, Pascal Geldsetzer, Sneha Sarah Mani, Aashish Gupta, Kavita Singh, Mohammed K. Ali, Dorairaj Prabhakaran, Nikhil Tandon, Nikkil Sudharsanan}, title = {Changing socioeconomic and geographic gradients in cardiovascular disease risk factors among Indians aged 15–49 years – evidence from nationally representative household surveys}, journal = {The Lancet Regional Health - Southeast Asia}, publisher = {Elsevier BV}, year = {2023}, volume = {12}, pages = {100188}, url = {https://api.elsevier.com/content/article/PII:S2772368223000483?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.lansea.2023.100188} }
Wetzel, S., Sarker, M., Hasan, M., Talukder, A., Sudharsanan, N. and Geldsetzer, P.	Rapidly rising diabetes and increasing body weight: A counterfactual analysis in repeated cross-sectional nationally representative data from Bangladesh [BibTeX]	2023	Epidemiology Vol. Publish Ahead of Print	article	DOI
BibTeX: @article{Wetzel2023a, author = {Sarah Wetzel, Malabika Sarker, Mehedi Hasan, Animesh Talukder, Nikkil Sudharsanan, Pascal Geldsetzer}, title = {Rapidly rising diabetes and increasing body weight: A counterfactual analysis in repeated cross-sectional nationally representative data from Bangladesh}, journal = {Epidemiology}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, year = {2023}, volume = {Publish Ahead of Print}, doi = {https://doi.org/10.1097/EDE.0000000000001622} }
Weyer, F.A., Gumiero, A., Lapouge, K., Bange, G., Kopp, J. and Sinning, I.	Structural basis of HypK regulating N-terminal acetylation by the NatA complex [Abstract] [BibTeX]	2017	Nature Communications Vol. 8(1), pp. 15726	article	DOI
Abstract: In eukaryotes, N-terminal acetylation is one of the most common protein modifications involved in a wide range of biological processes. Most N-acetyltransferase complexes (NATs) act co-translationally, with the heterodimeric NatA complex modifying the majority of substrate proteins. Here we show that the Huntingtin yeast two-hybrid protein K (HypK) binds tightly to the NatA complex comprising the auxiliary subunit Naa15 and the catalytic subunit Naa10. The crystal structures of NatA bound to HypK or to a N-terminal deletion variant of HypK were determined without or with a bi-substrate analogue, respectively. The HypK C-terminal region is responsible for high-affinity interaction with the C-terminal part of Naa15. In combination with acetylation assays, the HypK N-terminal region is identified as a negative regulator of the NatA acetylation activity. Our study provides mechanistic insights into the regulation of this pivotal protein modification.
BibTeX: @article{Weyer2017, author = {Weyer, Felix Alexander and Gumiero, Andrea and Lapouge, Karine and Bange, Gert and Kopp, Jürgen and Sinning, Irmgard}, title = {Structural basis of HypK regulating N-terminal acetylation by the NatA complex}, journal = {Nature Communications}, year = {2017}, volume = {8}, number = {1}, pages = {15726}, doi = {https://doi.org/10.1038/ncomms15726} }
Weyer, F.A., Gumiero, A., Gesé, G.V., Lapouge, K. and Sinning, I.	Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex [Abstract] [BibTeX]	2017	Nature Structural & Molecular Biology Vol. 24(2), pp. 144-151	article	DOI
Abstract: The yeast ribosome-associated complex (RAC) is formed by Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1. Structural analyses show Ssz1 in a hybrid conformation between the open and closed state and its substrate-binding domain completed by Zuo1.
BibTeX: @article{Weyer2017a, author = {Weyer, Felix Alexander and Gumiero, Andrea and Gesé, Genís Valentín and Lapouge, Karine and Sinning, Irmgard}, title = {Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex}, journal = {Nature Structural & Molecular Biology}, year = {2017}, volume = {24}, number = {2}, pages = {144--151}, doi = {https://doi.org/10.1038/nsmb.3349} }
Whitworth, D.J., Smith, R.J., Tress, R., Kay, S.T., Glover, S.C.O., Sormani, M.C. and Klessen, R.S.	Is the molecular KS relationship universal down to low metallicities? [Abstract] [BibTeX]	2021	Monthly Notices of the Royal Astronomical Society Vol. 510(3), pp. 4146-4165	article	DOI
Abstract: ABSTRACT In recent years, it has been speculated that in extreme low-metallicity galactic environments, stars form in regions that lack H2. In this paper, we investigate how changing the metallicity and ultraviolet (UV) field strength of a galaxy affects the star formation within, and the molecular gas Kennicutt–Schmidt (KS) relation. Using extremely high-resolution arepo simulations of isolated dwarf galaxies, we independently vary the metallicity and UV field to between 1 per cent and 10 per cent solar neighbourhood values. We include a non-equilibrium, time-dependent chemical network to model the molecular composition of the interstellar medium and include the effects of gas shielding from an ambient UV field. Crucially, our simulations directly model the gravitational collapse of gas into star-forming clumps and cores and their subsequent accretion using sink particles. In this first publication, we find that reducing the metallicity and UV field by a factor of 10 has no effect on star formation and minimal effect on the cold, dense star-forming gas. The cold gas depletion times are almost an order of magnitude longer than the molecular gas depletion time due to the presence of star formation in H i dominated cold gas. We study the H2 KS relationship that arises naturally within the simulations and find a near-linear power-law index of N = 1.09 ± 0.014 in our fiducial 10 rm per cent solar metallicity model. As the metallicity and UV field are reduced, this becomes moderately steeper, with a slope of N = 1.24 ± 0.022 for our 1 rm per cent solar metallicity and 1 rm per cent solar UV field model.
BibTeX: @article{Whitworth2021, author = {David J Whitworth, Rowan J Smith, Robin Tress, Scott T Kay, Simon C O Glover, Mattia C Sormani, Ralf S Klessen}, title = {Is the molecular KS relationship universal down to low metallicities?}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2021}, volume = {510}, number = {3}, pages = {4146--4165}, doi = {https://doi.org/10.1093/mnras/stab3622} }
Wichtmann, B.D., Albert, S., Zhao, W., Maurer, A., Rödel, C., Hofheinz, R.-D., Hesser, J., Zöllner, F.G. and Attenberger, U.I.	Are We There Yet? The Value of Deep Learning in a Multicenter Setting for Response Prediction of Locally Advanced Rectal Cancer to Neoadjuvant Chemoradiotherapy [Abstract] [BibTeX]	2022	Diagnostics Vol. 12(7), pp. 1601	article	DOI URL
Abstract: This retrospective study aims to evaluate the generalizability of a promising state-of-the-art multitask deep learning (DL) model for predicting the response of locally advanced rectal cancer (LARC) to neoadjuvant chemoradiotherapy (nCRT) using a multicenter dataset. To this end, we retrained and validated a Siamese network with two U-Nets joined at multiple layers using pre- and post-therapeutic T2-weighted (T2w), diffusion-weighted (DW) images and apparent diffusion coefficient (ADC) maps of 83 LARC patients acquired under study conditions at four different medical centers. To assess the predictive performance of the model, the trained network was then applied to an external clinical routine dataset of 46 LARC patients imaged without study conditions. The training and test datasets differed significantly in terms of their composition, e.g., T-/N-staging, the time interval between initial staging/nCRT/re-staging and surgery, as well as with respect to acquisition parameters, such as resolution, echo/repetition time, flip angle and field strength. We found that even after dedicated data pre-processing, the predictive performance dropped significantly in this multicenter setting compared to a previously published single- or two-center setting. Testing the network on the external clinical routine dataset yielded an area under the receiver operating characteristic curve of 0.54 (95% confidence interval [CI]: 0.41, 0.65), when using only pre- and post-therapeutic T2w images as input, and 0.60 (95% CI: 0.48, 0.71), when using the combination of pre- and post-therapeutic T2w, DW images, and ADC maps as input. Our study highlights the importance of data quality and harmonization in clinical trials using machine learning. Only in a joint, cross-center effort, involving a multidisciplinary team can we generate large enough curated and annotated datasets and develop the necessary pre-processing pipelines for data harmonization to successfully apply DL models clinically.
BibTeX: @article{Wichtmann2022, author = {Barbara D. Wichtmann, Steffen Albert, Wenzhao Zhao, Angelika Maurer, Claus Rödel, Ralf-Dieter Hofheinz, Jürgen Hesser, Frank G. Zöllner, Ulrike I. Attenberger}, title = {Are We There Yet? The Value of Deep Learning in a Multicenter Setting for Response Prediction of Locally Advanced Rectal Cancer to Neoadjuvant Chemoradiotherapy}, journal = {Diagnostics}, publisher = {MDPI AG}, year = {2022}, volume = {12}, number = {7}, pages = {1601}, url = {https://www.mdpi.com/2075-4418/12/7/1601/pdf}, doi = {https://doi.org/10.3390/diagnostics12071601} }
Wild, K., Aleksić, M., Lapouge, K., Juaire, K.D., Flemming, D., Pfeffer, S. and Sinning, I.	MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Wild2020, author = {Klemens Wild and Milan Aleksić and Karine Lapouge and Keven D. Juaire and Dirk Flemming and Stefan Pfeffer and Irmgard Sinning}, title = {MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-14603-7} }
Williams, M.P.I., Rigon, M., Straka, T., Hörner, S.J., Thiel, M., Gretz, N., Hafner, M., Reischl, M. and Rudolf, R.	A Novel Optical Tissue Clearing Protocol for Mouse Skeletal Muscle to Visualize Endplates in Their Tissue Context [Abstract] [BibTeX]	2019	Frontiers in Cellular Neuroscience Vol. 13, pp. 49	article	DOI
Abstract: Neuromuscular junctions (NMJs) mediate skeletal muscle contractions and play an important role in several neuromuscular disorders when their morphology and function are compromised. However, due to their small size and sparse distribution throughout the comparatively large, inherently opaque muscle tissue the analysis of NMJ morphology has been limited to teased fiber preparations, longitudinal muscle sections, and flat muscles. Consequently, whole mount analyses of NMJ morphology, numbers, their distribution, and assignment to a given muscle fiber have also been impossible to determine in muscle types that are frequently used in experimental paradigms. This impossibility is exacerbated by the lack of optical tissue clearing techniques that are compatible with clear and persistent NMJ stains. Here, we present MYOCLEAR, a novel and highly reproducible muscle tissue clearing protocol. Based on hydrogel-based tissue clearing methods, this protocol permits the labeling and detection of all NMJs in adult hindleg extensor digitorum longus muscles from wildtype and diseased mice. The method is also applicable to adult mouse diaphragm muscles and can be used for different staining agents, including toxins, lectins, antibodies, and nuclear dyes. It will be useful in understanding the distribution, morphological features, and muscle tissue context of NMJs in hindleg muscle whole mounts for biomedical and basic research.
BibTeX: @article{Williams2019, author = {Williams, Marion Patrick Ivey and Rigon, Matteo and Straka, Tatjana and Hörner, Sarah Janice and Thiel, Manfred and Gretz, Norbert and Hafner, Mathias and Reischl, Markus and Rudolf, Rüdiger}, title = {A Novel Optical Tissue Clearing Protocol for Mouse Skeletal Muscle to Visualize Endplates in Their Tissue Context}, journal = {Frontiers in Cellular Neuroscience}, year = {2019}, volume = {13}, pages = {49}, doi = {https://doi.org/10.3389/fncel.2019.00049} }
Winkler, M., Biswas, S., Berger, S.M., Küchler, M., Preisendörfer, L., Choo, M., Früh, S., Rem, P.D., Enkel, T., Arnold, B., Komljenovic, D., Sticht, C., Goerdt, S., Bettler, B., von Bohlen und Halbach, O., Bartsch, D. and Géraud, C.	Pianp deficiency links GABAB receptor signaling and hippocampal and cerebellar neuronal cell composition to autism-like behavior [Abstract] [BibTeX]	2019	Molecular Psychiatry	article	DOI
Abstract: Pianp (also known as Leda-1) is a type I transmembrane protein with preferential expression in the mammalian CNS. Its processing is characterized by proteolytic cleavage by a range of proteases including Adam10, Adam17, MMPs, and the γ-secretase complex. Pianp can interact with Pilrα and the GB1a subunit of the GABAB receptor (GBR) complex. A recent case description of a boy with global developmental delay and homozygous nonsense variant in PIANP supports the hypothesis that PIANP is involved in the control of behavioral traits in mammals. To investigate the physiological functions of Pianp, constitutive, global knockout mice were generated and comprehensively analyzed. Broad assessment did not indicate malformation or malfunction of internal organs. In the brain, however, decreased sizes and altered cellular compositions of the dentate gyrus as well as the cerebellum, including a lower number of cerebellar Purkinje cells, were identified. Functionally, loss of Pianp led to impaired presynaptic GBR-mediated inhibition of glutamate release and altered gene expression in the cortex, hippocampus, amygdala, and hypothalamus including downregulation of Erdr1, a gene linked to autism-like behavior. Behavioral phenotyping revealed that Pianp deficiency leads to context-dependent enhanced anxiety and spatial learning deficits, an altered stress response, severely impaired social interaction, and enhanced repetitive behavior, which all represent characteristic features of an autism spectrum disorder-like phenotype. Altogether, Pianp represents a novel candidate gene involved in autism-like behavior, cerebellar and hippocampal pathology, and GBR signaling.
BibTeX: @article{Winkler2019, author = {Winkler, Manuel and Biswas, Siladitta and Berger, Stefan M. and Küchler, Moritz and Preisendörfer, Laurens and Choo, Myeongjeong and Früh, Simon and Rem, Pascal D. and Enkel, Thomas and Arnold, Bernd and Komljenovic, Dorde and Sticht, Carsten and Goerdt, Sergij and Bettler, Bernhard and von Bohlen und Halbach, Oliver and Bartsch, Dusan and Géraud, Cyrill}, title = {Pianp deficiency links GABAB receptor signaling and hippocampal and cerebellar neuronal cell composition to autism-like behavior}, journal = {Molecular Psychiatry}, year = {2019}, doi = {https://doi.org/10.1038/s41380-019-0519-9} }
Winkler, M., Staniczek, T., Kürschner, S.W., Schmid, C.D., Schönhaber, H., Cordero, J., Kessler, L., Mathes, A., Sticht, C., Neßling, M., Uvarovskii, A., Anders, S., Zhang, X.-j., von Figura, G., Hartmann, D., Mogler, C., Dobreva, G., Schledzewski, K., Géraud, C., Koch, P.-S. and Goerdt, S.	Endothelial GATA4 controls liver fibrosis and regeneration by preventing a pathogenic switch in angiocrine signaling [BibTeX]	2021	Journal of Hepatology Vol. 74(2), pp. 380-393	article	DOI
BibTeX: @article{Winkler2021, author = {Manuel Winkler and Theresa Staniczek and Sina Wietje Kürschner and Christian David Schmid and Hiltrud Schönhaber and Julio Cordero and Linda Kessler and Arthur Mathes and Carsten Sticht and Michelle Neßling and Alexey Uvarovskii and Simon Anders and Xue-jun Zhang and Guido von Figura and Daniel Hartmann and Carolin Mogler and Gergana Dobreva and Kai Schledzewski and Cyrill Géraud and Philipp-Sebastian Koch and Sergij Goerdt}, title = {Endothelial GATA4 controls liver fibrosis and regeneration by preventing a pathogenic switch in angiocrine signaling}, journal = {Journal of Hepatology}, publisher = {Elsevier BV}, year = {2021}, volume = {74}, number = {2}, pages = {380--393}, doi = {https://doi.org/10.1016/j.jhep.2020.08.033} }
Winter, S.L. and Chlanda, P.	Dual-axis Volta phase plate cryo-electron tomography of Ebola virus-like particles reveals actin-VP40 interactions [BibTeX]	2021	Journal of Structural Biology Vol. 213(2), pp. 107742	article	DOI
BibTeX: @article{Winter2021, author = {Sophie L. Winter and Petr Chlanda}, title = {Dual-axis Volta phase plate cryo-electron tomography of Ebola virus-like particles reveals actin-VP40 interactions}, journal = {Journal of Structural Biology}, publisher = {Elsevier BV}, year = {2021}, volume = {213}, number = {2}, pages = {107742}, doi = {https://doi.org/10.1016/j.jsb.2021.107742} }
Winter, S.L., Golani, G., Lolicato, F., Vallbracht, M., Thiyagarajah, K., Ahmed, S.S., Lüchtenborg, C., Fackler, O.T., Brügger, B., Hoenen, T., Nickel, W., Schwarz, U.S. and Chlanda, P.	The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion [BibTeX]	2023	The EMBO Journal Vol. 42(11)	article	DOI
BibTeX: @article{Winter2023, author = {Sophie L Winter and Gonen Golani and Fabio Lolicato and Melina Vallbracht and Keerthihan Thiyagarajah and Samy Sid Ahmed and Christian Lüchtenborg and Oliver T Fackler and Britta Brügger and Thomas Hoenen and Walter Nickel and Ulrich S Schwarz and Petr Chlanda}, title = {The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion}, journal = {The EMBO Journal}, publisher = {EMBO}, year = {2023}, volume = {42}, number = {11}, doi = {https://doi.org/10.15252/embj.2023113578} }
Witt, R., Loos, L. and Zipf, A.	Analysing the Impact of Large Data Imports in OpenStreetMap [BibTeX]	2021	ISPRS International Journal of Geo-Information Vol. 10(8), pp. 528	article	DOI
BibTeX: @article{Witt2021, author = {Raphael Witt and Lukas Loos and Alexander Zipf}, title = {Analysing the Impact of Large Data Imports in OpenStreetMap}, journal = {ISPRS International Journal of Geo-Information}, publisher = {MDPI AG}, year = {2021}, volume = {10}, number = {8}, pages = {528}, doi = {https://doi.org/10.3390/ijgi10080528} }
Wittmer, P., Schmied, C.-M., Gasenzer, T. and Ewerz, C.	Vortex motion quantifies strong dissipation in a holographic superfluid [BibTeX]	2021	Vol. 127	article	DOI
BibTeX: @article{Wittmer2021, author = {Paul Wittmer and Christian-Marcel Schmied and Thomas Gasenzer and Carlo Ewerz}, title = {Vortex motion quantifies strong dissipation in a holographic superfluid}, publisher = {American Physical Society (APS)}, year = {2021}, volume = {127}, doi = {https://doi.org/10.1103/physrevlett.127.101601} }
Wohlfeil, S.A., Häfele, V., Dietsch, B., Schledzewski, K., Winkler, M., Zierow, J., Leibing, T., Mohammadi, M.M., Heineke, J., Sticht, C., Olsavszky, V., Koch, P.-S., Géraud, C. and Goerdt, S.	Hepatic Endothelial Notch Activation Protects against Liver Metastasis by Regulating Endothelial-Tumor Cell Adhesion Independent of Angiocrine Signaling [Abstract] [BibTeX]	2019	Cancer Research Vol. 79(3), pp. 598-610	article	DOI URL
Abstract: The interaction of tumor cells with organ-specific endothelial cells (EC) is an important step during metastatic progression. Notch signaling in organ-specific niches has been implicated in mediating opposing effects on organotropic metastasis to the lungs and the liver, respectively. In this study, we scrutinized the role of endothelial Notch activation during liver metastasis. To target hepatic EC (HEC), a novel EC subtype-specific Cre driver mouse was generated. Clec4g-Cretg/wt mice were crossed to Rosa26N1ICD-IRES-GFP to enhance Notch signaling in HEC (NICDOE-HEC). In NICDOE-HEC mice, hepatic metastasis of malignant melanoma and colorectal carcinoma was significantly reduced. These mice revealed reduced liver growth and impaired metabolic zonation due to suppression of hepatic angiocrine Wnt signaling. Hepatic metastasis, however, was not controlled by angiocrine Wnt signaling, as deficiency of the Wnt cargo receptor Wls in HEC of WlsHEC-KO mice did not affect hepatic metastasis. In contrast, the hepatic microvasculature in NICDOE-HEC mice revealed a special form of sinusoidal capillarization, with effacement of endothelial zonation functionally paralleled by reduced tumor cell adhesion in vivo. Notably, expression of endothelial adhesion molecule ICAM1 by HEC was significantly reduced. Treatment with an anti-ICAM1 antibody significantly inhibited tumor cell adhesion to HEC in wild-type mice confirming that Notch controls hepatic metastasis via modulation of HEC adhesion molecules. As endothelial Notch activation in the lung has been shown to promote lung metastasis, tumor therapy will require approaches that target Notch in an organ-, cell type-, and context-specific manner.Significance: Manipulation of Notch signaling in the endothelium has opposing, organ-specific effects on metastasis to the lung and the liver, demonstrating that this pathway should be targeted in a cell- and context-specific fashion.
BibTeX: @article{Wohlfeil2019, author = {Wohlfeil, Sebastian A. and Häfele, Verena and Dietsch, Bianca and Schledzewski, Kai and Winkler, Manuel and Zierow, Johanna and Leibing, Thomas and Mohammadi, Mona Malek and Heineke, Joerg and Sticht, Carsten and Olsavszky, Victor and Koch, Philipp-Sebastian and Géraud, Cyrill and Goerdt, Sergij}, title = {Hepatic Endothelial Notch Activation Protects against Liver Metastasis by Regulating Endothelial-Tumor Cell Adhesion Independent of Angiocrine Signaling}, journal = {Cancer Research}, publisher = {American Association for Cancer Research}, year = {2019}, volume = {79}, number = {3}, pages = {598--610}, url = {https://cancerres.aacrjournals.org/content/79/3/598}, doi = {https://doi.org/10.1158/0008-5472.CAN-18-1752} }
Wohlfeil, S.A., Häfele, V., Dietsch, B., Weller, C., Sticht, C., Jauch, A.S., Winkler, M., Schmid, C.D., Irkens, A.L., Olsavszky, A., Schledzewski, K., Reiners-Koch, P.-S., Goerdt, S. and Géraud, C.	Angiogenic and molecular diversity determine hepatic melanoma metastasis and response to anti-angiogenic treatment [BibTeX]	2022	Journal of Translational Medicine Vol. 20(1)	article	DOI
BibTeX: @article{Wohlfeil2022, author = {Sebastian A. Wohlfeil and Verena Häfele and Bianca Dietsch and Céline Weller and Carsten Sticht and Anna Sophia Jauch and Manuel Winkler and Christian David Schmid and Anna Lena Irkens and Ana Olsavszky and Kai Schledzewski and Philipp-Sebastian Reiners-Koch and Sergij Goerdt and Cyrill Géraud}, title = {Angiogenic and molecular diversity determine hepatic melanoma metastasis and response to anti-angiogenic treatment}, journal = {Journal of Translational Medicine}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {20}, number = {1}, doi = {https://doi.org/10.1186/s12967-022-03255-4} }
Wollenberg, K.M.J.	Diversity of Population III star formation [BibTeX]	2019		book
BibTeX: @book{Wollenberg2019, author = {Wollenberg, Katharina M. J.}, title = {Diversity of Population III star formation}, publisher = {Universität Heidelberg}, year = {2019} }
Wollenberg, K.M.J., Glover, S.C.O., Clark, P.C. and Klessen, R.S.	Formation sites of Population III star formation: The effects of different levels of rotation and turbulence on the fragmentation behaviour of primordial gas [BibTeX]	2020	Monthly Notices of the Royal Astronomical Society Vol. 494(2), pp. 1871-1893	article	DOI
BibTeX: @article{Wollenberg2020, author = {Katharina M J Wollenberg and Simon C O Glover and Paul C Clark and Ralf S Klessen}, title = {Formation sites of Population III star formation: The effects of different levels of rotation and turbulence on the fragmentation behaviour of primordial gas}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Oxford University Press (OUP)}, year = {2020}, volume = {494}, number = {2}, pages = {1871--1893}, doi = {https://doi.org/10.1093/mnras/staa289} }
Wolny, A., Cerrone, L., Vijayan, A., Tofanelli, R., Barro, A.V., Louveaux, M., Wenzl, C., Strauss, S., Wilson-Sánchez, D., Lymbouridou, R., Steigleder, S.S., Pape, C., Bailoni, A., Duran-Nebreda, S., Bassel, G.W., Lohmann, J.U., Tsiantis, M., Hamprecht, F.A., Schneitz, K., Maizel, A. and Kreshuk, A.	Accurate and versatile 3D segmentation of plant tissues at cellular resolution [BibTeX]	2020	eLife Vol. 9	article	DOI
BibTeX: @article{Wolny2020, author = {Adrian Wolny and Lorenzo Cerrone and Athul Vijayan and Rachele Tofanelli and Amaya Vilches Barro and Marion Louveaux and Christian Wenzl and Sören Strauss and David Wilson-Sánchez and Rena Lymbouridou and Susanne S Steigleder and Constantin Pape and Alberto Bailoni and Salva Duran-Nebreda and George W Bassel and Jan U Lohmann and Miltos Tsiantis and Fred A Hamprecht and Kay Schneitz and Alexis Maizel and Anna Kreshuk}, title = {Accurate and versatile 3D segmentation of plant tissues at cellular resolution}, journal = {eLife}, publisher = {eLife Sciences Publications, Ltd}, year = {2020}, volume = {9}, doi = {https://doi.org/10.7554/elife.57613} }
Wong, T., Hughes, A., Tokuda, K., Indebetouw, R., Onishi, T., Bandurski, J.B., Chen, C.-H.R., Fukui, Y., Glover, S.C.O., Klessen, R.S., Pineda, J.L., Roman-Duval, J., Sewiło, M., Wojciechowski, E. and Zahorecz, S.	Relations between Molecular Cloud Structure Sizes and Line Widths in the Large Magellanic Cloud [BibTeX]	2019	The Astrophysical Journal Vol. 885(1), pp. 50	article	DOI
BibTeX: @article{Wong2019, author = {Tony Wong and Annie Hughes and Kazuki Tokuda and Rémy Indebetouw and Toshikazu Onishi and Jeffrey B. Bandurski and C.-H. Rosie Chen and Yasuo Fukui and Simon C. O. Glover and Ralf S. Klessen and Jorge L. Pineda and Julia Roman-Duval and Marta Sewiło and Evan Wojciechowski and Sarolta Zahorecz}, title = {Relations between Molecular Cloud Structure Sizes and Line Widths in the Large Magellanic Cloud}, journal = {The Astrophysical Journal}, publisher = {American Astronomical Society}, year = {2019}, volume = {885}, number = {1}, pages = {50}, doi = {https://doi.org/10.3847/1538-4357/ab46ba} }
Woods, T.E., Agarwal, B., Bromm, V., Bunker, A., Chen, K.-J., Chon, S., Ferrara, A., Glover, S.C.O., Haemmerlé, L., Haiman, Z., Hartwig, T., Heger, A., Hirano, S., Hosokawa, T., Inayoshi, K., Klessen, R.S., Kobayashi, C., Koliopanos, F., Latif, M.A., Li, Y., Mayer, L., Mezcua, M., Natarajan, P., Pacucci, F., Rees, M.J., Regan, J.A., Sakurai, Y., Salvadori, S., Schneider, R., Surace, M., Tanaka, T.L., Whalen, D.J. and Yoshida, N.	Titans of the early Universe: The Prato statement on the origin of the first supermassive black holes [BibTeX]	2019	Publications of the Astronomical Society of Australia Vol. 36	article	DOI
BibTeX: @article{Woods2019, author = {Tyrone E. Woods and Bhaskar Agarwal and Volker Bromm and Andrew Bunker and Ke-Jung Chen and Sunmyon Chon and Andrea Ferrara and Simon C. O. Glover and Lionel Haemmerlé and Zoltán Haiman and Tilman Hartwig and Alexander Heger and Shingo Hirano and Takashi Hosokawa and Kohei Inayoshi and Ralf S. Klessen and Chiaki Kobayashi and Filippos Koliopanos and Muhammad A. Latif and Yuexing Li and Lucio Mayer and Mar Mezcua and Priyamvada Natarajan and Fabio Pacucci and Martin J. Rees and John A. Regan and Yuya Sakurai and Stefania Salvadori and Raffaella Schneider and Marco Surace and Takamitsu L. Tanaka and Daniel J. Whalen and Naoki Yoshida}, title = {Titans of the early Universe: The Prato statement on the origin of the first supermassive black holes}, journal = {Publications of the Astronomical Society of Australia}, publisher = {Cambridge University Press (CUP)}, year = {2019}, volume = {36}, doi = {https://doi.org/10.1017/pasa.2019.14} }
Würtz, M., Böhler, A., Neuner, A., Zupa, E., Rohland, L., Liu, P., Vermeulen, B.J.A., Pfeffer, S., Eustermann, S. and Schiebel, E.	Reconstitution of the recombinant human upgamma-tubulin ring complex [BibTeX]	2021	Open Biology Vol. 11(2)	article	DOI
BibTeX: @article{Wuertz2021, author = {Martin Würtz and Anna Böhler and Annett Neuner and Erik Zupa and Lukas Rohland and Peng Liu and Bram J. A. Vermeulen and Stefan Pfeffer and Sebastian Eustermann and Elmar Schiebel}, title = {Reconstitution of the recombinant human upgamma-tubulin ring complex}, journal = {Open Biology}, publisher = {The Royal Society}, year = {2021}, volume = {11}, number = {2}, doi = {https://doi.org/10.1098/rsob.200325} }
Würtz, M., Zupa, E., Atorino, E.S., Neuner, A., Böhler, A., Rahadian, A.S., Vermeulen, B.J.A., Tonon, G., Eustermann, S., Schiebel, E. and Pfeffer, S.	Modular assembly of the principal microtubule nucleator upgamma-TuRC [BibTeX]	2022	Nature Communications Vol. 13	article	DOI
BibTeX: @article{Wuertz2022, author = {Martin Würtz and Erik Zupa and Enrico S. Atorino and Annett Neuner and Anna Böhler and Ariani S. Rahadian and Bram J. A. Vermeulen and Giulia Tonon and Sebastian Eustermann and Elmar Schiebel and Stefan Pfeffer}, title = {Modular assembly of the principal microtubule nucleator upgamma-TuRC}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {13}, doi = {https://doi.org/10.1038/s41467-022-28079-0} }
Xia, L., Xu, Z., Zhou, X., Bergmann, F., Grabe, N., Büchler, M.W., Neoptolemos, J.P., Hackert, T., Kroemer, G. and Fortunato, F.	Impaired autophagy increases susceptibility to endotoxin-induced chronic pancreatitis [BibTeX]	2020	Cell Death & Disease Vol. 11(10)	article	DOI
BibTeX: @article{Xia2020, author = {L. Xia and Z. Xu and X. Zhou and F. Bergmann and N. Grabe and M. W. Büchler and J. P. Neoptolemos and T. Hackert and G. Kroemer and F. Fortunato}, title = {Impaired autophagy increases susceptibility to endotoxin-induced chronic pancreatitis}, journal = {Cell Death & Disease}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {10}, doi = {https://doi.org/10.1038/s41419-020-03050-3} }
Xydia, M., Rahbari, R., Ruggiero, E., Macaulay, I., Tarabichi, M., Lohmayer, R., Wilkening, S., Michels, T., Brown, D., Vanuytven, S., Mastitskaya, S., Laidlaw, S., Grabe, N., Pritsch, M., Fronza, R., Hexel, K., Schmitt, S., Müller-Steinhardt, M., Halama, N., Domschke, C., Schmidt, M., von Kalle, C., Schütz, F., Voet, T. and Beckhove, P.	Common clonal origin of conventional T cells and induced regulatory T cells in breast cancer patients [BibTeX]	2021	Nature Communications Vol. 12(1)	article	DOI
BibTeX: @article{Xydia2021, author = {Maria Xydia and Raheleh Rahbari and Eliana Ruggiero and Iain Macaulay and Maxime Tarabichi and Robert Lohmayer and Stefan Wilkening and Tillmann Michels and Daniel Brown and Sebastiaan Vanuytven and Svetlana Mastitskaya and Sean Laidlaw and Niels Grabe and Maria Pritsch and Raffaele Fronza and Klaus Hexel and Steffen Schmitt and Michael Müller-Steinhardt and Niels Halama and Christoph Domschke and Manfred Schmidt and Christof von Kalle and Florian Schütz and Thierry Voet and Philipp Beckhove}, title = {Common clonal origin of conventional T cells and induced regulatory T cells in breast cancer patients}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2021}, volume = {12}, number = {1}, doi = {https://doi.org/10.1038/s41467-021-21297-y} }
Yan, Y., Schultz, M. and Zipf, A.	An exploratory analysis of usability of Flickr tags for land use/land cover attribution [BibTeX]	2019	Geo-spatial Information Science Vol. 22(1), pp. 12-22	article	DOI
BibTeX: @article{Yan2019, author = {Yingwei Yan and Michael Schultz and Alexander Zipf}, title = {An exploratory analysis of usability of Flickr tags for land use/land cover attribution}, journal = {Geo-spatial Information Science}, publisher = {Informa UK Limited}, year = {2019}, volume = {22}, number = {1}, pages = {12--22}, doi = {https://doi.org/10.1080/10095020.2018.1560044} }
Zhan, T., Ambrosi, G., Wandmacher, A.M., Rauscher, B., Betge, J., Rindtorff, N., Häussler, R.S., Hinsenkamp, I., Bamberg, L., Hessling, B., Müller-Decker, K., Erdmann, G., Burgermeister, E., Ebert, M.P. and Boutros, M.	MEK inhibitors activate Wnt signalling and induce stem cell plasticity in colorectal cancer [Abstract] [BibTeX]	2019	Nature Communications Vol. 10(1), pp. 2197	article	DOI
Abstract: In colorectal cancer (CRC), aberrant Wnt signalling is essential for tumorigenesis and maintenance of cancer stem cells. However, how other oncogenic pathways converge on Wnt signalling to modulate stem cell homeostasis in CRC currently remains poorly understood. Using large-scale compound screens in CRC, we identify MEK1/2 inhibitors as potent activators of Wnt/β-catenin signalling. Targeting MEK increases Wnt activity in different CRC cell lines and murine intestine in vivo. Truncating mutations of APC generated by CRISPR/Cas9 strongly synergize with MEK inhibitors in enhancing Wnt responses in isogenic CRC models. Mechanistically, we demonstrate that MEK inhibition induces a rapid downregulation of AXIN1. Using patient-derived CRC organoids, we show that MEK inhibition leads to increased Wnt activity, elevated LGR5 levels and enrichment of gene signatures associated with stemness and cancer relapse. Our study demonstrates that clinically used MEK inhibitors inadvertently induce stem cell plasticity, revealing an unknown side effect of RAS pathway inhibition.
BibTeX: @article{Zhan2019, author = {Zhan, Tianzuo and Ambrosi, Giulia and Wandmacher, Anna Maxi and Rauscher, Benedikt and Betge, Johannes and Rindtorff, Niklas and Häussler, Ragna S. and Hinsenkamp, Isabel and Bamberg, Leonhard and Hessling, Bernd and Müller-Decker, Karin and Erdmann, Gerrit and Burgermeister, Elke and Ebert, Matthias P. and Boutros, Michael}, title = {MEK inhibitors activate Wnt signalling and induce stem cell plasticity in colorectal cancer}, journal = {Nature Communications}, year = {2019}, volume = {10}, number = {1}, pages = {2197}, doi = {https://doi.org/10.1038/s41467-019-09898-0} }
Zhang, Y., Gesé, G.V., Conz, C., Lapouge, K., Kopp, J., Wölfle, T., Rospert, S. and Sinning, I.	The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb [BibTeX]	2020	Nature Communications Vol. 11(1)	article	DOI
BibTeX: @article{Zhang2020, author = {Ying Zhang and Gen\is Valent\in Gesé and Charlotte Conz and Karine Lapouge and Jürgen Kopp and Tina Wölfle and Sabine Rospert and Irmgard Sinning}, title = {The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, number = {1}, doi = {https://doi.org/10.1038/s41467-020-15313-w} }
Zhang, Y., Jiang, Y., Kuster, D., Ye, Q., Huang, W., Fürbacher, S., Zhang, J., Tang, Z., Ibberson, D., Wild, K., Sinning, I., Hyman, A. and Jäschke, A.	Single-step discovery of high-affinity RNA ligands by UltraSelex [Abstract] [BibTeX]	2023	Research Square	article	DOI URL
Abstract: Abstract Aptamers, nucleic acid ligands against specific targets, have emerged as drug candidates, sensors, imaging tools, and nanotechnology building blocks. The most successful method for their development has been SELEX (Systematic Evolution of Ligands by EXponential Enrichment), an iterative procedure that is labor- and time-intensive and often enriches candidates for criteria other than those desired. Here we present UltraSelex, a non-iterative method that combines biochemical partitioning, high-throughput sequencing, and computational background minimization through statistical rank modeling. This approach avoids the common bias for abundant sequences and selects high-affinity ligands, even if they are extremely scarce. In six independent UltraSelex experiments (three towards each target), we discovered high-affinity aptamers for a fluorogenic silicon rhodamine dye, and a protein target, the SARS-CoV-2 RNA-dependent RNA polymerase. These aptamers enabled live-cell RNA imaging and efficient enzyme inhibition, respectively. The wet-lab partitioning part of UltraSelex can be completed in a few hours, and including sequencing and rank modeling via a public web server, the identification of lead candidates can be accomplished in about one day. UltraSelex provides a rapid route to novel drug candidates and diagnostic tools with greatly improved performance.
BibTeX: @article{Zhang2023, author = {Yaqing Zhang, Yuan Jiang, David Kuster, Qiwei Ye, Wenhao Huang, Simon Fürbacher, Jingye Zhang, Zhipeng Tang, David Ibberson, Klemens Wild, Irmgard Sinning, Anthony Hyman, Andres Jäschke}, title = {Single-step discovery of high-affinity RNA ligands by UltraSelex}, journal = {Research Square}, year = {2023}, url = {https://www.researchsquare.com/article/rs-2713959/v1}, doi = {https://doi.org/10.21203/rs.3.rs-2713959/v1} }
Zhao, W., Wang, H., Gemmeke, H., van Dongen, K.W.A., Hopp, T. and Hesser, J.	Ultrasound transmission tomography image reconstruction with a fully convolutional neural network [BibTeX]	2020	Vol. 65(23), pp. 235021	article	DOI
BibTeX: @article{Zhao2020, author = {Wenzhao Zhao and Hongjian Wang and Hartmut Gemmeke and Koen W A van Dongen and Torsten Hopp and Jürgen Hesser}, title = {Ultrasound transmission tomography image reconstruction with a fully convolutional neural network}, publisher = {IOP Publishing}, year = {2020}, volume = {65}, number = {23}, pages = {235021}, doi = {https://doi.org/10.1088/1361-6560/abb5c3} }
Zhao, W., Fan, Y., Wang, H., Gemmeke, H., van Dongen, K.W.A., Hopp, T. and Hesser, J.	Simulation-to-real generalization for deep-learning-based refraction-corrected ultrasound tomography image reconstruction [Abstract] [BibTeX]	2023	Physics in Medicine & Biology Vol. 68(3), pp. 035016	article	DOI
Abstract: Abstract Objective. The image reconstruction of ultrasound computed tomography is computationally expensive with conventional iterative methods. The fully learned direct deep learning reconstruction is promising to speed up image reconstruction significantly. However, for direct reconstruction from measurement data, due to the lack of real labeled data, the neural network is usually trained on a simulation dataset and shows poor performance on real data because of the simulation-to-real gap. Approach. To improve the simulation-to-real generalization of neural networks, a series of strategies are developed including a Fourier-transform-integrated neural network, measurement-domain data augmentation methods, and a self-supervised-learning-based patch-wise preprocessing neural network. Our strategies are evaluated on both the simulation dataset and real measurement datasets from two different prototype machines. Main results. The experimental results show that our deep learning methods help to improve the neural networks’ robustness against noise and the generalizability to real measurement data. Significance. Our methods prove that it is possible for neural networks to achieve superior performance to traditional iterative reconstruction algorithms in imaging quality and allow for real-time 2D-image reconstruction. This study helps pave the path for the application of deep learning methods to practical ultrasound tomography image reconstruction based on simulation datasets.
BibTeX: @article{Zhao2023, author = {Wenzhao Zhao, Yuling Fan, Hongjian Wang, Hartmut Gemmeke, Koen W A van Dongen, Torsten Hopp, Jürgen Hesser}, title = {Simulation-to-real generalization for deep-learning-based refraction-corrected ultrasound tomography image reconstruction}, journal = {Physics in Medicine & Biology}, publisher = {IOP Publishing}, year = {2023}, volume = {68}, number = {3}, pages = {035016}, doi = {https://doi.org/10.1088/1361-6560/acaeed} }
Zharov, Y., Ershov, A., Baumbach, T. and Heuveline, V.	Using the Order of Tomographic Slices as a Prior for Neural Networks Pre-Training [BibTeX]	2022		misc	DOI
BibTeX: @misc{Zharov2022, author = {Zharov, Yaroslav and Ershov, Alexey and Baumbach, Tilo and Heuveline, Vincent}, title = {Using the Order of Tomographic Slices as a Prior for Neural Networks Pre-Training}, publisher = {arXiv}, year = {2022}, doi = {https://doi.org/10.48550/ARXIV.2203.09372} }
Zhong, R., Zhang, F., Yang, Z., Li, Y., Xu, Q., Lan, H., Lang, S., Cyganek, L., Burgermeister, E., El-Battrawy, I., Zhou, X., Akin, I. and Borggrefe, M.	Regulation of Ion Channel Function in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes by Cancer Cell Secretion Through DNA Methylation [Abstract] [BibTeX]	2022	Frontiers in Cardiovascular Medicine Vol. 9	article	DOI
Abstract: BackgroundCardiac dysfunction including arrhythmias appear frequently in patients with cancers, which are expected to be caused mainly by cardiotoxic effects of chemotherapy. Experimental studies investigating the effects of cancer cell secretion without chemotherapy on ion channel function in human cardiomyocytes are still lacking.MethodsThe human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) generated from three healthy donors were treated with gastrointestinal (GI) cancer (AGS and SW480 cells) medium for 48 h. The qPCR, patch-clamp, western blotting, immunostaining, dot blotting, bisulfite sequence, and overexpression of the ten-eleven translocation (TET) enzyme were performed for the study.ResultsAfter treated with cancer cell secretion, the maximum depolarization velocity and the action potential amplitude were reduced, the action potential duration prolonged, peak Na+ current, and the transient outward current were decreased, late Na+ and the slowly activating delayed rectifier K+ current were increased. Changes of mRNA and protein level of respective channels were detected along with altered DNA methylation level in CpG island in the promoter regions of ion channel genes and increased protein levels of DNA methyltransferases. Phosphoinositide 3-kinase (PI3K) inhibitor attenuated and transforming growth factor-β (TGF-β) mimicked the effects of cancer cell secretion.ConclusionsGI cancer cell secretion could induce ion channel dysfunction, which may contribute to occurrence of arrhythmias in cancer patients. The ion channel dysfunction could result from DNA methylation of ion channel genes via activation of TGF-β/PI3K signaling. This study may provide new insights into pathogenesis of arrhythmia in cancer patients.
BibTeX: @article{Zhong2022, author = {Rujia Zhong, Feng Zhang, Zhen Yang, Yingrui Li, Qiang Xu, Huan Lan, Siegfried Lang, Lukas Cyganek, Elke Burgermeister, Ibrahim El-Battrawy, Xiaobo Zhou, Ibrahim Akin, Martin Borggrefe}, title = {Regulation of Ion Channel Function in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes by Cancer Cell Secretion Through DNA Methylation}, journal = {Frontiers in Cardiovascular Medicine}, publisher = {Frontiers Media SA}, year = {2022}, volume = {9}, doi = {https://doi.org/10.3389/fcvm.2022.839104} }
Zhou, F., Liu, Y., Rohde, C., Pauli, C., Gerloff, D., Köhn, M., Misiak, D., Bäumer, N., Cui, C., Göllner, S., Oellerich, T., Serve, H., Garcia-Cuellar, M.-P., Slany, R., Maciejewski, J.P., Przychodzen, B., Seliger, B., Klein, H.-U., Bartenhagen, C., Berdel, W.E., Dugas, M., Taketo, M.M., Farouq, D., Schwartz, S., Regev, A., Hébert, J., Sauvageau, G., Pabst, C., Hüttelmaier, S. and Müller-Tidow, C.	AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia [BibTeX]	2017	Nature Cell Biology Vol. 19(7), pp. 844-855	article	DOI
BibTeX: @article{Zhou2017, author = {Fengbiao Zhou and Yi Liu and Christian Rohde and Cornelius Pauli and Dennis Gerloff and Marcel Köhn and Danny Misiak and Nicole Bäumer and Chunhong Cui and Stefanie Göllner and Thomas Oellerich and Hubert Serve and Maria-Paz Garcia-Cuellar and Robert Slany and Jaroslaw P. Maciejewski and Bartlomiej Przychodzen and Barbara Seliger and Hans-Ulrich Klein and Christoph Bartenhagen and Wolfgang E. Berdel and Martin Dugas and Makoto Mark Taketo and Daneyal Farouq and Schraga Schwartz and Aviv Regev and Josée Hébert and Guy Sauvageau and Caroline Pabst and Stefan Hüttelmaier and Carsten Müller-Tidow}, title = {AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia}, journal = {Nature Cell Biology}, publisher = {Springer Science and Business Media LLC}, year = {2017}, volume = {19}, number = {7}, pages = {844--855}, doi = {https://doi.org/10.1038/ncb3563} }
Zhou, F., Aroua, N., Liu, Y., Rohde, C., Cheng, J., Wirth, A.-K., Fijalkowska, D., Göllner, S., Lotze, M., Yun, H., Yu, X., Pabst, C., Sauer, T., Oellerich, T., Serve, H., Röllig, C., Bornhäuser, M., Thiede, C., Baldus, C., Frye, M., Raffel, S., Krijgsveld, J., Jeremias, I., Beckmann, R., Trumpp, A. and Müller-Tidow, C.	A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia [Abstract] [BibTeX]	2022	Cancer Discovery Vol. 13(2), pp. 332-347	article	DOI
Abstract: Abstract The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2′-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2′-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2′-O-methylation specifically at exterior sites of ribosomes. The rRNA 2′-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2′-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2′-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2′-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. Significance: We establish the complete rRNA 2′-O-methylation landscape in human AML. Plasticity of rRNA 2′-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247
BibTeX: @article{Zhou2022, author = {Fengbiao Zhou, Nesrine Aroua, Yi Liu, Christian Rohde, Jingdong Cheng, Anna-Katharina Wirth, Daria Fijalkowska, Stefanie Göllner, Michelle Lotze, Haiyang Yun, Xiaobing Yu, Caroline Pabst, Tim Sauer, Thomas Oellerich, Hubert Serve, Christoph Röllig, Martin Bornhäuser, Christian Thiede, Claudia Baldus, Michaela Frye, Simon Raffel, Jeroen Krijgsveld, Irmela Jeremias, Roland Beckmann, Andreas Trumpp, Carsten Müller-Tidow}, title = {A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia}, journal = {Cancer Discovery}, publisher = {American Association for Cancer Research (AACR)}, year = {2022}, volume = {13}, number = {2}, pages = {332--347}, doi = {https://doi.org/10.1158/2159-8290.CD-22-0210} }
Zhu, L., Hissa, B., Győrffy, B., Jann, J.-C., Yang, C., Reissfelder, C. and Schölch, S.	Characterization of Stem-like Circulating Tumor Cells in Pancreatic Cancer [BibTeX]	2020	Diagnostics Vol. 10(5), pp. 305	article	DOI
BibTeX: @article{Zhu2020, author = {Lei Zhu and Barbara Hissa and Balázs Győrffy and Johann-Christoph Jann and Cui Yang and Christoph Reissfelder and Sebastian Schölch}, title = {Characterization of Stem-like Circulating Tumor Cells in Pancreatic Cancer}, journal = {Diagnostics}, publisher = {MDPI AG}, year = {2020}, volume = {10}, number = {5}, pages = {305}, doi = {https://doi.org/10.3390/diagnostics10050305} }
Zhu, L., Kan, K.-J., Grün, J.L., Hissa, B., Yang, C., Győrffy, B., Loges, S., Reißfelder, C. and Schölch, S.	GAS2L1 Is a Potential Biomarker of Circulating Tumor Cells in Pancreatic Cancer [BibTeX]	2020	Cancers Vol. 12(12), pp. 3774	article	DOI
BibTeX: @article{Zhu2020a, author = {Lei Zhu and Ke-Jia Kan and Johanna L. Grün and Barbara Hissa and Cui Yang and Balázs Győrffy and Sonja Loges and Christoph Reißfelder and Sebastian Schölch}, title = {GAS2L1 Is a Potential Biomarker of Circulating Tumor Cells in Pancreatic Cancer}, journal = {Cancers}, publisher = {MDPI AG}, year = {2020}, volume = {12}, number = {12}, pages = {3774}, doi = {https://doi.org/10.3390/cancers12123774} }
Ziegler, K., Folkard, R., Gonzalez, A.J., Burghardt, J., Antharvedi-Goda, S., Martin-Cortecero, J., Isaías-Camacho, E., Kaushalya, S., Tan, L.L., Kuner, T., Acuna, C., Kuner, R., Mease, R. and Groh, A.	Primary Somatosensory Cortex Bidirectionally Modulates Sensory Gain and Nociceptive Behavior in a Layer-Specific Manner [Abstract] [BibTeX]	2022	bioRxiv	article
Abstract: AbstractThe primary somatosensory cortex (S1) is a hub for body sensation of both innocuous and noxious signals, yet its role in somatosensation versus pain is debated. Despite known contributions of S1 to sensory gain modulation, its causal involvement in subjective sensory experiences remains elusive. Here, in mouse S1, we reveal the involvement of cortical output neurons in layers 5 (L5) and 6 (L6) in the perception of innocuous and noxious somatosensory signals. We find that L6 activation can drive aversive hypersensitivity and spontaneous nocifensive behavior. Linking behavior to neuronal mechanisms, we find that L6 enhances thalamic somatosensory responses, and in parallel, strongly suppresses L5 neurons. Directly suppressing L5 reproduced the pronociceptive phenotype induced by L6 activation, suggesting an anti-nociceptive function for L5 output. Indeed, L5 activation reduced sensory sensitivity and reversed inflammatory allodynia. Together, these findings reveal a layer-specific and bidirectional role for S1 in modulating subjective sensory experiences.
BibTeX: @article{Ziegler2022, author = {Katharina Ziegler, Ross Folkard, Antonio J Gonzalez, Jan Burghardt, Sailaja Antharvedi-Goda, Jesus Martin-Cortecero, Emilio Isaías-Camacho, Sanjeev Kaushalya, Linette Liqi Tan, Thomas Kuner, Claudio Acuna, Rohini Kuner, Rebecca Mease, Alexander Groh}, title = {Primary Somatosensory Cortex Bidirectionally Modulates Sensory Gain and Nociceptive Behavior in a Layer-Specific Manner}, journal = {bioRxiv}, year = {2022} }
Zila, V., Margiotta, E., Turoňová, B., Müller, T.G., Zimmerli, C.E., Mattei, S., Allegretti, M., Börner, K., Rada, J., Müller, B., Lusic, M., Kräusslich, H.-G. and Beck, M.	Cone-shaped HIV-1 capsids are transported through intact nuclear pores [BibTeX]	2021	Cell Vol. 184(4), pp. 1032-1046.e18	article	DOI
BibTeX: @article{Zila2021, author = {Vojtech Zila and Erica Margiotta and Beata Turoňová and Thorsten G. Müller and Christian E. Zimmerli and Simone Mattei and Matteo Allegretti and Kathleen Börner and Jona Rada and Barbara Müller and Marina Lusic and Hans-Georg Kräusslich and Martin Beck}, title = {Cone-shaped HIV-1 capsids are transported through intact nuclear pores}, journal = {Cell}, publisher = {Elsevier BV}, year = {2021}, volume = {184}, number = {4}, pages = {1032--1046.e18}, doi = {https://doi.org/10.1016/j.cell.2021.01.025} }
Zupa, E., Zheng, A., Neuner, A., Würtz, M., Liu, P., Böhler, A., Schiebel, E. and Pfeffer, S.	The cryo-EM structure of a upgamma-TuSC elucidates architecture and regulation of minimal microtubule nucleation systems [BibTeX]	2020	Nature Communications Vol. 11	article	DOI
BibTeX: @article{Zupa2020, author = {Erik Zupa and Anjun Zheng and Annett Neuner and Martin Würtz and Peng Liu and Anna Böhler and Elmar Schiebel and Stefan Pfeffer}, title = {The cryo-EM structure of a upgamma-TuSC elucidates architecture and regulation of minimal microtubule nucleation systems}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2020}, volume = {11}, doi = {https://doi.org/10.1038/s41467-020-19456-8} }
Zupa, E., Liu, P., Würtz, M., Schiebel, E. and Pfeffer, S.	The structure of the γ-TuRC: a 25-years-old molecular puzzle [BibTeX]	2021	Current Opinion in Structural Biology Vol. 66, pp. 15-21	article	DOI URL
BibTeX: @article{Zupa2021, author = {Erik Zupa, Peng Liu, Martin Würtz, Elmar Schiebel, Stefan Pfeffer}, title = {The structure of the γ-TuRC: a 25-years-old molecular puzzle}, journal = {Current Opinion in Structural Biology}, publisher = {Elsevier BV}, year = {2021}, volume = {66}, pages = {15--21}, url = {https://api.elsevier.com/content/article/PII:S0959440X20301433?httpAccept=text/xml}, doi = {https://doi.org/10.1016/j.sbi.2020.08.008} }
Zupa, E., Würtz, M., Neuner, A., Hoffmann, T., Rettel, M., Böhler, A., Vermeulen, B.J.A., Eustermann, S., Schiebel, E. and Pfeffer, S.	The augmin complex architecture reveals structural insights into microtubule branching [Abstract] [BibTeX]	2022	Nature Communications Vol. 13(1)	article	DOI URL
Abstract: AbstractIn mitosis, the augmin complex binds to spindle microtubules to recruit the γ-tubulin ring complex (γ-TuRC), the principal microtubule nucleator, for the formation of branched microtubules. Our understanding of augmin-mediated microtubule branching is hampered by the lack of structural information on the augmin complex. Here, we elucidate the molecular architecture and conformational plasticity of the augmin complex using an integrative structural biology approach. The elongated structure of the augmin complex is characterised by extensive coiled-coil segments and comprises two structural elements with distinct but complementary functions in γ-TuRC and microtubule binding, linked by a flexible hinge. The augmin complex is recruited to microtubules via a composite microtubule binding site comprising a positively charged unordered extension and two calponin homology domains. Our study provides the structural basis for augmin function in branched microtubule formation, decisively fostering our understanding of spindle formation in mitosis.
BibTeX: @article{Zupa2022, author = {Erik Zupa, Martin Würtz, Annett Neuner, Thomas Hoffmann, Mandy Rettel, Anna Böhler, Bram J. A. Vermeulen, Sebastian Eustermann, Elmar Schiebel, Stefan Pfeffer}, title = {The augmin complex architecture reveals structural insights into microtubule branching}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, year = {2022}, volume = {13}, number = {1}, url = {https://www.nature.com/articles/s41467-022-33228-6.pdf}, doi = {https://doi.org/10.1038/s41467-022-33228-6} }