Publikationen von Martin Vingron

Maarten P. Bebelman, Lenka Belicova, Elzbieta Gralinska, Tobias Jumel , Aparajita Lahree, Sarah Sommer, Andrej Shevchenko, Timofei Zatsepin, Yannis Kalaidzidis, Martin Vingron, and Marino Zerial, "Hepatocyte differentiation requires anisotropic expansion of bile canaliculi," Development 151 (22), Article dev202777 (2024).

Aybuge Altay and Martin Vingron, "scATAcat: cell-type annotation for scATAC-seq data," NAR: genomics and bioinformatics 6 (4), Article lqae135 (2024).

Maximilian Stötzel, Chieh-Yu Cheng, Ibrahim A. Ilik, Abhishek Sampath Kumar, Persia Akbari-Omgba, Vera A. van der Weijden, Yufei Zhang, Martin Vingron, Alexander Meissner, Tugce Aktas, Helene Kretzmer, and Aydan Bulut-Karslioglu, "TET activity safeguards pluripotency throughout embryonic dormancy," Nature Structural & Molecular Biology 31 (10), 1625-1639 (2024).

Julian Naderi, Alexandre P. Magalhães, Gözde Kibar, Gregoire Stik, Yaotian Zhang, Sebastian Mackowiak, Hannah M. Wieler, Francesca Rossi, René Buschow, Marie Christou-Kent, Marc Alcoverro-Bertran, Thomas Graf, Martin Vingron, and Denes Hnisz, "An activity-specificity trade-off encoded in human transcription factors," Nature Cell Biology 26 (8), 1309-1321 (2024).

Yan Zhao, Clemens Kohl, Daniel Rosebrock, Qinan Hu, Yuhui Hu, and Martin Vingron, "CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics," Nucleic Acids Research 52 (13), Article e57 (2024).

Daniel Rosebrock, Martin Vingron, and Peter F. Arndt, "Modeling gene expression cascades during cell state transitions," iScience 27 (4), Article 109386 (2024).

Mai H. Q. Phan, Tobias Zehnder, Fiona Puntieri, Bai-Wei Lo, Boris Lenhard, Ferenc Mueller, Martin Vingron, and Daniel M. Ibrahim, "Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances," bioRxiv (2024).

Mengxiao Yan, Ming Li, Yunze Wang, Xinyi Wang, Hossein-M. Moeinzadeh, Dora G. Quispe-Huamanquispe, Weijuan Fan, Yijie Fang, Yuqin Wang, Haozhen Nie, Zhangying Wang, Aiko Tanaka, Bettina Heider, Jan F. Kreuze, Godelieve Gheysen, Hongxia Wang, Martin Vingron, Ralph Bock, and Jun Yang, "Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato," Molecular Plant 17 (2), 277 -296 (2024).

Vera A. van der Weijden, Maximilian Stötzel, Dhanur P. Iyer, Beatrix Fauler, Elzbieta Gralinska, Mohammed Shahraz, David Meierhofer, Martin Vingron, Steffen Rulands, Theodore Alexandrov, Thorsten Mielke, and Aydan Bulut-Karslioglu, "FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy," Nature Cell Biology 26 (2), 181-193 (2024).

Trisevgeni Rapakoulia, Sara Lopez Ruiz de Vargas, Persia Akbari-Omgba, Verena Laupert, Igor Ulitsky, and Martin Vingron, "CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction," Bioinformatics 39 (11), btad687 (2023).

Jerome Jatzlau, Paul-Lennard Mendez, Aybuge Altay, Lion Raaz, Yufei Zhang, Sophia Mähr, Akin Sesver, Maria Reichenbach, Stefan Mundlos, Martin Vingron, and Petra Knaus, "Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription," iScience 26 (9), 107405 (2023).

Elzbieta Gralinska and Martin Vingron, "Association Plots: visualizing cluster-specific associations in high-dimensional correspondence analysis biplots," Journal of the Royal Statistical Society - Series C: Applied Statistics 72 (4), 1023-1040 (2023).

Matthias Lienhard, Twan van den Beucken , Bernd Timmermann, Myriam Hochradel, Stefan Boerno, Florian Caiment , Martin Vingron, and Ralf Herwig, "IsoTools: a flexible workflow for long-read transcriptome sequencing analysis," Bioinformatics 39 (6), btad364 (2023).

Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron, and Knut Reinert, "Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries," Genome Biology: Biology for the Post-Genomic Era 24 (1), 131 (2023).

Gözde Kibar and Martin Vingron, "Prediction of protein–protein interactions using sequences ofintrinsically disordered regions," Proteins: Structure, Function, and Bioinformatics 91 (7), 980-990 (2023).

M. Schindler, M. Osterwalder, I. Harabula, L. Wittler, A. C. Tzika, Dina K. N. Dechmann, M. Vingron, A. Visel, S. Haas, and F. M. Real, "Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes," Development 150 (17), dev201562 (2023).

Robert Schöpflin, Uirá Souto Melo, Mohammad Hossein Moeinzadeh, David Heller, Verena Laupert, Jakob Hertzberg, Manuel Holtgrewe, Nico Alavi, Marius-Konstantin Klever, Julius Jungnitsch, Emel Comak, Seval Türkmen, Denise Horn, Yannis Duffourd, Laurence Faivre, Patrick Callier, Damien Sanlaville, Orsetta Zuffardi, Romano Tenconi, Nehir Edibe Kurtas, Sabrina Giglio, Bettina Prager, Anna Latos-Bielenska, Ida Vogel, Merete Bugge, Niels Tommerup, Malte Spielmann, Antonio Vitobello, Vera M. Kalscheuer, Martin Vingron, and Stefan Mundlos, "Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes," Nature Communications 13 (1), 6470 (2022).

Magdalena Schindler, Marco Osterwalder, Izabela Harabula, Lars Wittler, Athanasia C. Tzika, Dina Dechmann, Martin Vingron, Axel Visel, Stefan Haas, and Francisca M. Real, "Co-option of the transcription factor SALL1 in mole ovotestis formation," bioRxiv , 514220 (2022).

Alessa Ringel, Quentin Szabo, Andrea M. Chiariello, Konrad Chudzik, Robert Schöpflin, Patricia Rothe, Alexandra L. Mattei, Tobias Zehnder, Dermot Harnett, Verena Laupert, Simona Bianco, Sara Hetzel, Juliane Glaser, Mai H. Q. Phan, Magdalena Schindler, Daniel M. Ibrahim, Christina Paliou, Andrea Esposito, César A. Prada-Medina, Stefan A. Haas, Peter Giere, Martin Vingron, Lars Wittler, Alexander Meissner, Mario Nicodemi, Giacomo Cavalli, Frédéric Bantignies, Stefan Mundlos, and Michael I. Robson, "Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes," Cell 185 (20), 3689-3704 (2022).

P. Pevzner, M. Vingron, C. Reidys, F. Sun, and S. Istrail, "Michael Waterman's Contributions to Computational Biology and Bioinformatics," Journal of Computational Biology 29 (7), 601-615 (2022).