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Prof. Dr. Firstname Lastname
Main Focus
- Research topic 01
- Research topic 02
- Research topic 03
- Research topic 04
- Research topic 05
Curriculum Vitae
Positions
Since 2025 Group Leader at the Max Planck Institute for Molecular Genetics
2020 - 2025 Postdoc at XY University, City, Country
Education
2015 - 2020 PhD Student at XY University, City, Country
2013 - 2015 Master studies in computer sciences at XY University, City, Country
2010 - 2013 Bachelor studies in biology at XY University, City, Country
Awards
2025 XY award
2024 XY fellowship
Memberships
Since 2025 Member of XY Organization
Contributions to the scientific Community
Since 2020 Review in the following journals
Selected publications
Abdullaev, E. T., Haridoss, D. A., & Arndt, P. F. (2025). Reconstruction of Segmental Duplication Rates and Associated Genomic Features by Network Analysis. Genome Biology and Evolution, 17(3), Article evaf011. doi:10.1093/gbe/evaf011
Bi, Y., Lankenau, T. L., Lienhard, M., & Herwig, R. (2025). IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data. Journal of Molecular Biology, Article 169049. doi:10.1016/j.jmb.2025.169049
Brändl, B., Steiger, M., Kubelt, C., Rohrandt, C., Zhu, Z., Evers, M., Wang, G., Schuldt, B., Afflerbach, A.-K., Wong, D., Lum, A., Halldorsson, S., Djirackor, L., Leske, H., Magadeeva, S., Smicius, R., Quedenau, C., Schmidt, N. O., Schüller, U., Vik-Mo, E. O., Proescholdt, M., Riemenschneider, M. J., Zadeh, G., Ammerpohl, O., Yip, S., Synowitz, M., van Bömmel, A., Kretzmer, H., & Müller, F.-J. (2025). Rapid brain tumor classification from sparse epigenomic data. Nature Medicine, 31(3), 840-848. doi:10.1038/s41591-024-03435-3
Hiepen, C., Benamar, M., Barrasa-Fano, J., Condor, M., Ilhan, M., Münch, J., Hastar, N., Kerkhoff, Y., Harms, G. S., Mielke, T., Koenig, B., Block, S., Rocks, O., Abdelilah-Seyfried, S., Van Oosterwyck, H., & Knaus, P. (2025). Endothelial tip-cell position, filopodia formation and biomechanics require BMPR2 expression and signaling. Communications Biology, 8(1), Article 21. doi:10.1038/s42003-024-07431-8
Lauer, S. M., Gasse, J., Krizsan, A., Reepmeyer, M., Sprink, T., Nikolay, R., Spahn, C. M. T., & Hoffmann, R. (2025). The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding. Nature Communications, 16(1), Article 567. doi:10.1038/s41467-025-55836-8
Complete Publication List
Europe PMC
Publications with affiliation of the Max Planck Institute for Molecular Genetics
Journal Article (226)
1.
Journal Article
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).
2.
Journal Article
Aybuge Altay and Martin Vingron, "scATAcat: cell-type annotation for scATAC-seq data," NAR: genomics and bioinformatics 6 (4), Article lqae135 (2024).
3.
Journal Article
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).
4.
Journal Article
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).
5.
Journal Article
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).
6.
Journal Article
Daniel Rosebrock, Martin Vingron, and Peter F. Arndt, "Modeling gene expression cascades during cell state transitions," iScience 27 (4), Article 109386 (2024).
7.
Journal Article
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).
8.
Journal Article
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).
9.
Journal Article
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).
10.
Journal Article
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).
11.
Journal Article
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).
12.
Journal Article
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).
13.
Journal Article
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).
14.
Journal Article
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).
15.
Journal Article
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).
16.
Journal Article
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).
17.
Journal Article
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).
18.
Journal Article
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).
19.
Journal Article
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).
20.
Journal Article
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).
21.
Journal Article
Damir Baranasic, Matthias Hörtenhuber, Piotr Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez- Gonzalez, Nan Li, Joseph Wragg, Fabio D’Orazio, Noelia Díaz, Benjamín Hernández- Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Pelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, and Ferenc Müller, "Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements," Nature Genetics 54 (7), 1037-1050 (2022).
22.
Journal Article
Daniel Rosebrock, Sneha Arora, Naresh Mutukula, Rotem Volkman, Elzbieta Gralinska, Anastasios Balaskas, Amèlia Aragonés Hernández, Rene Buschow, Björn Brändl, Franz-Josef Müller, Peter F. Arndt, Martin Vingron, and Yechiel Elkabetz, "Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells," Nature Cell Biology 24 (6), 981-995 (2022).
23.
Journal Article
Elzbieta Gralinska, Clemens Kohl, Sokhandan Fadakar, and Martin Vingron, "Visualizing Cluster-specific Genes from Single-cell Transcriptomics Data Using Association Plots," Journal of Molecular Biology 434 (11), 167525 (2022).
24.
Journal Article
J. Hertzberg, S. Mundlos, M. Vingron, and G. Gallone, "TADA – a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs," Genome Biology 23 (1), 67 (2022).
25.
Journal Article
Lam-Ha Ly and Martin Vingron, "Effect of imputation on gene network reconstruction from single-cell RNA-seq data," Patterns 3 (2), 100414 (2021).
26.
Journal Article
Laura Viola Glaser, Mara Steiger, Alisa Fuchs, Alena van Bömmel, Edda Einfeldt, Ho-Ryun Chung, Martin Vingron, and Sebastiaan H. Meijsing, "Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq," Nucleic Acids Research (London) 49 (21), 12178-12195 (2021).
27.
Journal Article
Elin Enervald, Lynn Marie Powell, Lora Boteva, Rossana Foti, Nerea Blanes Ruiz, Gözde Kibar, Agnieszka Piszczek, Fatima Cavaleri, Martin Vingron, Andrea Cerase, and Sara B. C. Buonomo, "RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes," The EMBO Journal 40 (24), e105862 (2021).
28.
Journal Article
Philipp Benner and Martin Vingron, "Quantifying the tissue-specific regulatory information within enhancer DNA sequences," NAR: genomics and bioinformatics 3 (4), lqab095 (2021).
29.
Journal Article
Magdalena Socha, Anna Sowińska-Seidler, Uirá Souto Melo, Bjørt K. Kragesteen, Martin Franke, Verena Heinrich, Robert Schöpflin, Inga Nagel, Nicolas Gruchy, Stefan Mundlos, Varun K. A. Sreenivasan, Cristina López, Martin Vingron, Ewelina Bukowska-Olech, Malte Spielmann, and Aleksander Jamsheer, "Position effects at the FGF8 locus are associated with femoral hypoplasia," The American Journal of Human Genetics 108 (9), 1725-1734 (2021).
30.
Journal Article
Lenka Belicova , Urska Repnik , Julien Delpierre , Elzbieta Gralinska, Sarah Seifert , José Ignacio Valenzuela , Hernán Andrés Morales-Navarrete , Christian Franke , Helin Räägel , Evgeniya Shcherbinina , Tatiana Prikazchikova , Victor Koteliansky , Martin Vingron, Yannis L. Kalaidzidis , Timofei Zatsepin , and Marino Zerial , "Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads," The Journal of Cell Biology: JCB 220 (10), e202103003 (2021).
31.
Journal Article
Franziska Witte, Jorge Ruiz-Orera, Camilla Ciolli Mattioli, Susanne Blachut, Eleonora Adami, Jana Felicitas Schulz, Valentin Schneider-Lunitz, Oliver Hummel, Giannino Patone, Michael Benedikt Mücke, Jan Šilhavý, Matthias Heinig, Leonardo Bottolo, Daniel Sanchis, Martin Vingron, Marina Chekulaeva, Michal Pravenec, Norbert Hubner, and Sebastiaan van Heesch, "A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion," Genome Biology 22 (1), 191 (2021).
32.
Journal Article
Martyna Gajos, Olga Jasnovidova, Alena van Bömmel, Susanne Freier, Martin Vingron, and Andreas Mayer, "Conserved DNA sequence features underlie pervasive RNA polymerase pausing," Nucleic Acids Research (London) 49 (8), 4402-4420 (2021).
33.
Journal Article
David Heller and Martin Vingron, "SVIM-asm: structural variant detection from haploid and diploid genome assemblies," Bioinformatics 36 (22-23), 5519-5521 (2020).
34.
Journal Article
Francisca M. Real, Stefan A. Haas, Paolo Franchini, Peiwen Xiong, Oleg Simakov, Heiner Kuhl, Robert Schöpflin, David Heller, Mohammad Hossein Moeinzadeh, Verena Heinrich, Thomas Krannich , Annkatrin Bressin, Michaela F. Hartmann, Stefan A. Wudy, Dina K. N. Dechmann, Alicia Hurtado, Francisco J. Barrionuevo, Magdalena Schindler, Izabela Harabula, Marco Osterwalder, Michael Hiller, Lars Wittler, Axel Visel, Bernd Timmermann, Axel Meyer, Martin Vingron, Rafael Jiménez, Stefan Mundlos, and Dario G. Lupiáñez, "The mole genome reveals regulatory rearrangements associated with adaptive intersexuality," Science 370 (6513), 208-214 (2020).
35.
Journal Article
Uirá Souto Melo, Robert Schöpflin, Rocio Acuna-Hidalgo, Martin Atta Mensah, Björn Fischer-Zirnsak, Manuel Holtgrewe, Marius-Konstantin Klever, Seval Türkmen, Verena Heinrich, Ilina Datkhaeva Pluym, Eunice Matoso, Sérgio Bernardo de Sousa, Pedro Louro, Wiebke Hülsemann, Monika Cohen, Andreas Dufke, Anna Latos-Bieleńska, Martin Vingron, Vera Kalscheuer, Fabiola Quintero-Rivera, Malte Spielmann, and Stefan Mundlos, "Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases," The American Journal of Human Genetics 106 (6), 872-884 (2020).
36.
Journal Article
M-Hossein Moeinzadeh, Yang, Jun, Evgeny Muzychenko, Giuseppe Gallone, David Heller, Knut Reinert, Stefan Haas, and Martin Vingron, "Ranbow: A fast and accurate method for polyploid haplotype reconstruction," PLOS Computational Biology 16 (5), e1007843 (2020).
37.
Journal Article
Philipp Benner and Martin Vingron, "ModHMM: A Modular Supra-Bayesian Genome Segmentation Method," Journal of Computational Biology 27 (4), 442-457 (2020).
38.
Journal Article
Christina E. Herkt, Brian Caffrey, Kristin Surmann, Sascha Blankenburg, Manuela Gesell Salazar, Anna L. Jung, Stefanie M. Herbel, Kerstin Hoffmann, Leon N. Schulte, Wei Chen, Alexandra Sittka-Stark, Uwe Völker, Martin Vingron, Annalisa Marsico, Wilhelm Bertrams, and Bernd Schmeck, "A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1," mBio 11 (2), e03155-19 (2020).
39.
Journal Article
Sascha Young Kupke, Lam-Ha Ly, Stefan T. Börno, Alexander Ruff, Bernd Timmermann, Martin Vingron, and Stefan Haas, "Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication," Viruses 12 (1), 71 (2020).
40.
Journal Article
Anna Ramisch, Verena Heinrich, Laura V. Glaser, Alisa Fuchs, Xinyi Yang, Philipp Benner, Robert Schöpflin, Na Li, Sarah Kinkley, Anja Römer-Hillmann, John Longinotto, Steffen Heyne, Beate Czepukojc, Sonja M. Kessler, Alexandra K. Kiemer, Cristina Cadenas, Laura Arrigoni, Nina Gasparoni, Thomas Manke, Thomas Pap, Andrew Pospisilik, Jan Hengstler, Jörn Walter, Sebastiaan Meijsing, Ho-Ryun Chung, and Martin Vingron, "CRUP: a comprehensive framework to predict condition-specific regulatory units," Genome Biology: Biology for the Post-Genomic Era 20 (1), 227 (2019).
41.
Journal Article
David Heller and Martin Vingron, "SVIM: Structural Variant Identification using Mapped Long Reads," Bioinformatics 35 (17), 2907-2915 (2019).
42.
Journal Article
W. Kopp and Martin Vingron, "DNA Motif Match Statistics Without Poisson Approximation," Journal of Computational Biology 26 (8), 846-865 (2019).
43.
Journal Article
Alexandra Despang, Robert Schöpflin, Martin Franke, Salaheddine Ali, Ivana Jerković, Christina Paliou, Wing-Lee Chan, Bernd Timmermann, Lars Wittler, Martin Vingron, Stefan Mundlos, and Daniel M. Ibrahim, "Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture," Nature Genetics 51 (8), 1263-1271 (2019).
44.
Journal Article
S. van Heesch, F. Witte, V. Schneider-Lunitz, J. F. Schulz, E. Adami, A. B. Faber, M. Kirchner, H. Maatz, S. Blachut, C. L. Sandmann, M. Kanda, C. L. Worth, S. Schafer, L. Calviello, R. Merriott, G. Patone, O. Hummel, E. Wyler, B. Obermayer, M. B. Mucke, E. L. Lindberg, F. Trnka, S. Memczak, M. Schilling, L. E. Felkin, P. J. R. Barton, N. M. Quaife, K. Vanezis, S. Diecke, M. Mukai, N. Mah, S. J. Oh, A. Kurtz, C. Schramm, D. Schwinge, M. Sebode, M. Harakalova, F. W. Asselbergs, A. Vink, R. A. de Weger, S. Viswanathan, A. A. Widjaja, A. Gartner-Rommel, H. Milting, C. Dos Remedios, C. Knosalla, P. Mertins, M. Landthaler, Martin Vingron, W. A. Linke, J. G. Seidman, C. E. Seidman, N. Rajewsky, U. Ohler, S. A. Cook, and N. Hubner, "The Translational Landscape of the Human Heart," Cell 178 (1), 242-260 (2019).
45.
Journal Article
Christina Paliou, Philine Guckelberger, Robert Schöpflin, Verena Heinrich, Andrea Esposito, Andrea M. Chiariello, Simona Bianco, Carlo Annunziatella, Johannes Helmuth, Stefan Haas, Ivana Jerković, Norbert Brieske, Lars Wittler, Bernd Timmermann, Mario Nicodemi, Martin Vingron, Stefan Mundlos, and Guillaume Andrey, "Preformed Chromatin Topology Assists Transcriptional Robustness of Shh during Limb Development," Proceedings of the National Academy of Sciences of the United States of America 116 (25), 12390-12399 (2019).
46.
Journal Article
J. P. Mallm, M. Iskar, N. Ishaque, L. C. Klett, S. J. Kugler, Jose M. Muino, V. B. Teif, A. M. Poos, S. Grossmann, F. Erdel, D. Tavernari, S. D. Koser, S. Schumacher, B. Brors, R. Konig, D. Remondini, Martin Vingron, S. Stilgenbauer, P. Lichter, M. Zapatka, D. Mertens, and K. Rippe, "Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks," Molecular Systems Biology 15 (5), e8339 (2019).
47.
Journal Article
Tobias Zehnder, Philipp Benner, and Martin Vingron, "Predicting enhancers in mammalian genomes using supervised hidden Markov models," BMC Bioinformatics 20 (1), 157 (2019).
48.
Journal Article
Mahsa Ghanbari, Julia Lasserre, and Martin Vingron, "The Distance Precision Matrix: computing networks from non-linear relationships," Bioinformatics 35 (6), 1009-1017 (2019).
49.
Journal Article
Katerina Kraft, Andreas Magg, Verena Heinrich, Christina Riemenschneider, Robert Schöpflin, Julia Markowski, Daniel Ibrahim, Rocío Acuna-Hidalgo, Alexandra Despang, Guillaume Andrey, Lars Wittler, Bernd Timmermann, Martin Vingron, and Stefan Mundlos, "Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations," Nature Cell Biology 21 (3), 305-310 (2019).
50.
Journal Article
Kenjiro Adachi, Wolfgang Kopp, Guangming Wu, Sandra Heising, Boris Greber, Martin Stehling, Marcos J. Araúzo-Bravo, Stefan T. Boerno, Bernd Timmermann, Martin Vingron, and Hans R. Schöler, "Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency - Correction," Cell Stem Cell 23 (6), 900-904 (2018).
51.
Journal Article
Xinyi Yang and Martin Vingron, "Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions," BMC Biology 16 (1), 138 (2018).
52.
Journal Article
Stefanie Schöne, Anna Melissa Bothe, Edda Einfeldt, Marina Borschiwer, Philipp Florian Benner, Martin Vingron, Morgane Thomas-Chollier, and Sebastiaan H. Meijsing, "Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise," PLoS Genetics 14 (11), e1007793 (2018).
53.
Journal Article
Bjørt K. Kragesteen , Malte Spielmann, Christina Paliou, Verena Heinrich, Robert Schöpflin, Andrea Esposito, Carlo Annunziatella, Simona Bianco , Andrea M. Chiariello, Ivana Jerković , Izabela Harabula, Philine Guckelberger, Michael Pechstein, Lars Wittler, Wing-Lee Chan, Martin Franke, Darío G. Lupiáñez , Katerina Kraft, Bernd Timmermann, Martin Vingron, Axel Visel, Mario Nicodemi, Stefan Mundlos, and Guillaume Andrey, "Dynamic 3D chromatin architecture determines enhancer specificity and morphogenetic identity in limb development," Nature Genetics 50 (10), 1463-1473 (2018).
54.
Journal Article
L. Grassi, F. Pourfarzad, S. Ullrich, A. Merkel, F. Were, E. Carrillo-de-Santa-Pau, G. Yi, I. H. Hiemstra, A. T. J. Tool, E. Mul, J. Perner, E. Janssen-Megens, K. Berentsen, H. Kerstens, E. Habibi, M. Gut, M. L. Yaspo, M. Linser, E. Lowy, A. Datta, L. Clarke, P. Flicek, M. Vingron, D. Roos, T. K. van den Berg, S. Heath, D. Rico, M. Frontini, M. Kostadima, I. Gut, A. Valencia, W. H. Ouwehand, H. G. Stunnenberg, J. H. A. Martens, and T. W. Kuijpers, "Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils," Cell Reports 24 (10), 2784-2794 (2018).
55.
Journal Article
Alena van Bömmel, Michael I. Love, Ho-Ryun Chung, and Martin Vingron, "coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers," PLoS Computational Biology 14 (8), e1006372 (2018).
56.
Journal Article
Kenjiro Adachi, Wolfgang Kopp, Guangming Wu, Sandra Heising, Boris Greber, Martin Stehling , Marcos J. Araúzo-Bravo, Stefan T. Boerno, Bernd Timmermann, Martin Vingron, and Hans R. Schöler, "Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency," Cell Stem Cell 23 (2), 266-275 (2018).
57.
Journal Article
Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael Becker, Felix Dreher, Uwe Schirmer, Stefan T. Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, Heike Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, and Ruth M. Schweiger, "Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance," Genome Medicine 10 (1), 10:55 (2018).
58.
Journal Article
Simona Bianco, Darío G. Lupiáñez, Andrea M. Chiariello, Carlo Annunziatella, Katerina Kraft, Robert Schöpflin, Lars Wittler, Guillaume Andrey, Martin Vingron, Ana Pombo, Stefan Mundlos, and Mario Nicodemi, "Polymer physics predicts the effects of structural variants on chromatin architecture," Nature Genetics 50 (5), 662-667 (2018).
59.
Journal Article
Verena Thormann, Maika C. Rothkegel, Robert Schöpflin, Laura V. Glaser, Peter Djuric, Na Li, Ho-Ryun Chung, Kevin Schwahn, Martin Vingron, and Sebastiaan Meijsing, "Genomic dissection of enhancers uncovers principles of combinatorial regulation and dynamic wiring of enhancer-promoter contacts," Nucleic Acids Research (London) 46 (6), 2868-2882 (2018).
60.
Journal Article
J. George, V. Walter, M. Peifer, L. B. Alexandrov, D. Seidel, F. Leenders, L. Maas, C. Müller, I. Dahmen, T. M. Delhomme, M. Ardin, N. Leblay, G. Byrnes, R. Sun, A. De Reynies, A. McLeer-Florin, G. Bosco, F. Malchers, R. Menon, J. Altmüller, C. Becker, P. Nürnberg, V. Achter, U. Lang, P. M. Schneider, M. Bogus, M. G. Soloway, M. D. Wilkerson, Y. Cun, J. D. McKay, D. Moro-Sibilot, C. G. Brambilla, S. Lantuejoul, N. Lemaitre, A. Soltermann, W. Weder, V. Tischler, O. T. Brustugun, M. Lund-Iversen, A. Helland, S. Solberg, S. Ansen, G. Wright, B. Solomon, L. Roz, U. Pastorino, I. Petersen, J. H. Clement, J. Sanger, J. Wolf, Martin Vingron, T. Zander, S. Perner, W. D. Travis, S. A. Haas, M. Olivier, M. Foll, R. Buttner, D. N. Hayes, E. Brambilla, L. Fernandez-Cuesta, and R. K. Thomas, "Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors," Nature Communications 9 (1), 1048 (2018).
61.
Journal Article
W. Kopp and M. Vingron, "An improved compound Poisson model for the number of motif hits in DNA sequences," Bioinformatics 33 (24), 3929-3937 (2017).
62.
Journal Article
D. Heller, R. Krestel, U. Ohler, M. Vingron, and A. Marsico, "ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data," Nucleic Acids Research (London) 45 (19), 11004-11018 (2017).
63.
Journal Article
J. Bhat, J. Helmuth, G. Chitadze, L. Kouakanou, C. Peters, M. Vingron, O. Ammerpohl, and D. Kabelitz, "Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity," Scand J Immunol 86 (4), 184-195 (2017).
64.
Journal Article
A. J. Will , G. Cova, M. Osterwalder, W. L. Chan, L. Wittler, N. Brieske, V. Heinrich, J. P. de Villartay, M. Vingron, E. Klopocki, A. Visel, D. G. Lupianez, and S. Mundlos, "Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)," Nature Genetics 49 (10), 1539-1545 (2017).
65.
Journal Article
Jun Yang, Mohammad Hossein Moeinzadeh, Heiner Kuhl, Johannes Helmuth, Peng Xiao, Stefan Haas, Guiling Liu, Jianli Zheng, Zhe Sun, Weijuan Fan, Gaifang Deng, Hongxia Wang, Fenhong Hu, Shanshan Zhao, Alisdair R. Fernie, Stefan T. Börno, Bernd Timmermann, Peng Zhang, and Martin Vingron, "Haplotype-resolved sweet potato genome traces back its hexaploidization history," Nature Plants 2017 (3), 696-703 (2017).
66.
Journal Article
M. I. Love, M. Huska, M. Jurk, R. Schöpflin, S. R. Starick, K. Schwahn, S. B. Cooper, K. R. Yamamoto, M. Thomas-Chollier, M. Vingron, and S. H. Meijsing, "Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation," Nucleic Acids Research (London) 45 (4), 1805-1819 (2017).
67.
Journal Article
Guillaume Andrey, Robert Schöpflin, Ivana Jerković, Verena Heinrich, Daniel Ibrahim, Christina Paliou, Myriam Hochradel, Bernd Timmermann, Stefan Haas, Martin Vingron, and Stefan Mundlos, "Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding," Genome Research 27 (2), 223-233 (2017).
68.
Journal Article
Martin Franke, Daniel Ibrahim, Guillaume Andrey, Wibke Schwarzer, Verena Heinrich, Robert Schöpflin, Katerina Kraft, Rieke Kempfer, Ivana Jerković, Wing-Lee Chan, Malte Spielmann, Bernd Timmermann, Lars Wittler, Ingo Kurth, Paola Cambiaso, Orsetta Zuffardi, Gunnar Houge, Lindsay Lambie, Francesco Brancati, Ana Pombo, Martin Vingron, Francois Spitz, and Stefan Mundlos, "Formation of novel chromatin domains determines pathogenicity of genomic duplications," Nature 538 (7624), 265-269 (2016).
69.
Journal Article
I. Du Bois, A. Marsico, W. Bertrams, M. R. Schweiger, B. Caffrey, A. Sittka-Stark, M. Eberhardt, J. Vera, M. Vingron, and B. T. Schmeck, "Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2," The Journal of Infectious Diseases 214 (3), 454-463 (2016).
70.
Journal Article
D. Juan, J. Perner, E. Carrillo de Santa Pau, S. Marsili, D. Ochoa, H. R. Chung, M. Vingron, D. Rico, and A. Valencia, "Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs," Cell Reports 14 (5), 1246-1257 (2016).
71.
Journal Article
S. Ancherbak, E. E. Kuruoglu, and M. Vingron, "Time-Dependent Gene Network Modelling by Sequential Monte Carlo," IEEE ACM Transactions on Computational Biology and Bioinformatics 13 (6), 1183-1193 (2016).
72.
Journal Article
H. Hu, S. A. Haas, J. Chelly, H. Van Esch, M. Raynaud, A. P. M. de Brouwer, S. Weinert, G. Froyen, S. G. M. Frints, F. Laumonnier, T. Zemojtel, M. I. Love, H. Richard, A.-K. Emde, M. Bienek, C. Jensen, M. Hambrock, U. Fischer, C. Langnick, M. Feldkamp, W. Wissink-Lindhout, N. Lebrun, L. Castelnau, J. Rucci, R. Montjean, O. Dorseuil, P. Billuart, T. Stuhlmann, M. Shaw, M. A. Corbett, A. Gardner, S. Willis-Owen, C. Tan, K. L. Friend, S. Belet, K. E. P. van Roozendaal, M. Jimenez-Pocquet, M.-P. Moizard, N. Ronce, R. Sun, S. O'Keeffe, R. Chenna, A. van Bömmel, J. Göke, A. Hackett, M. Field, L. Christie, J. Boyle, E. Haan, J. Nelson, G. Turner, G. Baynam, G. Gillessen-Kaesbach, U. Müller, D. Steinberger, B. Budny, M. Badura-Stronka, A. Latos-Bieleńska, L. B. Ousager, P. Wieacker, G. Rodríguez Criado, M.-L. Bondeson, G. Annerén, A. Dufke, M. Cohen, L. Van Maldergem, C. Vincent-Delorme, B. Echenne, B. Simon-Bouy, T. Kleefstra, M. Willemsen, J.-P. Fryns, K. Devriendt, R. Ullmann, M. Vingron, K. Wrogemann, T. F. Wienker, A. Tzschach, H. van Bokhoven, J. Gecz, T. J. Jentsch, W. Chen, H.-H. Ropers, and V. M. Kalscheuer, "X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes," Molecular Psychiatry 21 (1), 133-148 (2016).
73.
Journal Article
M. Huska and M. Vingron, "Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns," PLoS Computational Biology 12 (12), e1005249 (2016).
74.
Journal Article
J. M. Muino, S. de Bruijn, A. Pajoro, K. Geuten, M. Vingron, G. C. Angenent, and K. Kaufmann, "Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor," Molecular Biology and Evolution 33 (1), 185-200 (2016).
75.
Journal Article
S. Schöne, M. Jurk, M. B. Helabad, I. Dror, I. Lebars, B. Kieffer, P. Imhof, R. Rohs, M. Vingron, M. Thomas-Chollier, and S. Meijsing, "Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity," Nature Communications 7, 13784 (2016).
76.
Journal Article
S. Schöne, M. Jurk, M. B. Helabad, I. Dror, I. Lebars, B. Kieffer, P. Imhof, R. Rohs, M. Vingron, M. Thomas-Chollier, and S. Meijsing, "Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity," Nature Communications 7, 12621 (2016).
77.
Journal Article
M. Ganbari, Julia Lasserre, and M. Vingron, "Reconstruction of gene networks using prior knowledge," BMC Systems Biology 9, 9:84 (2015).
78.
Journal Article
F. Eduati, L. M. Mangravite, T. Wang, H. Tang, J. C. Bare, R. Huang, T. Norman, M. Kellen, M. P. Menden, J. Yang, X. Zhan, R. Zhong, G. Xiao, M. Xia, N. Abdo, O. Kosyk, Niehs-Ncats-Unc Dream Toxicogenetics Collaboration, A. van Bömmel, B. Caffrey, M. Heinig, M. Huska, A. Mammana, J. Perner, M. Vingron, S. Friend, A. Dearry, A. Simeonov, R. R. Tice, I. Rusyn, F. A. Wright, G. Stolovitzky, Y. Xie, and J. Saez-Rodriguez, "Prediction of human population responses to toxic compounds by a collaborative competition," Nat Biotechnol 33 (9), 933-940 (2015).
79.
Journal Article
J. George, J. S. Lim, S. J. Jang, Y. Cun, L. Ozretic, G. Kong, F. Leenders, X. Lu, L. Fernandez-Cuesta, G. Bosco, C. Müller, I. Dahmen, N. S. Jahchan, K. S. Park, D. Yang, A. N. Karnezis, D. Vaka, A. Torres, M. S. Wang, J. O. Korbel, R. Menon, S. M. Chun, D. Kim, M. Wilkerson, N. Hayes, D. Engelmann, B. Putzer, M. Bos, S. Michels, I. Vlasic, D. Seidel, B. Pinther, P. Schaub, C. Becker, J. Altmuller, J. Yokota, T. Kohno, R. Iwakawa, K. Tsuta, M. Noguchi, T. Muley, H. Hoffmann, P. A. Schnabel, I. Petersen, Y. Chen, A. Soltermann, V. Tischler, C. M. Choi, Y. H. Kim, P. P. Massion, Y. Zou, D. Jovanovic, M. Kontic, G. M. Wright, P. A. Russell, B. Solomon, I. Koch, M. Lindner, L. A. Muscarella, A. la Torre, J. K. Field, M. Jakopovic, J. Knezevic, E. Castanos-Velez, L. Roz, U. Pastorino, O. T. Brustugun, M. Lund-Iversen, E. Thunnissen, J. Köhler, M. Schuler, J. Botling, M. Sandelin, M. Sanchez-Cespedes, H. B. Salvesen, V. Achter, U. Lang, M. Bogus, P. M. Schneider, T. Zander, S. Ansen, M. Hallek, J. Wolf, M. Vingron, Y. Yatabe, W. D. Travis, P. Nurnberg, C. Reinhardt, S. Perner, L. Heukamp, R. Büttner, S. A. Haas, E. Brambilla, M. Peifer, J. Sage, and R. K. Thomas, "Comprehensive genomic profiles of small cell lung cancer," Nature 524 (7563), 47-53 (2015).
80.
Journal Article
Denise Emmerich, Tomasz Zemojtel, Jochen Hecht, Peter Krawitz, Malte Spielmann, Jirko Kühnisch, Karolina Kobus, Monika Oßwald, Verena Heinrich, Peter Berlien, Ute Müller, Victor-F. Mautner, Katharina Wimmer, Peter N. Robinson, Martin Vingron, Sigrid Tinschert, Stefan Mundlos, and Mateusz Kolanczyk, "Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient," European journal of human genetics 23 (6), 1870-1873 (2015).
81.
Journal Article
Stephan R. Starick, Jonas Ibn-Salem, Marcel Jurk, Céline Hernandez, Michael I. Love, Ho-Ryun Chung, Martin Vingron, Morgane Thomas-Chollier, and Sebastian H. Meijsing, "ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors," Genome Res 25 (6), 825-835 (2015).
82.
Journal Article
S. Schafer, E. Adami, M. Heinig, K. E. Rodrigues, F. Kreuchwig, J. Silhavy, S. van Heesch, D. Simaite, N. Rajewsky, E. Cuppen, M. Pravenec, M. Vingron, S. A. Cook, and N. Hubner, "Translational regulation shapes the molecular landscape of complex disease phenotypes," Nat Commun 6, 6:7200 (2015).
83.
Journal Article
Lynnette Fernandez-Cuesta, Ruping Sun, Roopika Menon, Julie George, Susanne Lorenz, Leonardo A. Meza-Zepeda, Martin Peifer, Dennis Plenker, Johannes M. Heuckmann, Frauke Leenders, Thomas Zander, Ilona Dahmen, Mirjam Koker, Jakob Schöttle, Roland T. Ullrich, Janine Altmüller, Christian Becker, Peter Nürnberg, Henrik Seidel, Diana Böhm, Friederike Göke, Sascha Ansen, Prudence A. Russell, Gavin M. Wright, Zoe Wainer, Benjamin Solomon, Iver Petersen, Joachim H. Clement, Jörg Sänger, Odd Terje Brustugun, Aslaug Helland, Steinar Solberg, Marius Lund-Iversen, Reinhard Büttner, Jürgen Wolf, Elisabeth Brambilla, Martin Vingron, Sven Perner, Stefan A. Haas, and Roman K. Thomas, "Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data," Genome Biology: Biology for the Post-Genomic Era 16, 16:7 (2015).
84.
Journal Article
M. Heinig, M. Colome-Tatche, A. Taudt, C. Rintisch, S. Schafer, M. Pravenec, N. Hubner, M. Vingron, and F. Johannes, "histoneHMM: Differential analysis of histone modifications with broad genomic footprints," BMC Bioinformatics 16, 16:60 (2015).
85.
Journal Article
Juliane Perner, Julia Lasserre, Sarah Kinkley, Martin Vingron, and Ho-Ryun Chung, "Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling," Nucleic Acids Research (London) 42 (22), 13689-13695 (2014).
86.
Journal Article
Navodit Misra, Ewa Szczurek, and Martin Vingron, "Inferring the paths of somatic evolution in cancer," Bioinformatics 30 (17), 2456-2463 (2014).
87.
Journal Article
G. Meng and M. Vingron, "Condition-specific target prediction from motifs and expression," Bioinformatics 30 (12), 1643-1650 (2014).
88.
Journal Article
Xianbin Yu, Guangyong Zheng, Lanlan Shan, Guofeng Meng, Martin Vingron, Qi Liu, and Xin-Guang Zhu, "Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana," Frontiers in Plant Science 5, 5:273-5:273 (2014).
89.
Journal Article
C. Rintisch, M. Heinig, A. Bauerfeind, S. Schafer, C. Mieth, G. Patone, O. Hummel, W. Chen, S. Cook, E. Cuppen, M. Colome-Tatche, F. Johannes, R. C. Jansen, H. Neil, M. Werner, M. Pravenec, M. Vingron, and N. Hubner, "Natural variation of histone modification and its impact on gene expression in the rat genome," Genome Research 24 (6), 942-953 (2014).
90.
Journal Article
L. Fernandez-Cuesta, D. Plenker, H. Osada, R. Sun, R. Menon, F. Leenders, S. Ortiz-Cuaran, M. Peifer, M. Bos, J. Dassler, F. Malchers, J. Schöttle, W. Vogel, I. Dahmen, M. Koker, R. T. Ullrich, G. M. Wright, P. A. Russell, Z. Wainer, B. Solomon, E. Brambilla, H. Nagy-Mignotte, D. Moro-Sibilot, C. G. Brambilla, S. Lantuejoul, J. Altmüller, C. Becker, P. Nürnberg, J. M. Heuckmann, E. Stoelben, I. Petersen, J. H. Clement, J. Sänger, L. A. Muscarella, A. la Torre, V. M. Fazio, I. Lahortiga, T. Perera, S. Ogata, M. Parade, D. Brehmer, M. Vingron, L. C. Heukamp, R. Buettner, T. Zander, J. Wolf, S. Perner, S. Ansen, S. A. Haas, Y. Yatabe, and R. K. Thomas, "CD74-NRG1 Fusions in Lung Adenocarcinoma," Cancer Discovery 4 (4), 415-422 (2014).
91.
Journal Article
L. Fernandez-Cuesta, M. Peifer, X. Lu, R. Sun, L. Ozretic, D. Seidel, T. Zander, F. Leenders, J. George, C. Müller, I. Dahmen, B. Pinther, G. Bosco, K. Konrad, J. Altmüller, P. Nürnberg, V. Achter, U. Lang, P. M. Schneider, M. Bogus, A. Soltermann, O. T. Brustugun, A. Helland, S. Solberg, M. Lund-Iversen, S. Ansen, E. Stoelben, G. M. Wright, P. Russell, Z. Wainer, B. Solomon, J. K. Field, R. Hyde, M. P. Davies, L. C. Heukamp, I. Petersen, S. Perner, C. M. Lovly, F. Cappuzzo, W. D. Travis, J. Wolf, M. Vingron, E. Brambilla, S. A. Haas, R. Buettner, and R. K. Thomas, "Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids," Nature Communications 5, 5:3518 (2014).
92.
Journal Article
E. Szczurek, N. Misra, and M. Vingron, "Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma," International Journal of Cancer 133 (9), 2123-2132 (2013).
93.
Journal Article
M. Thomas-Chollier, L. C. Watson, S. B. Cooper, M. A. Pufall, J. S. Liu, K. Borzym, M. Vingron, K. R. Yamamoto, and S. H. Meijsing, "A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms," Proceedings of the National Academy of Sciences of the United States of America 110 (44), 17826-17831 (2013).
94.
Journal Article
Alessandro Mammana, Martin Vingron, and Ho-Ryun Chung, "Inferring nucleosome positions with their histone mark annotation from ChIP data," Bioinformatics 29 (20), 2547-2554 (2013).
95.
Journal Article
Annalisa Marsico, Matthew Huska, Julia Lasserre, Haiyang Hu, Dubravka Vucicevic, Anne Musahl, Ulf Andersson Ørom, and Martin Vingron, "PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs," Genome Biology 14 (8), R84-R84 (2013).
96.
Journal Article
J. Göke, Y. S. Chan, J. L. Yan, M. Vingron, and H. H. Ng, "Genome-wide Kinase-Chromatin Interactions Reveal the Regulatory Network of ERK Signaling in Human Embryonic Stem Cells," Molecular Cell 50 (6), 844-855 (2013).
97.
Journal Article
Radmila Feldmann, Cornelius Fischer, Vitam Kodelja, Sarah Behrens, Stefan Haas, Martin Vingron, Bernd Timmermann, Anne Geikowski, and Sascha Sauer, "Genome-wide analysis of LXRalpha activation reveals new transcriptional networks in human atherosclerotic foam cells," Nucleic Acids Research (London) 41 (6), 3518-3531 (2013).
98.
Journal Article
Radmila Feldmann, Cornelius Fischer, Vitam Kodelja, Sarah Behrens, Stefan Haas, Martin Vingron, Bernd Timmermann, Anne Geikowski, and Sascha Sauer, "Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells," Nucleic Acids Research (London) 41 (6), 3518-3531 (2013).
99.
Journal Article
M. T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T. R. Riley, J. Saez-Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, Dream Consortium, P. Agius, A. Arvey, P. Bucher, C. G., Jr. Callan, C. W. Chang, C. Y. Chen, Y. S. Chen, Y. W. Chu, J. Grau, I. Grosse, V. Jagannathan, J. Keilwagen, S. M. Kielbasa, J. B. Kinney, H. Klein, M. B. Kursa, H. Lahdesmaki, K. Laurila, C. Lei, C. Leslie, C. Linhart, A. Murugan, A. Mysickova, W. S. Noble, M. Nykter, Y. Orenstein, S. Posch, J. Ruan, W. R. Rudnicki, C. D. Schmid, R. Shamir, W. K. Sung, M. Vingron, Z. Zhang, H. J. Bussemaker, Q. D. Morris, M. L. Bulyk, G. Stolovitzky, and T. R. Hughes, "Evaluation of methods for modeling transcription factor sequence specificity," Nature biotechnology 31 (2), 126-34 (2013).