List of publications

Pockrandt, C. M.; Alzamel, M.; Iliopoulos, C. S.; Reinert, K.: GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics, btaa222 (2020)

Benner, P.; Vingron, M.: ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. Journal of Computational Biology 27 (4), pp. 442 - 457 (2020)

Kupke, S. Y.; Ly, L.-H.; Börno, S. T.; Ruff, A.; Timmermann, B.; Vingron, M.; Haas, S.: 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), pii: E71 (2020)

Ramisch, A.; Heinrich, V.; Glaser, L. V.; Fuchs, A.; Yang, X.; Benner, P.; Schöpflin, R.; Li, N.; Kinkley, S.; Römer-Hillmann, A. et al.; Longinotto, J.; Heyne, S.; Czepukojc, B.; Kessler, S. M.; Kiemer, A. K.; Cadenas, C.; Arrigoni, L.; Gasparoni, N.; Manke, T.; Pap, T.; Pospisilik, A.; Hengstler, J.; Walter, J.; Meijsing, S.; Chung, H.-R.; Vingron, M.: CRUP: a comprehensive framework to predict condition-specific regulatory units. Genome Biology: Biology for the Post-Genomic Era 20, 20:227 (2019)

Heller, D.; Vingron, M.: SVIM: Structural Variant Identification using Mapped Long Reads. Bioinformatics 35 (17), pp. 2907 - 2915 (2019)

Kopp, W.; Vingron, M.: DNA Motif Match Statistics Without Poisson Approximation. Journal of Computational Biology 26 (8), pp. 846 - 865 (2019)

Despang, A.; Schöpflin, R.; Franke, M.; Ali, S.; Jerković, I.; Paliou, C.; Chan, W.-L.; Timmermann, B.; Wittler, L.; Vingron, M. et al.; Mundlos, S.; Ibrahim, D. M.: Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture. Nature Genetics 51 (8), pp. 1263 - 1271 (2019)

van Heesch, S.; Witte, F.; Schneider-Lunitz, V.; Schulz, J. F.; Adami, E.; Faber, A. B.; Kirchner, M.; Maatz, H.; Blachut, S.; Sandmann, C. L. et al.; Kanda, M.; Worth, C. L.; Schafer, S.; Calviello, L.; Merriott, R.; Patone, G.; Hummel, O.; Wyler, E.; Obermayer, B.; Mucke, M. B.; Lindberg, E. L.; Trnka, F.; Memczak, S.; Schilling, M.; Felkin, L. E.; Barton, P. J. R.; Quaife, N. M.; Vanezis, K.; Diecke, S.; Mukai, M.; Mah, N.; Oh, S. J.; Kurtz, A.; Schramm, C.; Schwinge, D.; Sebode, M.; Harakalova, M.; Asselbergs, F. W.; Vink, A.; de Weger, R. A.; Viswanathan, S.; Widjaja, A. A.; Gartner-Rommel, A.; Milting, H.; Dos Remedios, C.; Knosalla, C.; Mertins, P.; Landthaler, M.; Vingron, M.; Linke, W. A.; Seidman, J. G.; Seidman, C. E.; Rajewsky, N.; Ohler, U.; Cook, S. A.; Hubner, N.: The Translational Landscape of the Human Heart. Cell 178 (1), e29, pp. 242 - 260 (2019)

Paliou, C.; Guckelberger, P.; Schöpflin, R.; Heinrich, V.; Esposito, A.; Chiariello, A. M.; Bianco, S.; Annunziatella, C.; Helmuth, J.; Haas, S. et al.; Jerković, I.; Brieske, N.; Wittler, L.; Timmermann, B.; Nicodemi, M.; Vingron, M.; Mundlos, S.; Andrey, G.: Preformed Chromatin Topology Assists Transcriptional Robustness of Shh during Limb Development. bioRxiv (Preprint Server) 2019, 528877 (2019)

Mallm, J. P.; Iskar, M.; Ishaque, N.; Klett, L. C.; Kugler, S. J.; Muino, J. M.; Teif, V. B.; Poos, A. M.; Grossmann, S.; Erdel, F. et al.; Tavernari, D.; Koser, S. D.; Schumacher, S.; Brors, B.; Konig, R.; Remondini, D.; Vingron, M.; Stilgenbauer, S.; Lichter, P.; Zapatka, M.; Mertens, D.; Rippe, K.: Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Molecular Systems Biology 15 (5), e8339 (2019)

Zehnder, T.; Benner, P.; Vingron, M.: Predicting enhancers in mammalian genomes using supervised hidden Markov models. BMC Bioinformatics 20, 157 (2019)

Ghanbari, M.; Lasserre, J.; Vingron, M.: The Distance Precision Matrix: computing networks from non-linear relationships. Bioinformatics 35 (6), pp. 1009 - 1017 (2019)

Kraft, K.; Magg, A.; Heinrich, V.; Riemenschneider, C.; Schöpflin, R.; Markowski, J.; Ibrahim, D.; Acuna-Hidalgo, R.; Despang, A.; Andrey, G. et al.; Wittler, L.; Timmermann, B.; Vingron, M.; Mundlos, S.: Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations. Nature Cell Biology 21 (3), pp. 305 - 310 (2019)

Adachi, K.; Kopp, W.; Wu, G.; Heising, S.; Greber, B.; Stehling, M.; Araúzo-Bravo, M. J.; Boerno, S. T.; Timmermann, B.; Vingron, M. et al.; Schöler, H. R.: Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency - Correction. Cell Stem Cell 23 (6), pp. 900 - 904 (2018)

Yang, X.; Vingron, M.: Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions. BMC Biology 16 (1), 138 (2018)

Schöne, S.; Bothe, A. M.; Einfeldt, E.; Borschiwer, M.; Benner, P. F.; Vingron, M.; Thomas-Chollier, M.; Meijsing, S. H.: Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genetics 14 (11), e1007793 (2018)

Kragesteen , B. K.; Spielmann, M.; Paliou, C.; Heinrich, V.; Schöpflin, R.; Esposito, A.; Annunziatella, C.; Bianco , S.; Chiariello, A. M.; Jerković , I. et al.; Harabula, I.; Guckelberger, P.; Pechstein, M.; Wittler, L.; Chan, W.-L.; Franke, M.; Lupiáñez , D. G.; Kraft, K.; Timmermann, B.; Vingron, M.; Visel, A.; Nicodemi, M.; Mundlos, S.; Andrey, G.: Dynamic 3D chromatin architecture determines enhancer specificity and morphogenetic identity in limb development. Nature Genetics 50 (10), pp. 1463 - 1473 (2018)

Grassi, L.; Pourfarzad, F.; Ullrich, S.; Merkel, A.; Were, F.; Carrillo-de-Santa-Pau, E.; Yi, G.; Hiemstra, I. H.; Tool, A. T. J.; Mul, E. et al.; Perner, J.; Janssen-Megens, E.; Berentsen, K.; Kerstens, H.; Habibi, E.; Gut, M.; Yaspo, M. L.; Linser, M.; Lowy, E.; Datta, A.; Clarke, L.; Flicek, P.; Vingron, M.; Roos, D.; van den Berg, T. K.; Heath, S.; Rico, D.; Frontini, M.; Kostadima, M.; Gut, I.; Valencia, A.; Ouwehand, W. H.; Stunnenberg, H. G.; Martens, J. H. A.; Kuijpers, T. W.: Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils. Cell Reports 24 (10), pp. 2784 - 2794 (2018)

van Bömmel, A.; Love, M. I.; Chung, H.-R.; Vingron, M.: coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLoS Computational Biology 14 (8), e1006372 (2018)

Adachi, K.; Kopp, W.; Wu, G.; Heising, S.; Greber, B.; Stehling , M.; Araúzo-Bravo, M. J.; Boerno, S. T.; Timmermann, B.; Vingron, M. et al.; Schöler, H. R.: Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency. Cell Stem Cell 23 (2), pp. 266 - 275 (2018)