Benner, P.: Computing Leapfrog Regularization Paths with Applications to Large-Scale K-mer Logistic Regression. Journal of Computational Biology 28 (6), pp. 560 - 569 (2021)

Allou, L.; Balzano, S.; Magg, A.; Quinodoz, M.; Royer-Bertrand, B.; Schöpflin, R.; Chan, W.-L.; Speck-Martins, C. E.; Rocha Carvalho, D.; Farage, L. et al.; Marques Lourenço, C.; Albuquerque, R.; Rajagopal, S.; Nampoothiri, S.; Campos-Xavier, B.; Chiesa, C.; Niel-Bütschi, F.; Wittler, L.; Timmermann, B.; Spielmann, M.; Robson, M.; Ringel, A.; Heinrich, V.; Cova, G.; Andrey , G.; Prada-Medina, C. A.; Pescini-Gobert, R.; Unger, S.; Bonafé, L.; Grote, P.; Rivolta, C.; Mundlos, S.; Superti-Furga, A.: Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 592 (7852), pp. 93 - 98 (2021)

Heller, D.; Vingron, M.: SVIM-asm: structural variant detection from haploid and diploid genome assemblies. Bioinformatics 36 (22-23), pp. 5519 - 5521 (2020)

Real, F. M.; Haas, S. A.; Franchini, P.; Xiong, P.; Simakov, O.; Kuhl, H.; Schöpflin, R.; Heller, D.; Moeinzadeh, M. H.; Heinrich, V. et al.; Krannich , T.; Bressin, A.; Hartmann, M. F.; Wudy, S. A.; Dechmann, D. K. N.; Hurtado, A.; Barrionuevo, F. J.; Schindler, M.; Harabula, I.; Osterwalder, M.; Hiller, M.; Wittler, L.; Visel, A.; Timmermann, B.; Meyer, A.; Vingron, M.; Jiménez, R.; Mundlos, S.; Lupiáñez, D. G.: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 370 (6513), pp. 208 - 214 (2020)

Melo, U. S.; Schöpflin, R.; Acuna-Hidalgo, R.; Mensah, M. A.; Fischer-Zirnsak, B.; Holtgrewe, M.; Klever, M.-K.; Türkmen, S.; Heinrich, V.; Datkhaeva Pluym, I. et al.; Matoso, E.; de Sousa, S. B.; Louro, P.; Hülsemann, W.; Cohen, M.; Dufke, A.; Latos-Bieleńska, A.; Vingron, M.; Kalscheuer, V.; Quintero-Rivera, F.; Spielmann, M.; Mundlos, S.: Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases. The American Journal of Human Genetics 106 (6), pp. 872 - 884 (2020)

Moeinzadeh, M.-H.; Yang, Jun; Muzychenko, E.; Gallone, G.; Heller, D.; Reinert, K.; Haas, S.; Vingron, M.: Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLOS Computational Biology 16 (5), e1007843 (2020)

Pockrandt, C. M.; Alzamel, M.; Iliopoulos, C. S.; Reinert, K.: GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics 36 (12), pp. 3687 - 3692 (2020)

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

Herkt, C. E.; Caffrey, B.; Surmann, K.; Blankenburg, S.; Gesell Salazar, M.; Jung, A. L.; Herbel, S. M.; Hoffmann, K.; Schulte, L. N.; Chen, W. et al.; Sittka-Stark, A.; Völker, U.; Vingron, M.; Marsico, A.; Bertrams, W.; Schmeck, B.: A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1. mBio 11 (2), e03155-19 (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), 71 (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 (1), 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), 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. Proceedings of the National Academy of Sciences of the United States of America 116 (25), pp. 12390 - 12399 (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 (1), 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)