Publications of Martin Vingron

Lienhard, M.; van den Beucken , T.; Timmermann, B.; Hochradel, M.; Boerno, S.; Caiment , F.; Vingron, M.; Herwig, R.: IsoTools: a flexible workflow for long-read transcriptome sequencing analysis. Bioinformatics, btad364 (2023)

Kibar, G.; Vingron, M.: Prediction of protein–protein interactions using sequences ofintrinsically disordered regions. Proteins: Structure, Function, and Bioinformatics, prot.26486 (2023)

Schöpflin, R.; Melo, U. S.; Moeinzadeh, M. H.; Heller, D.; Laupert, V.; Hertzberg, J.; Holtgrewe, M.; Alavi, N.; Klever, M.-K.; Jungnitsch, J. et al.; Comak, E.; Türkmen, S.; Horn, D.; Duffourd, Y.; Faivre, L.; Callier, P.; Sanlaville, D.; Zuffardi, O.; Tenconi, R.; Kurtas, N. E.; Giglio, S.; Prager, B.; Latos-Bielenska, A.; Vogel, I.; Bugge, M.; Tommerup, N.; Spielmann, M.; Vitobello, A.; Kalscheuer, V. M.; Vingron, M.; Mundlos, S.: Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes. Nature Communications 13, 6470 (2022)

Schindler, M.; Osterwalder, M.; Harabula, I.; Wittler, L.; Tzika, A. C.; Dechmann, D.; Vingron, M.; Visel, A.; Haas, S.; Real, F. M.: Co-option of the transcription factor SALL1 in mole ovotestis formation. bioRxiv, 514220 (2022)

Ringel, A.; Szabo, Q.; Chiariello, A. M.; Chudzik, K.; Schöpflin, R.; Rothe, P.; Mattei, A. L.; Zehnder, T.; Harnett, D.; Laupert, V. et al.; Bianco, S.; Hetzel, S.; Glaser, J.; Phan, M. H. Q.; Schindler, M.; Ibrahim, D. M.; Paliou, C.; Esposito, A.; Prada-Medina, C. A.; Haas, S. A.; Giere, P.; Vingron, M.; Wittler, L.; Meissner, A.; Nicodemi, M.; Cavalli, G.; Bantignies, F.; Mundlos, S.; Robson, M. I.: Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 185 (20), e21, pp. 3689 - 3704 (2022)

Rosebrock, D.; Arora, S.; Mutukula, N.; Volkman, R.; Gralinska, E.; Balaskas, A.; Aragonés Hernández, A.; Buschow, R.; Brändl, B.; Müller, F.-J. et al.; Arndt, P. F.; Vingron, M.; Elkabetz, Y.: 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, pp. 981 - 995 (2022)

Gralinska, E.; Kohl, C.; Fadakar, S.; Vingron, M.: Visualizing Cluster-specific Genes from Single-cell Transcriptomics Data Using Association Plots. Journal of Molecular Biology 434 (11), 167525 (2022)

Hertzberg, J.; Mundlos, S.; Vingron, M.; Gallone, G.: TADA – a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs. Genome Biology 23, 67 (2022)

Ly, L.-H.; Vingron, M.: Effect of imputation on gene network reconstruction from single-cell RNA-seq data. Patterns 3, 100414 (2022)

Glaser, L. V.; Steiger, M.; Fuchs, A.; van Bömmel, A.; Einfeldt, E.; Chung, H.-R.; Vingron, M.; Meijsing, S. H.: Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq. Nucleic Acids Research (London) 49 (21), gkab1100, pp. 12178 - 12195 (2021)

Enervald, E.; Powell, L. M.; Boteva, L.; Foti, R.; Ruiz, N. B.; Kibar, G.; Piszczek, A.; Cavaleri, F.; Vingron, M.; Cerase, A. et al.; Buonomo, S. B. C.: RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes. The EMBO Journal 40, e105862 (2021)

Benner, P.; Vingron, M.: Quantifying the tissue-specific regulatory information within enhancer DNA sequences. NAR: genomics and bioinformatics 3 (4), lqab095 (2021)

Socha, M.; Sowińska-Seidler, A.; Melo, U. S.; Kragesteen, B. K.; Franke, M.; Heinrich, V.; Schöpflin, R.; Nagel, I.; Gruchy, N.; Mundlos, S. et al.; Sreenivasan, V. K. A.; López, C.; Vingron, M.; Bukowska-Olech, E.; Spielmann, M.; Jamsheer, A.: Position effects at the FGF8 locus are associated with femoral hypoplasia. The American Journal of Human Genetics 108 (9), pp. 1725 - 1734 (2021)

Belicova , L.; Repnik , U.; Delpierre , J.; Gralinska, E.; Seifert , S.; Valenzuela , J. I.; Morales-Navarrete , H. A.; Franke , C.; Räägel , H.; Shcherbinina , E. et al.; Prikazchikova , T.; Koteliansky , V.; Vingron, M.; Kalaidzidis , Y. L.; Zatsepin , T.; Zerial , M.: Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads. The Journal of Cell Biology: JCB 220 (10), e202103003 (2021)

Witte, F.; Ruiz-Orera, J.; Ciolli Mattioli, C.; Blachut, S.; Adami, E.; Schulz, J. F.; Schneider-Lunitz, V.; Hummel, O.; Patone, G.; Mücke, M. B. et al.; Šilhavý, J.; Heinig, M.; Bottolo, L.; Sanchis, D.; Vingron, M.; Chekulaeva, M.; Pravenec, M.; Hubner, N.; van Heesch, S.: A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biology 22, 191 (2021)

Gajos, M.; Jasnovidova, O.; van Bömmel, A.; Freier, S.; Vingron, M.; Mayer, A.: Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Research (London) 49 (8), pp. 4402 - 4420 (2021)

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

Gralinska, E.; Vingron, M.: Association Plots: Visualizing associations in high-dimensional correspondence analysis biplots. bioRxiv (Preprint Server) (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)