Publications of Martin Vingron

Baranasic, D.; Hörtenhuber, M.; Balwierz, P.; Zehnder, T.; Mukarram, A. K.; Nepal, C.; Varnai, C.; Hadzhiev, Y.; Jimenez- Gonzalez, A.; Li, N. et al.; Wragg, J.; D’Orazio, F.; Díaz, N.; Hernández- Rodríguez, B.; Chen, Z.; Stoiber, M.; Dong, M.; Stevens, I.; Ross, S. E.; Eagle, A.; Martin, R.; Obasaju, P.; Rastegar, S.; McGarvey, A. C.; Kopp, W.; Chambers, E.; Wang, D.; Kim, H. R.; Acemel, R. D.; Naranjo, S.; Lapinski, M.; Chong, V.; Mathavan, S.; Peers, B.; Sauka-Spengler, T.; Vingron, M.; Carninci, P.; Ohler, U.; Lacadie, S. A.; Burgess, S.; Winata, C.; van Eeden, F.; Vaquerizas, J. M.; Gómez-Skarmeta, J. L.; Onichtchouk, D.; Brown, B. J.; Bogdanovic, O.; Westerfield, M.; Wardle, F. C.; Daub, C. O.; Lenhard, B.; Müller, F.: Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics 54 (7), pp. 1037 - 1050 (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 (6), 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 (1), 67 (2022)

Ly, L.-H.; Vingron, M.: Effect of imputation on gene network reconstruction from single-cell RNA-seq data. Patterns 3 (2), 100414 (2021)

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), 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 (24), 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 (1), 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)

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)

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)