Publications of Martin Vingron

Starick, S. R.; Ibn-Salem, J.; Jurk, M.; Hernandez, C.; Love, M. I.; Chung, H.-R.; Vingron, M.; Thomas-Chollier, M.; Meijsing, S. H.: 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), pp. 825 - 835 (2015)

Schafer, S.; Adami, E.; Heinig, M.; Rodrigues, K. E.; Kreuchwig, F.; Silhavy, J.; van Heesch, S.; Simaite, D.; Rajewsky, N.; Cuppen, E. et al.; Pravenec, M.; Vingron, M.; Cook, S. A.; Hubner, N.: Translational regulation shapes the molecular landscape of complex disease phenotypes. Nat Commun 6, 6:7200 (2015)

Fernandez-Cuesta, L.; Sun, R.; Menon, R.; George, J.; Lorenz, S.; Meza-Zepeda, L. A.; Peifer, M.; Plenker, D.; Heuckmann, J. M.; Leenders, F. et al.; Zander, T.; Dahmen, I.; Koker, M.; Schöttle, J.; Ullrich, R. T.; Altmüller, J.; Becker, C.; Nürnberg, P.; Seidel, H.; Böhm, D.; Göke, F.; Ansen, S.; Russell, P. A.; Wright, G. M.; Wainer, Z.; Solomon, B.; Petersen, I.; Clement, J. H.; Sänger, J.; Brustugun, O. T.; Helland, A.; Solberg, S.; Lund-Iversen, M.; Büttner, R.; Wolf, J.; Brambilla, E.; Vingron, M.; Perner, S.; Haas, S. A.; Thomas, R. K.: 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)

Heinig, M.; Colome-Tatche, M.; Taudt, A.; Rintisch, C.; Schafer, S.; Pravenec, M.; Hubner, N.; Vingron, M.; Johannes, F.: histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics 16, 16:60 (2015)

Perner, J.; Lasserre, J.; Kinkley, S.; Vingron, M.; Chung, H.-R.: Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling. Nucleic Acids Research (London) 42 (22), pp. 13689 - 13695 (2014)

Misra, N.; Szczurek, E.; Vingron, M.: Inferring the paths of somatic evolution in cancer. Bioinformatics 30 (17), pp. 2456 - 2463 (2014)

Meng, G.; Vingron, M.: Condition-specific target prediction from motifs and expression. Bioinformatics 30 (12), pp. 1643 - 1650 (2014)

Yu, X.; Zheng, G.; Shan, L.; Meng, G.; Vingron, M.; Liu, Q.; Zhu, X.-G.: Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Frontiers in Plant Science 5, p. 5:273 - 5:273 (2014)

Rintisch, C.; Heinig, M.; Bauerfeind, A.; Schafer, S.; Mieth, C.; Patone, G.; Hummel, O.; Chen, W.; Cook, S.; Cuppen, E. et al.; Colome-Tatche, M.; Johannes, F.; Jansen, R. C.; Neil, H.; Werner, M.; Pravenec, M.; Vingron, M.; Hubner, N.: Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Research 24 (6), pp. 942 - 953 (2014)

Fernandez-Cuesta, L.; Plenker, D.; Osada, H.; Sun, R.; Menon, R.; Leenders, F.; Ortiz-Cuaran, S.; Peifer, M.; Bos, M.; Dassler, J. et al.; Malchers, F.; Schöttle, J.; Vogel, W.; Dahmen, I.; Koker, M.; Ullrich, R. T.; Wright, G. M.; Russell, P. A.; Wainer, Z.; Solomon, B.; Brambilla, E.; Nagy-Mignotte, H.; Moro-Sibilot, D.; Brambilla, C. G.; Lantuejoul, S.; Altmüller, J.; Becker, C.; Nürnberg, P.; Heuckmann, J. M.; Stoelben, E.; Petersen, I.; Clement, J. H.; Sänger, J.; Muscarella, L. A.; la Torre, A.; Fazio, V. M.; Lahortiga, I.; Perera, T.; Ogata, S.; Parade, M.; Brehmer, D.; Vingron, M.; Heukamp, L. C.; Buettner, R.; Zander, T.; Wolf, J.; Perner, S.; Ansen, S.; Haas, S. A.; Yatabe, Y.; Thomas, R. K.: CD74-NRG1 Fusions in Lung Adenocarcinoma. Cancer Discovery 4 (4), pp. 415 - 422 (2014)

Fernandez-Cuesta, L.; Peifer, M.; Lu, X.; Sun, R.; Ozretic, L.; Seidel, D.; Zander, T.; Leenders, F.; George, J.; Müller, C. et al.; Dahmen, I.; Pinther, B.; Bosco, G.; Konrad, K.; Altmüller, J.; Nürnberg, P.; Achter, V.; Lang, U.; Schneider, P. M.; Bogus, M.; Soltermann, A.; Brustugun, O. T.; Helland, A.; Solberg, S.; Lund-Iversen, M.; Ansen, S.; Stoelben, E.; Wright, G. M.; Russell, P.; Wainer, Z.; Solomon, B.; Field, J. K.; Hyde, R.; Davies, M. P.; Heukamp, L. C.; Petersen, I.; Perner, S.; Lovly, C. M.; Cappuzzo, F.; Travis, W. D.; Wolf, J.; Vingron, M.; Brambilla, E.; Haas, S. A.; Buettner, R.; Thomas, R. K.: Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Nature Communications 5, 5:3518 (2014)

Szczurek, E.; Misra, N.; Vingron, M.: Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma. International Journal of Cancer 133 (9), pp. 2123 - 2132 (2013)

Thomas-Chollier, M.; Watson, L. C.; Cooper, S. B.; Pufall, M. A.; Liu, J. S.; Borzym, K.; Vingron, M.; Yamamoto, K. R.; Meijsing, S. H.: 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), pp. 17826 - 17831 (2013)

Mammana, A.; Vingron, M.; Chung, H.-R.: Inferring nucleosome positions with their histone mark annotation from ChIP data. Bioinformatics 29 (20), pp. 2547 - 2554 (2013)

Marsico, A.; Huska, M.; Lasserre, J.; Hu, H.; Vucicevic, D.; Musahl, A.; Ørom, U. A.; Vingron, M.: PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biology 14 (8), p. R84 - R84 (2013)

Göke, J.; Chan, Y. S.; Yan, J. L.; Vingron, M.; Ng, H. H.: Genome-wide Kinase-Chromatin Interactions Reveal the Regulatory Network of ERK Signaling in Human Embryonic Stem Cells. Molecular Cell 50 (6), pp. 844 - 855 (2013)

Feldmann, R.; Fischer, C.; Kodelja, V.; Behrens, S.; Haas, S.; Vingron, M.; Timmermann, B.; Geikowski, A.; Sauer, S.: Genome-wide analysis of LXRalpha activation reveals new transcriptional networks in human atherosclerotic foam cells. Nucleic Acids Research (London) 41 (6), pp. 3518 - 3531 (2013)

Feldmann, R.; Fischer, C.; Kodelja, V.; Behrens, S.; Haas, S.; Vingron, M.; Timmermann, B.; Geikowski, A.; Sauer, S.: Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. Nucleic Acids Research (London) 41 (6), pp. 3518 - 3531 (2013)

Weirauch, M. T.; Cote, A.; Norel, R.; Annala, M.; Zhao, Y.; Riley, T. R.; Saez-Rodriguez, J.; Cokelaer, T.; Vedenko, A.; Talukder, S. et al.; Consortium, D.; Agius, P.; Arvey, A.; Bucher, P.; Callan, C. G.,. J.; Chang, C. W.; Chen, C. Y.; Chen, Y. S.; Chu, Y. W.; Grau, J.; Grosse, I.; Jagannathan, V.; Keilwagen, J.; Kielbasa, S. M.; Kinney, J. B.; Klein, H.; Kursa, M. B.; Lahdesmaki, H.; Laurila, K.; Lei, C.; Leslie, C.; Linhart, C.; Murugan, A.; Mysickova, A.; Noble, W. S.; Nykter, M.; Orenstein, Y.; Posch, S.; Ruan, J.; Rudnicki, W. R.; Schmid, C. D.; Shamir, R.; Sung, W. K.; Vingron, M.; Zhang, Z.; Bussemaker, H. J.; Morris, Q. D.; Bulyk, M. L.; Stolovitzky, G.; Hughes, T. R.: Evaluation of methods for modeling transcription factor sequence specificity. Nature biotechnology 31 (2), pp. 126 - 34 (2013)

Lasserre, J.; Chung, H.-R.; Vingron, M.: Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks. PLoS Computational Biology 9 (9), p. e1003168 - e1003168 (2013)