Publications of M. Vingron

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)

Odoardi, F.; Sie, C.; Streyl, K.; Ulaganathan, V. K.; Schlaeger, C.; Lodygin, D.; Heckelsmiller, K.; Nietfeld, W.; Ellwart, J.; Klinkert, W. E. F. et al.; Lottaz, C.; Nosov, M.; Brinkmann, V.; Spang, R.; Lehrach, H.; Vingron, M.; Wekerle, H.; Fluegel-Koch, C.; Fluegel, A.: T cells become licensed in the lung to enter the central nervous system. Nature 488 (7413), pp. 675 - 679 (2012)

Ni, S.; Vingron, M.: R2KS: a novel measure for comparing gene expression based on ranked gene lists. Journal of Computational Biology 19 (6), pp. 766 - 775 (2012)

Schulz, M. H.; Zerbino, D. R.; Vingron, M.; Birney, E.: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28 (8), pp. 1086 - 92 (2012)

Zemojtel, T.; Vingron, M.: p53 binding sites in transposons. Frontiers in Genetics 3, 40 (2012)

Lasserre, J.; Arnold, S.; Vingron, M.; Reinke, P.; Hinrichs, C.: Predicting the outcome of renal transplantation. Journal of the American Medical Informatics Association 19 (2), pp. 255 - 262 (2012)

Mysickova, A.; Vingron, M.: Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. BMC Genomics 13 Suppl 1, p. S2 - S2 (2012)

Adams, D.; Altucci, L.; Antonarakis, S. E.; Ballesteros, J.; Beck, S.; Bird, A.; Bock, C.; Boehm, B.; Campo, E.; Caricasole, A. et al.; Dahl, F.; Dermitzakis, E. T.; Enver, T.; Esteller, M.; Estivill, X.; Ferguson-Smith, A.; Fitzgibbon, J.; Flicek, P.; Giehl, C.; Graf, T.; Grosveld, F.; Guigo, R.; Gut, I.; Helin, K.; Jarvius, J.; Kuppers, R.; Lehrach, H.; Lengauer, T.; Lernmark, A.; Leslie, D.; Loeffler, M.; Macintyre, E.; Mai, A.; Martens, J. H.; Minucci, S.; Ouwehand, W. H.; Pelicci, P. G.; Pendeville, H.; Porse, B.; Rakyan, V.; Reik, W.; Schrappe, M.; Schubeler, D.; Seifert, M.; Siebert, R.; Simmons, D.; Soranzo, N.; Spicuglia, S.; Stratton, M.; Stunnenberg, H. G.; Tanay, A.; Torrents, D.; Valencia, A.; Vellenga, E.; Vingron, M.; Walter, J.; Willcocks, S.: BLUEPRINT to decode the epigenetic signature written in blood. Nature biotechnology 30 (3), pp. 224 - 226 (2012)

Emde, A. K.; Schulz, M. H.; Weese, D.; Sun, R.; Vingron, M.; Kalscheuer, V. M.; Haas, S.; Reinert, K.: Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics 28 (5), pp. 619 - 27 (2012)

Göke, J.; Schulz, M. H.; Lasserre, J.; Vingron, M.: Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics 28 (5), pp. 656 - 63 (2012)