Publications of Martin Vingron

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)

Heise, F.; Chung, H.-R.; Weber, J. M.; Xu, Z.; Klein-Hitpass, L.; Steinmetz, L. M.; Vingron, M.; Ehrenhofer-Murray, A. E.: Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange. Nucleic Acids Research (London) 40 (1), pp. 65 - 74 (2012)

Sun, R.; Love, M.; Zemojtel, T.; Emde, A.-K.; Chung, H.-R.; Vingron, M.; Haas, S.: Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics 28 (7), pp. 1024 - 1025 (2012)

Hallen, L.; Klein, H.; Stoschek, C.; Wehrmeyer, S.; Nonhoff, U.; Ralser, M.; Wilde, J.; Rohr, C.; Schweiger, M. R.; Zatloukal, K. et al.; Vingron, M.; Lehrach, H.; Konthur, Z.; Krobitsch, S.: The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. Human Molecular Genetics 20, pp. 104 - 114 (2011)

Goke, J.; Jung, M.; Behrens, S.; Chavez, L.; O'Keeffe, S.; Timmermann, B.; Lehrach, H.; Adjaye, J.; Vingron, M.: Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Comput Biol 7 (12), e1002304 (2011)

Kolanczyk, M.; Pech, M.; Zemojte, T.; Yamamoto, H.; Mikula, I.; Calvaruso, M.-A.; van den Brand, M.; Richter, R.; Fischer, B.; Ritz, A. et al.; Kossler, N.; Thurisch, B.; Spoerle, R.; Smeitink, J.; Kornak, U.; Chan, D.; Vingron, M.; Martasek, P.; Lightowlers, R. N.; Nijtmans, L.; Schuelke, M.; Nierhaus, K. H.; Mundlos, S.: NOA1 is an essential GTPase required for mitochondrial protein synthesis. Molecular Biology of the Cell 22 (1), pp. 1 - 11 (2011)

Lin, S.; Haas, S.; Zemojtel, T.; Xiao, P.; Vingron, M.; Li, R.: Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. Gene 473 (2), pp. 139 - 49 (2011)

Love, M. I.; Mysickova, A.; Sun, R.; Kalscheuer, V. M.; Vingron, M.; Haas, S. A.: Modeling read counts for CNV detection in exome sequencing data. Statistical Applications in Genetics and Molecular Biology 10 (1) (2011)

Roepcke, S.; Stahlberg, S.; Klein, H.; Schulz, M. H.; Theobald, L.; Gohlke, S.; Vingron, M.; Walther, D. J.: A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ. BMC Genomics 12, p. 624 (2011)

Serin, A.; Vingron, M.: DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach. Algorithms Mol Biol 6 (1), p. 18 (2011)

Szczurek, E.; Markowetz, F.; Gat-Viks, I.; Biecek, P.; Tiuryn, J.; Vingron, M.: Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. BMC Bioinformatics 12, p. 249 (2011)

Thomas-Chollier, M.; Hufton, A.; Heinig, M.; O'Keeffe, S.; Masri, N. E.; Roider, H. G.; Manke, T.; Vingron, M.: Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat Protoc 6 (12), pp. 1860 - 9 (2011)