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)

Warnatz, H. J.; Schmidt, D.; Manke, T.; Piccini, I.; Sultan, M.; Borodina, T.; Balzereit, D.; Wruck, W.; Soldatov, A.; Vingron, M. et al.; Lehrach, H.; Yaspo, M. L.: The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. The Journal of Biological Chemistry 286 (26), pp. 23521 - 32 (2011)

Yuan, Y.; Chen, Y. P.; Ni, S.; Xu, A. G.; Tang, L.; Vingron, M.; Somel, M.; Khaitovich, P.: Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics 12, p. 347 (2011)

Zemojtel, T.; Kielbasa, S. M.; Arndt, P. F.; Behrens, S.; Bourque, G.; Vingron, M.: CpG deamination creates transcription factor-binding sites with high efficiency. Genome Biol Evol 3, pp. 1304 - 11 (2011)

Chung, H.-R.; Dunkel, I.; Heise, F.; Linke, C.; Krobitsch, S.; Ehrenhofer-Murray, A. E.; Sperling, S. R.; Vingron, M.: The effect of MNase on nucleosome positioning data. PLoS ONE 5 (12), p. e15754 - e15754 (2010)

Behrens, S.; Vingron, M.: Studying the evolution of promoter sequences: a waiting time problem. Journal Computational Biology 17 (12), pp. 1591 - 1606 (2010)

Warnatz, H. J.; Querfurth, R.; Guerasimova, A.; Cheng, X.; Haas, S. A.; Hufton, A. L.; Manke, T.; Vanhecke, D.; Nietfeld, W.; Vingron, M. et al.; Janitz, M.; Lehrach, H.; Yaspo, M. L.: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Research 38 (18), pp. 6112 - 6123 (2010)

Heinig, M.; Petretto, E.; Wallace, C.; Bottolo, L.; Rotival, M.; Lu, H.; Li, Y.; Sarwar, R.; Langley, S. R.; Bauerfeind, A. et al.; Hummel, O.; Lee, Y. A.; Paskas, S.; Rintisch, C.; Saar, K.; Cooper, J.; Buchan, R.; Gray, E. E.; Cyster, J. G.; Erdmann, J.; Hengstenberg, C.; Maouche, S.; Ouwehand, W. H.; Rice, C. M.; Samani, N. J.; Schunkert, H.; Goodall, A. H.; Schulz, H.; Roider, H. G.; Vingron, M.; Blankenberg, S.; Munzel, T.; Zeller, T.; Szymczak, S.; Ziegler, A.; Tiret, L.; Smyth, D. J.; Pravenec, M.; Aitman, T. J.; Cambien, F.; Clayton, D.; Todd, J. A.; Hubner, N.; Cook, S. A.: A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 467 (7314), pp. 460 - 464 (2010)

Szczurek, E.; Biecek, P.; Tiuryn, J.; Vingron, M.: Introducing knowledge into differential expression analysis. Journal of Computational Biology 17 (8), pp. 953 - 967 (2010)

Kielbasa, S. M.; Klein, H.; Roider, H. G.; Vingron, M.; Blüthgen, N.: TransFind--predicting transcriptional regulators for gene sets. Nucleic Acids Research 38 Suppl, pp. W275 - W280 (2010)

Richard, H.; Schulz, M. H.; Sultan, M.; Nurnberger, A.; Schrinner, S.; Balzereit, D.; Dagand, E.; Rasche, A.; Lehrach, H.; Vingron, M. et al.; Haas, S. A.; Yaspo, M. L.: Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Research 38 (10), p. e112 - e112 (2010)

Manke, T.; Heinig, M.; Vingron, M.: Quantifying the effect of sequence variation on regulatory interactions. Hum Mutation 31 (4), pp. 477 - 483 (2010)

Schütze, T.; Arndt, P. F.; Menger, M.; Wochner, A.; Vingron, M.; Erdmann, V. A.; Lehrach, H.; Kaps, C.; Glökler, J.: A calibrated diversity assay for nucleic acid libraries using DiStRO-a Diversity Standard of Random Oligonucleotides. Nucleic Acids Research 38 (4), p. e23 - e23 (2010)

Karlic, R.; Chung, H. R.; Lasserre, J.; Vlahovicek, K.; Vingron, M.: Histone modification levels are predictive for gene expression. Proceedings of the National Academy of Sciences USA 107 (7), pp. 2926 - 2931 (2010)

Meng, G.; Mosig, A.; Vingron, M.: A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. BMC Bioinformatics 11, p. 11:267 - 11:267 (2010)

Hufton, A. L.; Mathia, S.; Braun, H.; Georgi, U.; Lehrach, H.; Vingron, M.; Poustka, A. J.; Panopoulou, G.: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Resaerch 19, pp. 2036 - 2051 (2009)

Roider, H. G.; Lenhard, B.; Kanhere, A.; Haas, S. A.; Vingron, M.: CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses. Nucleic Acids Research 37 (19), pp. 6305 - 6315 (2009)

Chavez, L.; Bais, A. S.; Vingron, M.; Lehrach, H.; Adjaye, J.; Herwig, R.: In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. BMC Genomics 10, p. 314 - 314 (2009)

Huang, X.; Vingron, M.: Maximum Similarity: A New Formulation of Phylogenetic Reconstruction. Journal of Computational Biology 16 (7), pp. 887 - 896 (2009)