Computational Biology

• Pape UJ*equal contribution, Pastor WA*, Huang Y*, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Huang Y, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S, Rao A., Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature, 2011, 473: 394-397. [Link] [Summary]
• Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS, Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology, 2011, 12 (R83). [Link]
• Ko M, Huang Y, Jankowska A, Pape UJ, Tahiliani M, Bandukwala H, An J, Lamperti E, Koh KP, Aravind L, Liu XS, Agarwal S, Maciejewski J, Rao A, Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature, 2010, 468: 839-843. [Link] [Summary]
• Wang H, Wang Q, Pape UJ, Shen B, Huang J, Wu B, Li X, Systematic investigation of global coordination among mRNA and protein in cellular society. BMC Genomics, 2010, 11: 364. [Link]
• Pape UJ, Klein H, Vingron M, Statistical detection of co-operative transcription factors with similarity adjustment, Bioinformatics, 2009, 25 (16), 2103-2109. [Link]
• Pape UJ, Statistics for Transcription Factor Binding Sites, PhD thesis, Free University of Berlin, 2008.
• Pape UJ, Klein H, Vingron M, Statistical detection of co-operative transcription factors with similarity adjustment. In Beyer A, Schroeder M (eds), Lecture Notes in Informatics: Proc. of German Conference on Bioinformatics, 2008, 96-105.
• Pape UJ, Vingron M, Statistics for Co-Occurrence of DNA Motifs. In Chiquet J, Glaz J, Limnios N, Moyal P (eds), Proc. of International Workshop for Applied Probability (IWAP), 2008.
• Pape UJ, Rahmann S, Sun F, Vingron M, Compound Poisson approximation of DNA motif counts on both strands, Journal of Computational Biology, 2008, 15 (6), 547-564. [Link]
• Toenjes M, Schueler M, Hammer S, Pape UJ, Fischer JJ, Berger F, Vingron M, Sperling S, Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes, Molecular BioSystems, 2008, 4 (6), 589-598. [Link]
• Pape UJ, Rahmann S, Vingron M, Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering, Bioinformatics, 2008, 24 (3), 350-357. [Link]
• Pape UJ, Grossmann S, Hammer S, Sperling S, Vingron M, A new statistical model to select target sequences bound by transcription factors, Genome Informatics, 2006, 17 (1), 134-140.
• Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohman JU, A gene expression map of Arabidopsis development, Nature Genetics, 2005, 37 (5), 501-506. [Link]