Publications - Benedikt Zacher

  • 2015

  • J. Glas, S. Dumcke, B. Zacher, D. Poron, J. Gagneur, A. Tresch. Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model Nucleic Acids Research (2015)

    Link

  • 2014

  • B. Zacher, M. Lidschreiber, P. Cramer, J. Gagneur, A. Tresch. Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. Molecular Systems Biology (2014)

    Link

  • 2012

  • T. Griebel, B. Zacher, P. Ribeca, E. Raineri, V. Lacroix, R. Guigó, and M. Sammeth, Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Res. (2012)

    Link

  • C. Schmidt, S. Bultmann, D. Meilinger, B. Zacher, A.Tresch, K. Maier, C. Peter, D. Martin, H. Leonhardt, F. Spada. Global DNA hypomethylation prevents consolidation of differentiation programs and allows reversion to the embryonic stem cell state, Plos One (2012)

    Link

  • B. Zacher, K. Abnaof, S. Gade, E. Younesi, A. Tresch, H. Fröhlich. Joint Bayesian Inference of Condition Specific miRNA and Transcription Factor Activities from Combined Gene and microRNA Expression Data, Bioinformatics (2012)

    Link

  • B. Schwalb, D. Schulz, M. Sun, B. Zacher, S. Dümcke, D. Martin, P. Cramer, A.Tresch. Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA). Bioinformatics (2012)

    Link

  • 2011

  • B. Zacher, P. Torkler, A. Tresch. Analysis of Affymetrix ChIP-chip data using Starr and Bioconductor. Cold Spring Harbor Protocols (2011)

    Link

  • C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Dümcke, B. Zacher, A. Mayer, J. Sydow, L. Marcinowski, L. Dölken, D. Martin, A. Tresch, P. Cramer. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Molecular Systems Biology (2011)

    Link

  • 2010

  • B. Zacher, P.F. Kuan, A. Tresch. Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. BMC Bioinformatics (2010)

    Link

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