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Gergely Csaba

Gergely Csaba
E-Mail: csaba * at * bio.ifi.lmu.de
Phone: +49-89-2180-4046
Fax: +49-89-2180-99-4046
Address:

Teaching and Research Unit Bioinformatics

Institut für Informatik

Ludwig-Maximilians-Universität München

Amalienstr. 17, 80333 Munich, Germany
Raum: 4-07, 4. Etage
Publications
Submitted
Papers
Fabian Birzele, E. Hoffmann, Gergely Csaba, Ralf Zimmer. Alternative Splicing of Protein Repeats. BMC Structural Biology, Submitted.
    Gergely Csaba, Fabian Birzele, Ralf Zimmer. On the Similarity of Protein Structures. submitted, Submitted.
      Gergely Csaba, Evi Berchtold, Ralf Zimmer. Explaining data via networks - Gene Set Enrichment using Significant Area Search on mined regulatory relation networks. submitted, Submitted.
        Gergely Csaba, Simone Wolf, Ralf Zimmer. SynTree: a fast context speci c NER method and its application on correctly identify psychiatric disorders in publications. submitted, Submitted.
          Robert Pesch, Gergely Csaba, Ralf Zimmer. Isoform Structure Alignment Representation. submitted, Submitted.
            2016
            Papers
            Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer. Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinformatics, vol 17, pp. 45, January 2016.
            Patricia Schöppner, Gergely Csaba, T. Braun, M. Daake, B. Richter, Oliver F. Lange, Martin Zacharias, Ralf Zimmer, Martin Haslbeck. Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins. Journal of Molecular Biology, vol 428, no. 8, pp. 1544-57, Apr 2016.
            2015
            Papers
            Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. ContextMap 2: fast and accurate context-based RNA-seq mapping.. BMC bioinformatics, vol 16, pp. 122, 2015.
            Konrad Schreiber, Gergely Csaba, Martin Haslbeck, Ralf Zimmer. Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae. PLoS ONE, October 15 2015.
            2013
            Papers
            Ludwig Geistlinger, Gergely Csaba, Simon Dirmeier, Robert Küffner, Ralf Zimmer. A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Research, vol 41, no. 18, pp. 8452-8463, July 2013.
            Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. Mining RNA-Seq Data for Infections and Contaminations. PloS one, vol 8, pp. e73071, Sep 2013.
            Theses
            Gergely Csaba. Context Based Bioinformatics. PhD Thesis, LMU München, 2013.
            2012
            Papers
            Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics, vol 13(Suppl 6), pp. S9, 2012.
            2011
            Papers
            Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola Mulder, Ralf Zimmer. From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems. Bioinformatics, Bioinformatics, vol 27, no. 13, pp. i366-i373, July 2011.
            2010
            Papers
            Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer. miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics, vol 11, pp. 135, 16 March 2010 2010.
            Gergely Csaba, Ralf Zimmer. Vorescore - fold recognition improved by rescoring of protein structure models. Bioinformatics, vol 26, no. 18, pp. i482-i488, September 2010.
            2009
            Papers
            Gergely Csaba, Fabian Birzele, Ralf Zimmer. Systematic Comparison of SCOP and CATH: A new Gold Standard for Protein Structure Analysis. BMC Structural Biology, vol 9, no. 23, 2009.
            Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel, R. Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer. Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen. Informatik-Spektrum, vol 32, no. 4, pp. 310-319, 2009.
            • DOI
            • Journal version
            2008
            Papers
            Fabian Birzele, Gergely Csaba, Ralf Zimmer. Alternative splicing and protein structure evolution. Nucleic Acids Res., vol 36, pp. 550–558, Feb 2008.
            Gergely Csaba, Fabian Birzele, Ralf Zimmer. Protein structure alignment considering phenotypic plasticity. Bioinformatics, vol 24, pp. 98–104, Aug 2008.
            2007
            Papers
            Fabian Birzele, Jan Gewehr, Gergely Csaba, Ralf Zimmer. Vorolign - Fast Structural Alignment using Voronoi Contacts. Bioinformatics, vol 23, no. 2, pp. e205-e211, 2007.
            Theses
            Gergely Csaba. Phenotypic Plasticity as a Measure for Protein Structural Similarity. Master Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, November 2007.
              2006
              Theses
              Gergely Csaba. Analysis of Protein Sequence-Structure Alignments. Bachelor Thesis, LMU München, December 2006.
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