Lehr- und Forschungseinheit Bioinformatik
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Dr. Gergely Csaba

Gergely Csaba
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Telefon: Phone: +49-89-2180-4046
Fax: +49-89-2180-99-4046
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Lehr- und Forschungseinheit Bioinformatik Teaching and Research Unit Bioinformatics

Institut für Informatik

Ludwig-Maximilians-Universität München

Amalienstr. 17, 80333 München Munich, Germany
Raum: 4-07, 4. Etage
PublikationenPublications
2019
Papers
Evi Berchtold, Martina Vetter, Melanie Gündert, Gergely Csaba, Christine Fathke, Susanne E Ulbrich, Christoph Thomssen, Ralf Zimmer, Eva J Kantelhardt, Comparison of six breast cancer classifiers using qPCR, Bioinformatics, 2019.
Evi Berchtold, Gergely Csaba, Ralf Zimmer, YESdb: integrative analysis of environmental stress in yeast, Database, vol. 2019, 2019.
Moritz Mühlhofer, Evi Berchtold, Christopher G Stratil, Gergely Csaba, Elena Kunold, Nina C. Bach, Stephan A. Sieber, Martin Haslbeck, Ralf Zimmer, Johannes Buchner, The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins, Cell Reports, vol. 29, no. 13, pp. 4593-4607, 2019.
Constantin Ammar, Evi Berchtold, Gergely Csaba, Andreas Schmidt, Axel Imhof, Ralf Zimmer, Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets, Journal of Proteome Research, vol. 18, no. 4, pp. 1553-1566, 2019.
2017
Papers
Evi Berchtold, Gergely Csaba, Ralf Zimmer, RelExplain—integrating data and networks to explain biological processes, Bioinformatics, vol. 33, no. 12, pp. 1837-1844, 2017.
2016
Papers
Evi Berchtold, Gergely Csaba, Ralf Zimmer, Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data, PLoS ONE, vol. 11, no. 10, 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, 2016.
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, 2016.
2015
Papers
Konrad Schreiber, Gergely Csaba, Martin Haslbeck, Ralf Zimmer, Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae, PLoS ONE, 2015.
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.
2013
Papers
Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel, Mining RNA-Seq Data for Infections and Contaminations, PloS one, vol. 8, pp. e73071, 2013.
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, 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, vol. 27, no. 13, pp. i366-i373, 2011.
2010
Papers
Gergely Csaba, Ralf Zimmer, Vorescore - fold recognition improved by rescoring of protein structure models, Bioinformatics, vol. 26, no. 18, pp. i482-i488, 2010.
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, 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.
2008
Papers
Gergely Csaba, Fabian Birzele, Ralf Zimmer, Protein structure alignment considering phenotypic plasticity, Bioinformatics, vol. 24, pp. 98–104, 2008.
Fabian Birzele, Gergely Csaba, Ralf Zimmer, Alternative splicing and protein structure evolution, Nucleic Acids Res., vol. 36, pp. 550–558, 2008.
2007
Papers
Fabian Birzele, Jan Erik 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, 2007.
2006
Theses
Gergely Csaba, Analysis of Protein Sequence-Structure Alignments, Bachelor Thesis, LMU München, 2006.

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