accepted
Papers
Laura V. Glaser, Simone Rieger, Sybille Thumann, Cornelia Kuklik-Roos, Dietmar E Martin, Kerstin C. Maier, Marie L. Harth-Hertle, Björn Grüning, Rolf Backofen, Stefan Krebs, Helmut Blum,
Ralf Zimmer,
Florian Erhard, Bettina Kempkes,
EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells, PLoS Pathogens, accepted.
2019
Papers
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.
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.
2017
Papers
Matthias Barann,
Ralf Zimmer,
Fabian Birzele,
Manananggal - A Novel Viewer For Alternative Splicing Events, BMC Bioinformatics, vol. 18, pp. 120, 2017.
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
Robert Pesch,
Ralf Zimmer,
Cross-Species Conservation of Context-Specific Networks, BMC Systems Biology, vol. 10, no. 76, 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.
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.
Vinicius Henrique Silva, Luciana Correia Almeida Regitano,
Ludwig Geistlinger, Fábio Pértille, Poliana Fernanda Giachetto, Ricardo Augusto Brassaloti, Natália Silva Morosini,
Ralf Zimmer, Luiz Lehmann Coutinho,
Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle, PLOS ONE, vol. 11, no. 6, pp. e0157711, 2016.
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.
2015
Papers
Andrzej J. Rutkowski,
Florian Erhard, Anne L’Hernault,
Thomas Bonfert, Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou,
Ralf Zimmer,
Caroline C. Friedel, Lars Dölken,
Wide-spread disruption of host transcription termination in HSV-1 infection, Nature Communications, vol. 6, no. 7126, 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.
Florian Erhard,
Ralf Zimmer,
Count ratio model reveals bias affecting NGS fold changes, Nucleic Acids Research, pp. pii: gkv696., 2015.
Sabine Hünten, Markus Kaller, Friedel Drepper, Silke Oeljeklaus,
Thomas Bonfert,
Florian Erhard, Anne Dueck, Norbert Eichner,
Caroline C. Friedel, Gunter Meister,
Ralf Zimmer, Bettina Warscheid, Heiko Hermeking,
p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses., Molecular & cellular proteomics : MCP, 2015.
Konrad Schreiber,
Gergely Csaba, Martin Haslbeck,
Ralf Zimmer,
Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae, PLoS ONE, 2015.
Tobias Petri, Stefan Altmann,
Ludwig Geistlinger,
Ralf Zimmer,
Robert Küffner,
Addressing false discoveries in network inference, Bioinformatics, vol. 31, no. 17, pp. 2836-43, 2015.
2014
Papers
Robert Pesch,
Ralf Zimmer,
To be, or not to be: konservierte eukaryotische Regulationsnetzwerke?, BIOspektrum, vol. 20, no. 5, pp. 514-516, 2014.
Florian Erhard, Jürgen Haas, Diana Lieber, Georg Malterer, Lukasz Jaskiewicz, Mihaela Zavolan, Lars Dölken,
Ralf Zimmer,
Widespread context-dependency of microRNA-mediated regulation., Genome research, 2014.
2013
Papers
Ronny Kramer,
Simone Wolf,
Tobias Petri, Dirk von Soosten, Sven Dänicke, Eva-Maria Weber,
Ralf Zimmer, Juergen Rehage, Gerhard Jahreis,
A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation, Lipids in Health and Disease, vol. 12, no. 96, 2013.
Robert Pesch,
Ralf Zimmer,
Complementing the Eukaryotic Protein Interactome, PLOS One, vol. 8, no. 6, pp. e66635, 2013.
Samantha J. Griffiths, Manfred Koegl, Chris Boutell, Helen L. Zenner, Colin Crump,
Orland Gonzalez,
Caroline C. Friedel, Gerald Barry, Kimberley Martin, Marie H. Craigon, Rui Chen, Lakshmi N. Kaza, Even Fossum, John K. Fazakerley, Stacey Efstathiou,
Ralf Zimmer, Peter Ghazal, Jürgen Haas,
A systematic analysis of host factors reveals a Med23-interferon-lambda regulatory axis against Herpes simplex virus Type 1 replication, PLoS Pathogens, vol. 9, no. 8, pp. e1003514, 2013.
Harth-Hertle ML, Scholz BA,
Florian Erhard, Glaser LV, Dölken L,
Ralf Zimmer, Bettina Kempkes,
Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9, PLoS Pathogens, vol. 9, no. 9, pp. e1003638, 2013.
Robert Maier,
Ralf Zimmer,
Robert Küffner,
A Turing test for artificial expression data, Bioinformatics, vol. 29, no. 20, pp. 2603-2609, 2013.
Florian Erhard, Lars Dölken, Lukasz Jaskiewicz,
Ralf Zimmer,
PARma: identification of microRNA target sites in AGO-PAR-CLIP data., Genome biology, vol. 14, pp. R79, 2013.
Florian Erhard, Lars Dölken,
Ralf Zimmer,
RIP-chip enrichment analysis, Bioinformatics, vol. 29, no. 1, September 2012, Basel, Switzerland, pp. 77–83, 2013.
Mayuko Kurome,
Ludwig Geistlinger, Barbara Keßler, Valeri Zakhartchenko, Nikolai Klymiuk, Annegret Wünsch, Anne Richter, Andrea Bähr, Katrin Krähe, Katinka Burkhardt, Krzysztof Flisikowski, Tatiana Flisikowska, Claudia Merkl, Martina Landmann, Marina Durkovic, Alexander Tschukes, Simone Kraner, Dirk Schindelhauer,
Tobias Petri, Alexander Kind, Hiroshi Nagashima, Angelika Schnieke,
Ralf Zimmer, Eckhard Wolf,
Factors Influencing the Efficiency of Generating Genetically Engineered Pigs by Nuclear Transfer: Multi-Factorial Analysis of a Large Data Set, BMC Biotechnology, vol. 13, no. 43, 2013.
Sorg D, Danowski K, Korenkova V, Rusnakova V,
Robert Küffner,
Ralf Zimmer, Meyer HH, Kliem H,
Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens, Animal, vol. 7, no. 5, pp. 799-805, 2013.
Lenac Roviš T, Bailer SM, Pothineni VR, Ouwendijk WJ, Šimić H, Babić M, Miklić K, Malić S, Verweij MC, Baiker A,
Gonzalez O, von Brunn A,
Ralf Zimmer, Früh K, Verjans GM, Jonjić S, Jürgen Haas,
Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection, J Virol. 2013, vol. 87, no. 12, pp. 6943-54, 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.
Thomas Bonfert,
Gergely Csaba,
Ralf Zimmer,
Caroline C. Friedel,
Mining RNA-Seq Data for Infections and Contaminations, PloS one, vol. 8, pp. e73071, 2013.
2012
Papers
Tobias Petri,
Evi Berchtold,
Ralf Zimmer,
Caroline C. Friedel,
Detection and correction of probe-level artefacts on microarrays, BMC Bioinformatics, vol. 13, pp. 114, 2012.
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.
Tobias Stögbauer,
Lukas Windhager,
Ralf Zimmer, Joachim O. Rädler,
Experiment and Mathematical Modeling of Gene Expression Dynamics in a Cell-Free System, Integrative Biology, vol. 4 (5), pp. 494 - 501, 2012.
Robert Pesch, Matthias Böck,
Ralf Zimmer,
ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes, Proceedings of the German Conference on Bioinformatics (GCB), vol. 26, pp. 69-81, 2012.
Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z,
Florian Erhard, Benkartek C, Babic M,
Ralf Zimmer, Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Lars Dölken,
Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathogens, vol. 8, no. 2, pp. e1002510, 2012.
Lisa Marcinowski, Michael Lidschreiber,
Lukas Windhager, Martina Rieder, Jens B. Bosse, Bernd Rädle,
Thomas Bonfert, Ildiko Györy, Miranda de Graaf, Olivia Prazeres da Costa, Philip Rosenstiel,
Caroline C. Friedel,
Ralf Zimmer, Zsolt Ruzsics, Lars Dölken,
Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection, PLoS Pathog, vol. 8, no. 9, pp. e1002908, 2012.
Lukas Windhager,
Thomas Bonfert, Kaspar Burger, Zsolt Ruzsics, Stefan Krebs, Stefanie Kaufmann, Georg Malterer, Anne L’Hernault, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel,
Ralf Zimmer, Dirk Eick,
Caroline C. Friedel, Lars Dölken,
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution., Genome research, vol. 22, pp. 2031-42, 2012.
Florian Erhard,
Ralf Zimmer,
Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Journal of Proteomics, vol. 75, no. 11, pp. 3230-9, 2012.
Robert Küffner,
Tobias Petri,
Pegah Tavakkolkhah,
Lukas Windhager,
Ralf Zimmer,
Inferring Gene Regulatory Networks by ANOVA, Bioinformatics, vol. 28, no. 10, pp. 1376-1382, 2012.
Haroon Naeem,
Ralf Zimmer,
Pegah Tavakkolkhah,
Robert Küffner,
Rigorous assessment of gene set enrichment tests, Bioinformatics, vol. bts164v1-bts164, pp. 7, 2012.
2011
Papers
Florian Erhard,
Ralf Zimmer,
Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Detecting outlier peptides in quantitative high-throughput mass spectrometry data, September 2011, Weihenstephan, Germany, 2011.
Tobias Petri,
Robert Küffner,
Ralf Zimmer,
Experiment Specific Expression Patterns, RECOMB 2011, Research in Computational Molecular Biology (Vineet Bafna, S. Cenk Sahinalp, eds.), Springer, vol. 15, pp. 339-354, 2011.
Susanne Pfefferle, Julia Schöpf, Manfred Kögl,
Caroline C. Friedel, Marcel A. Müller, Javier Carbajo-Lozoya, Thorsten Stellberger, Ekatarina von Dall’Armi, Petra Herzog, Stefan Kallies, Daniela Niemeyer, Vanessa Ditt, Thomas Kuri, Roland Züst, Ksenia Pumpor, Rolf Hilgenfeld, Frank Schwarz,
Ralf Zimmer, Imke Steffen, Friedemann Weber, Volker Thiel, Georg Herrler, Heinz-Jürgen Thiel, Christel Schwegmann-Weßels, Stefan Pöhlmann, Jürgen Haas, Christian Drosten, Albrecht von Brunn,
The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors, PLoS Pathog, vol. 7, no. 10, pp. e1002331, 2011.
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.
Orland Gonzalez,
Ralf Zimmer,
Contextual analysis of RNAi-based functional screens using interaction networks, Bioinformatics, vol. 27, pp. 2707-2713, 2011.
2010
Papers
Orland Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeifer, Eduardo Mendoza,
Ralf Zimmer, Dieter Oesterhelt,
Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis, PLoS Computational Biology, vol. 6, no. 6, pp. e1000799, 2010.
Florian Erhard,
Caroline C. Friedel,
Ralf Zimmer,
FERN - Stochastic Simulation and Evaluation of Reaction Networks, Systems Biology for Signaling Networks (Sangdun Choi, ed.), Springer, vol. 1, Part 4, pp. 751-775, 2010.
Lukas Windhager,
Florian Erhard,
Ralf Zimmer,
Fuzzy modeling, Modeling in Systems Biology: The Petri Net Approach (Ina Koch, Wolfgang Reisig, Falk Schreiber, eds.), Springer, 2010.
Wolfgang Fischer,
Lukas Windhager, Stefanie Rohrer, Matthias Zeiller, Arno Karnholz, Reinhard Hoffmann,
Ralf Zimmer, Rainer Haas,
Strain-specific genes of Helicobacter pylori: Genome evolution driven by a novel type IV secretion system and genomic island transfer, Nucleic Acids Research, vol. 38, no. 18, pp. 6089-101, 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.
R Küffner,
Tobias Petri,
Lukas Windhager,
Ralf Zimmer,
Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization, PLoS One, vol. 5, pp. e12807, 2010.
Lars Dölken, Georg Malterer,
Florian Erhard, Sheila Kothe,
Caroline C. Friedel, Guillaume Suffert, Lisa Marcinowski, Natalie Motsch, Stephanie Barth, Michaela Beizinger, Diana Lieber, Susanne M. Bailer, Reinhard Hoffmann, Zsolt Ruzsics, Elisabeth Kremmer, Sebastien Pfeffer,
Ralf Zimmer, Ulrich H Koszinowski, Friedrich Grässer, Gunter Meister, Jürgen Haas,
Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays, Cell Host & Microbe, vol. 7, no. 4, pp. 324-334, 2010.
Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken,
Ralf Zimmer,
HALO - A Java framework for precise transcript half-life determination, Bioinformatics, vol. 26, no. 9, pp. 1264-1266, 2010.
Florian Erhard,
Ralf Zimmer,
Classification of ncRNAs using position and size information in deep sequencing data, Bioinformatics, vol. 26, no. 18, pp. i426-i432, 2010.
Gergely Csaba,
Ralf Zimmer,
Vorescore - fold recognition improved by rescoring of protein structure models, Bioinformatics, vol. 26, no. 18, pp. i482-i488, 2010.
2009
Papers
Caroline C. Friedel, Jan Krumsiek,
Ralf Zimmer,
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Journal of Computational Biology, vol. 16, no. 8, pp. 1-17, 2009.
O. Gonzalez, S. Gronau, F. Pfeiffer, E. Mendoza,
Ralf Zimmer, D. Oesterhelt,
Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 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.
Orland Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza,
Ralf Zimmer, Dieter Oesterhelt,
Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 2009.
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.
AG Moll, MT Lindenmeyer, M Kretzler, PJ Nelson,
Ralf Zimmer, CD Cohen,
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays, PLoS ONE, vol. 4, no. 3, pp. e4702, 2009.
Caroline C. Friedel,
Ralf Zimmer,
Identifying the topology of protein complexes from affinity purification assays, Bioinformatics, vol. 25, no. 16, pp. 2140-2146, 2009.
Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski,
Ralf Zimmer,
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life, Nucleic Acids Research, vol. 37, no. 17, pp. e115, 2009.
Even Fossum,
Caroline C. Friedel, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke,
Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz,
Ralf Zimmer, Jürgen Haas,
Evolutionarily conserved herpesviral protein interaction networks., PLoS Pathog, vol. 5, no. 9, pp. e1000570, 2009.
2008
Papers
Florian Erhard,
Caroline C. Friedel,
Ralf Zimmer,
FERN - a Java framework for stochastic simulation and evaluation of reaction networks, BMC Bioinformatics, vol. 9, no. 1, pp. 356, 2008.
Caroline C. Friedel, Jan Krumsiek,
Ralf Zimmer,
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008 (Sorin Istrail, Pavel Pevzner, Michael Waterman, eds.), Springer, vol. 4955, Singapore, March 30 - April 2, 2008, pp. 3-16, 2008.
Lukas Windhager,
Ralf Zimmer,
Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic, German Conference on Bioinformatics, Gesellschaft für Informatik, vol. P-136, September 9-12, 2008, Dresden, Germany, pp. 106-115, 2008.
R Küffner, Tatjana Schilling,
Ralf Zimmer, Ludger Klein-Hitpass, Franz Jakob, Norbert Schütze,
Microarray analyses of transdifferentiated mesenchymal stem cells, Journal of Cellular Biochemistry, vol. 103, no. 2, pp. 413-433, 2008.
Katrin Fundel, Jochen Haag, Pia M. Gebhard,
Ralf Zimmer, Thomas Aigner,
Normalization strategies for mRNA expression data in cartilage research, Osteoarthritis Cartilage, vol. 16, pp. 947-955, 2008.
Orland Gonzalez, S. Gronau, M. Falb, F. Pfeiffer, E. Mendoza,
Ralf Zimmer, D. Oesterhelt,
Reconstruction, modeling & analysis of Halobacterium salinarum R-1metabolism, Mol Biosyst, vol. 4, no. 2, pp. 148-59, 2008.
Orland Gonzalez,
Ralf Zimmer,
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes, Bioinformatics, vol. 24, no. 10, pp. 1257-63, 2008.
Caroline C. Friedel,
Ralf Zimmer,
Identifying the topology of protein complexes from affinity purification assays, Proceedings of the German Conference on Bioinformatics (GCB 2008), GI, vol. P-136, September 9-12, 2008, Dresden, Germany, pp. 30-43, 2008.
Katrin Fundel,
R Küffner, T. Aigner,
Ralf Zimmer,
Normalization and gene p-value estimation: issues in microarray data processing, Bioinform Biol Insights, vol. 2, pp. 291-305, 2008.
Fabian Birzele, Jan Erik Gewehr,
Ralf Zimmer,
AutoPSI: a database for automatic structural classification of protein sequences and structures, Nucleic Acids Res., vol. 36, pp. 398–401, 2008.
Fabian Birzele,
R Küffner, Franziska Meier, Florian Oefinger, Christian Potthast,
Ralf Zimmer,
ProSAS: a database for analyzing alternative splicing in the context of protein structures, Nucleic Acids Res., vol. 36, pp. D63–68, 2008.
Fabian Birzele,
Gergely Csaba,
Ralf Zimmer,
Alternative splicing and protein structure evolution, Nucleic Acids Res., vol. 36, pp. 550–558, 2008.
Gergely Csaba,
Fabian Birzele,
Ralf Zimmer,
Protein structure alignment considering phenotypic plasticity, Bioinformatics, vol. 24, pp. 98–104, 2008.
Lars Dölken, Zsolt Ruzsics, Bernd Rädle,
Caroline C. Friedel,
Ralf Zimmer, Jörg Mages, Reinhard Hoffmann, Paul Dickinson, Thorsten Forster, Peter Ghazal, Ulrich H Koszinowski,
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay, RNA, vol. 14, no. 9, pp. 1959–1972, 2008.
Jan Krumsiek,
Caroline C. Friedel,
Ralf Zimmer,
ProCope–protein complex prediction and evaluation, Bioinformatics, vol. 24, no. 18, pp. 2115–2116, 2008.
2007
Papers
Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok,
Caroline C. Friedel,
Ralf Zimmer, Rhonda Roberts, Jürgen Haas,
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome, PLoS ONE, vol. 2, no. 5, pp. e459, 2007.
Caroline C. Friedel,
Ralf Zimmer,
Influence of degree correlations on network structure and stability in protein-protein interaction networks, BMC Bioinformatics, vol. 8, pp. 297, 2007.
Katrin Fundel,
R Küffner,
Ralf Zimmer,
RelEx - Relation extraction using dependency parse trees, Bioinformatics, vol. 23, no. 3, pp. 365-371, 2007.
Katrin Fundel,
Ralf Zimmer,
Human Gene Normalization by an Integrated Approach including Abbreviation Resolution and Disambiguation, Second BioCreative Challenge Evaluation Workshop, 2007.
Thomas Aigner, Jochen Haag,
Ralf Zimmer,
Functional genomics, evo-devo and systems biology: a chance to overcome complexity?, Curr Opin Rheumatol, vol. 19, no. 5, pp. 463-470, 2007.
Jan Erik Gewehr, Martin Szugat,
Ralf Zimmer,
BioWeka–extending the Weka framework for bioinformatics, Bioinformatics, vol. 23, no. 5, pp. 651-653, 2007.
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.
Jan Erik Gewehr, Volker Hintermair,
Ralf Zimmer,
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings, Bioinformatics, vol. 23, no. 10, pp. 1203-1210, 2007.
2006
Papers
Chad A. Davis, Fabian Gerick, Volker Hintermair,
Caroline C. Friedel,
Katrin Fundel,
R Küffner,
Ralf Zimmer,
Reliable gene signatures for microarray classification: assessment of stability and performance, Bioinformatics, vol. 22, no. 19, pp. 2356-2363, 2006.
R Küffner, T. Duchrow,
Katrin Fundel,
Ralf Zimmer,
Characterization of Protein Interactions, German Conference on Bioinformatics (GCB) (Daniel Huson, Oliver Kohlbacher, Andrei Lupas, Kay Nieselt, Andreas Zell, eds.), Gesellschaft für Informatik, vol. P-83, Tübingen, Germany, September 19-22, 2006, pp. 64-73, 2006.
Thomas Aigner,
Katrin Fundel, Joachim Saas, Pia M. Gebhard, Jochen Haag, Tilo Weiss, Alexander Zien, Franz Obermayer,
Ralf Zimmer, Eckart Bartnik,
Large-Scale Gene Expression Profiling of Osteoarthritic Cartilage Degeneration, Arthritis&Rheumatism, vol. 54, no. 11, pp. 3533-3544, 2006.
Dong-Yup Lee,
Ralf Zimmer, Sang-Yup Lee,
Colored Petri Net Modeling and Simulation of Signal Transduction Pathways, Metabolic Engineering, vol. 8, no. 2, pp. 112-122, 2006.
H. Redestig,
Florian Sohler,
Ralf Zimmer, J. Selbig,
Unsupervised Decision Trees Based on Gene Ontology Terms for the Interpretation of Gene Expression Data, Advances in Data Analysis. Proc. 30th Annual Conference of the German Classification Society (GfKl) (R. Decker, H.-J. Lenz, eds.), Springer-Verlag, Heidelberg-Berlin, 2007, pp. 385-594, 2006.
Joachim Saas, Jochen Haag, D. Rueger, S. Chubinskaya,
Florian Sohler,
Ralf Zimmer, Eckart Bartnik, Thomas Aigner,
IL-1beta, but not BMP-7 leads to a dramatic change in the gene expression pattern of human adult articular chondrocytes–portraying the gene expression pattern in two donors, Cytokine, vol. 36, no. 1-2, pp. 90-99, 2006.
Jan Erik Gewehr,
Ralf Zimmer,
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles, Bioinformatics, vol. 22, no. 2, pp. 181-187, 2006.
Caroline C. Friedel,
Ralf Zimmer,
Toward the complete interactome, Nat Biotechnol, vol. 24, no. 6, pp. 614-615, 2006.
Caroline C. Friedel,
Ralf Zimmer,
Inferring topology from clustering coefficients in protein-protein interaction networks, BMC Bioinformatics, vol. 7, pp. 519, 2006.
2005
Papers
R Küffner,
Katrin Fundel,
Ralf Zimmer,
Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts, Bioinformatics, vol. 21, no. Suppl 2, pp. 259-267, 2005.
Martin Szugat, Daniel Güttler,
Florian Sohler,
Ralf Zimmer,
Web Servicing the Biological Office, Bioinformatics, vol. 21, no. (Suppl. 2), pp. 268-269, 2005.
Thomas Aigner, L. McKenna, Alexander Zien, Z. Fan, Pia M. Gebhard,
Ralf Zimmer,
Gene expression profiling of serum- and interleukin-1beta-stimulated primary human adult articular chondrocytes–a molecular analysis based on chondrocytes isolated from one donor, Cytokine, vol. 31, no. 3, pp. 227-240, 2005.
Thomas Aigner, Joachim Saas, Alexander Zien,
Ralf Zimmer, Pia M. Gebhard, Thomas Knorr,
Analysis of Differential Gene Expression in Healthy and Osteoarthritic Cartilage and Isolated Chondrocytes by Microarray Analysis, Methods in Molecular Medicine, vol. 100, pp. 109-128, 2005.
M. Gebauer, Joachim Saas,
Florian Sohler, Jochen Haag, S. Soder, M. Pieper, Eckart Bartnik, J. Beninga,
Ralf Zimmer, Thomas Aigner,
Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1beta, Osteoarthritis Cartilage, vol. 13, no. 8, pp. 697-708, 2005.
Florian Sohler,
Ralf Zimmer,
Identifying active transcription factors and kinases from expression data, Bioinformatics, vol. 21, no. Suppl 2, pp. 115-122, 2005.
Katrin Fundel,
R Küffner, Thomas Aigner,
Ralf Zimmer,
Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments, German Conference on Bioinformatics (GCB) 2005 (A. Torda, S. Kurtz, Matthias Rarey, eds.), GI, vol. P-71, pp. 77-91, 2005.
Katrin Fundel, Daniel Güttler,
Ralf Zimmer,
Joannis Apostolakis,
A simple approach for protein name identification: prospects and limits, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S15, 2005.
Katrin Fundel,
Daniel Hanisch, Heinz-Theodor Mevissen,
Ralf Zimmer, Juliane Fluck,
ProMiner: rule-based protein and gene entity recognition, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S14, 2005.
Fabian Birzele, Jan Erik Gewehr,
Ralf Zimmer,
QUASAR–scoring and ranking of sequence-structure alignments, Bioinformatics, vol. 21, no. 24, pp. 4425–4426, 2005.
2004
Papers
Katrin Fundel, Daniel Güttler,
Ralf Zimmer,
Joannis Apostolakis,
Exact versus approximate string matching for protein name identification, BioCreative Challenge Evaluation Workshop, 2004.
Daniel Hanisch,
Katrin Fundel, Heinz-Theodor Mevissen,
Ralf Zimmer, Juliane Fluck,
ProMiner: Organism-specific protein name detection using approximate string matching, BioCreative Challenge Evaluation Workshop, 2004.
Christoph Best,
Ralf Zimmer,
Joannis Apostolakis,
Probabilistic methods for predicting protein functions in protein-protein interaction networks, German Conference on Bioinformatics, GCB 2004 (Robert Giegerich, Jens Stoye, eds.), Gesellschaft für Informatik, vol. P-53, Bielefeld, Germany, October 4-6, 2004, pp. 159-168, 2004.
Thomas Aigner, E. Bartnik, F. Sohler,
Ralf Zimmer,
Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses, Clin Orthop Relat Res, no. 427 Suppl, pp. 138-143, 2004.
T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claussen, C. Ebeling, P. Ernst, K. Heidtke, A. Herrmann, S. O’Keeffe, O. Kiesslich, S. Kolibal, J. O. Korbel, T. Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, H. T. Mevissen, HW Mewes, H. Michael, M. Mokrejs, T. Muller, H. Pospisil, M. Rarey, J. G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, I. Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender,
Ralf Zimmer,
The Helmholtz Network for Bioinformatics: an integrative web portal forbioinformatics resources, Bioinformatics, vol. 20, no. 2, pp. 268-70, 2004.
Jan Erik Gewehr, Niklas Von Öhsen,
Ralf Zimmer,
Combining Secondary Structure Element Alignment and Profile Alignment for Fold Recognition, German Conference on Bioinformatics, GCB 2004 (Robert Giegerich, Jens Stoye, eds.), Gesellschaft für Informatik, vol. P-53, Bielefeld, Germany, October 4-6, 2004, pp. 141-148, 2004.
Dong-Yup Lee,
Ralf Zimmer, Sang-Yup Lee,
Knowledge representation model for systems-level analysis of signal transduction networks, Genome Inform Ser Workshop Genome Inform, vol. 15, no. 2, pp. 234-243, 2004.
Florian Sohler,
Daniel Hanisch,
Ralf Zimmer,
New methods for joint analysis of biological networks and expression data, Bioinformatics, vol. 20, no. 10, pp. 1517-1521, 2004.
Niklas Von Öhsen,
Joannis Apostolakis,
Ralf Zimmer,
Dopro: Automatic Protein Domain Structure Prediction using a Stochastic Model for Analyzing Homology Search Results, CAFASP 2004, pp. extended abstract, 2004.
Niklas Von Öhsen, Ingolf Sommer,
Ralf Zimmer,
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures, Bioinformatics, vol. 20, no. 14, pp. 2228-35, 2004.
Daniel Hanisch,
Florian Sohler,
Ralf Zimmer,
ToPNet - an application for interactive analysis of expression data and biological networks, Bioinformatics, vol. 20, no. 9, pp. 1470-1471, 2004.
Patents
Ralf Zimmer, D. Hoffmann,
Fluorescent Energy for Elucidating the 3D Structure of Biological Macromolecules (FETMA), no. PCT Patent application, European patent office 10.08.2001, 2004.
Ralf Zimmer,
R Küffner, Alexander Zien,
Method for Evaluation of Gene Expression and DNA Chip Data using Metabolic/Regulatory Pathways and Statistical Significance Measures with Applications to Drug Target Finding, GMD Forschungszentrum Informationstechnik GmbH, no. PCT Patent application, European patent office 12.11.1999, 2004.
2003
Papers
Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen,
Ralf Zimmer,
Playing biology’s name game: identifying protein names in scientific text, Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003) (Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, eds.), Lihue, Hawaii, USA, January 3-7, 2003, pp. 403-414, 2003.
Thomas Aigner, Alexander Zien,
Daniel Hanisch,
Ralf Zimmer, J. Bone,
Gene expression in chondrocytes assessed with use of microarrays, Joint Surg Am, vol. 85-A, no. Suppl 2, pp. 117-123, 2003.
Florian Sohler,
Daniel Hanisch,
Ralf Zimmer,
New methods for joint analysis of biological networks and expression data, Proceedings of the German Conference on Bioinformatics, GCB 2003 (W. Mewes, D. Frishman, V. Heun, S. Kramer, eds.), belleville Verlag, München, Neuherberg and Garching, Germany, October 12-14, 2003, pp. 141-146, 2003.
Alexander Zien, Juliane Fluck,
Ralf Zimmer, Thomas Lengauer,
Microarrays: How Many Do You Need?, Journal of Computational Biology, vol. 10, no. 3-4, pp. 653-667, 2003.
Thomas Aigner,
Ralf Zimmer,
The promise and limitations of DNA microarray analysis: comment on the editorial by Firestein and Pisetsky, Arthritis Rheum, vol. 48, no. 3, pp. 860; author reply 862, 2003.
Niklas Von Öhsen, Ingolf Sommer,
Ralf Zimmer,
Profile-profile alignment: a powerful tool for protein structure prediction, Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003) (Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, eds.), Lihue, Hawaii, USA, January 3-7, 2003, pp. 252-63, 2003.
2002
Papers
Daniel Hanisch, Alexander Zien,
Ralf Zimmer, Thomas Lengauer,
Co-clustering of biological networks and gene expression data, Bioinformatics, vol. 18, no. 90001, pp. S145-S154, 2002.
Thomas Aigner, E. Bartnik, Alexander Zien,
Ralf Zimmer,
Functional genomics of osteoarthritis, Pharmacogenomics, vol. 3, no. 5, pp. 635-50, 2002.
Mario Albrecht,
Daniel Hanisch,
Ralf Zimmer, Thomas Lengauer,
Improving fold recognition of protein threading by experimental distance constraints, In Silico Biol, vol. 2, no. 3, pp. 325-337, 2002.
Joannis Apostolakis, D. Güttler,
Florian Sohler,
Ralf Zimmer,
Biological context and the analysis of gene expression data, ECCB 2002 (H.-P. Lenhof, ed.), vol. Poster, 2002.
Joannis Apostolakis, D. Güttler,
Florian Sohler,
Ralf Zimmer,
Prediction of gene functions from biological interactions, RECOMB 2002 (M. Vingron, ed.), vol. Poster, 2002.
J. Freudenberg,
Ralf Zimmer,
Daniel Hanisch, Thomas Lengauer,
A hypergraph-based method for unification of existing protein structure-and sequence-families, In Silico Biol, vol. 2, no. 3, pp. 339-349, 2002.
Daniel Hanisch,
Ralf Zimmer, Thomas Lengauer,
ProML - the protein markup language for specification of protein sequences, structures and families, In Silico Biol, vol. 2, no. 3, pp. 313-24, 2002.
Ingolf Sommer, Alexander Zien, Niklas Von Öhsen,
Ralf Zimmer, Thomas Lengauer,
Confidence measures for protein fold recognition, Bioinformatics, vol. 18, no. 6, pp. 802-812, 2002.
Alexander Zien, Juliane Fluck, Thomas Lengauer,
Ralf Zimmer,
Microarrays: How many do you need?, Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002 (E Myers, et al, eds.), ACM Press, New York, Washington, DC, USA, April 18-21, 2002, pp. 321-330, 2002.
2001
Papers
Alexander Zien, Thomas Aigner,
Ralf Zimmer, Thomas Lengauer,
Centralization: a new method for the normalization of gene expression data, Bioinformatics, vol. 17, no. Suppl.1, pp. S323-S331, 2001.
Mario Albrecht,
Daniel Hanisch,
Ralf Zimmer, Thomas Lengauer,
Improving fold recognition of protein threading by experimental distance constraints, German Conference on Bioinformatics (GCB 2001) (E. Windender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 68-77, 2001.
Mario Albrecht,
Ralf Zimmer,
Protein structure prediction by threading with experimental constraints, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
J. Freudenberg,
Ralf Zimmer,
Daniel Hanisch, Thomas Lengauer,
A new method for unification of existing protein structure- and sequence-families, German Conference on Bioinformatics (GCB 2001) (E. Wingender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 78-84, 2001.
Daniel Hanisch,
Ralf Zimmer, Thomas Lengauer,
Evaluation of structure prediction models using the ProML specification language, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
Daniel Hanisch,
Ralf Zimmer, Thomas Lengauer,
ProML - The protein markup language for specification of protein sequences, structures and families, German Conference on Bioinformatics (GCB 2001) (E. Wingender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 58-67, 2001.
Ingolf Sommer, Niklas Von Öhsen, Alexander Zien,
Ralf Zimmer, Thomas Lengauer,
Confidence Measures for fold recognition, German Conference on Bioinformatics (E. Wingender, ed.), pp. 26-33, 2001.
Niklas Von Öhsen,
Ralf Zimmer,
Improving profile-profile alignments via log average scoring, Proceedings of the First International Workshop on Algorithms in Bioinformatics (WABI 2001) (O. Gascuel, B.M.E. Moret, eds.), Springer-Verlag, vol. 2149, Århus, Denmark, August 28-31, 2001, pp. 11-26, 2001.
Ralf Zimmer, Thomas Lengauer,
Protein Structure Prediction, Bioinformatics - From Genomes to Drugs (Thomas Lengauer, ed.), Wiley-VCH, pp. 237-313, 2001.
Patents
Ralf Zimmer,
Frei programmierbares, universelles Parallel-rechnersystem zur Durchführung von allgemeinen Berechnungen, GMD - Forschungszentrum Informationstechnik GmbH, Sankt Augustin, no. PCT Patent application, European patent office 15.04.1998, 2001.
