Ralf Zimmer

Florian Erhard, Lars Dölken, Ralf Zimmer: RIP-chip enrichment analysis. Bioinformatics 29(1): 77-83 (2013)

Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer: Inferring gene regulatory networks by ANOVA. Bioinformatics 28(10): 1376-1382 (2012)

Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner: Rigorous assessment of gene set enrichment tests. Bioinformatics 28(11): 1480-1486 (2012)

Tobias Petri, Evi Berchtold, Ralf Zimmer, Caroline C. Friedel: Detection and correction of probe-level artefacts on microarrays. BMC Bioinformatics 13: 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 13(S-6): S9 (2012)

Robert Pesch, Matthias Böck, Ralf Zimmer: ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes. GCB 2012: 69-81

Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer: From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics [ISMB/ECCB] 27(13): 366-373 (2011)

Orland R. Gonzalez, Ralf Zimmer: Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics 27(19): 2707-2713 (2011)

Tobias Petri, Robert Küffner, Ralf Zimmer: Experiment Specific Expression Patterns. Journal of Computational Biology 18(11): 1423-1435 (2011)

Tobias Petri, Robert Küffner, Ralf Zimmer: Experiment Specific Expression Patterns. RECOMB 2011: 339-354

Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer: HALO - a Java framework for precise transcript half-life determination. Bioinformatics 26(9): 1264-1266 (2010)

Gergely Csaba, Ralf Zimmer: Vorescore - fold recognition improved by rescoring of protein structure models. Bioinformatics 26(18) (2010)

Florian Erhard, Ralf Zimmer: Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics 26(18) (2010)

Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer: miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics 11: 135 (2010)

Orland R. Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt: Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis. PLoS Computational Biology 6(6) (2010)

Caroline C. Friedel, Ralf Zimmer: Identifying the topology of protein complexes from affinity purification assays. Bioinformatics 25(16): 2140-2146 (2009)

Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel, Robert Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer: Algorithmische Systembiologie mit Petrinetzen - Von qualitativen zu quantitativen Systemmodellen. Informatik Spektrum 32(4): 310-319 (2009)

Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer: Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. Journal of Computational Biology 16(8): 971-987 (2009)

Orland R. 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 5(4) (2009)

Orland R. Gonzalez, Ralf Zimmer: Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics 24(10): 1257-1263 (2008)

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer: ProCope - protein complex prediction and evaluation. Bioinformatics 24(18): 2115-2116 (2008)

Florian Erhard, Caroline C. Friedel, Ralf Zimmer: FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics 9 (2008)

Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer: ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Research 36(Database-Issue): 63-68 (2008)

Fabian Birzele, Jan E. Gewehr, Ralf Zimmer: AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Research 36(Database-Issue): 398-401 (2008)

Gergely Csaba, Fabian Birzele, Ralf Zimmer: Protein structure alignment considering phenotypic plasticity. ECCB 2008: 98-104

Caroline C. Friedel, Ralf Zimmer: Identifying the Topology of Protein Complexes from Affinity Purification Assays. German Conference on Bioinformatics 2008: 30-43

Lukas Windhager, Ralf Zimmer: Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics 2008: 106-115

Volker Heun, Ralf Zimmer: Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. GI Jahrestagung (2) 2008: 988-991

Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer: Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008: 3-16

Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer: Vorolign - fast structural alignment using Voronoi contacts. Bioinformatics 23(2): 205-211 (2007)

Katrin Fundel, Robert Küffner, Ralf Zimmer: RelEx - Relation extraction using dependency parse trees. Bioinformatics 23(3): 365-371 (2007)

Jan E. Gewehr, Martin Szugat, Ralf Zimmer: BioWeka - extending the Weka framework for bioinformatics. Bioinformatics 23(5): 651-653 (2007)

Jan E. Gewehr, Volker Hintermair, Ralf Zimmer: AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics 23(10): 1203-1210 (2007)

Caroline C. Friedel, Ralf Zimmer: Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics 8 (2007)

Jan E. Gewehr, Ralf Zimmer: SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics 22(2): 181-187 (2006)

Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer: Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics 22(19): 2356-2363 (2006)

Katrin Fundel, Ralf Zimmer: Gene and protein nomenclature in public databases. BMC Bioinformatics 7: 372 (2006)

Caroline C. Friedel, Ralf Zimmer: Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 7: 519 (2006)

Robert Küffner, Timo Duchrow, Katrin Fundel, Ralf Zimmer: Characterization of Protein Interactions. German Conference on Bioinformatics 2006: 64-73

Henning Redestig, Florian Sohler, Ralf Zimmer, Joachim Selbig: Unsupervised Decision Trees Structured by Gene Ontology (GO-UDTs) for the Interpretation of Microarray Data. GfKl 2006: 585-592

Fabian Birzele, Jan E. Gewehr, Ralf Zimmer: QUASAR - scoring and ranking of sequence-structure alignments. Bioinformatics 21(24): 4425-4426 (2005)

Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis: A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 6(S-1) (2005)

Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck: ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 6(S-1) (2005)

Florian Sohler, Ralf Zimmer: Identifying active transcription factors and kinases from expression data using pathway queries. ECCB/JBI 2005: 122

Robert Küffner, Katrin Fundel, Ralf Zimmer: Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. ECCB/JBI 2005: 267

Martin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler, Ralf Zimmer: Web servicing the biological office. ECCB/JBI 2005: 269

Katrin Fundel, Robert Küffner, Thomas Aigner, Ralf Zimmer: Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. German Conference on Bioinformatics 2005: 77-91

Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer: The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics 20(2): 268-270 (2004)

Florian Sohler, Daniel Hanisch, Ralf Zimmer: New methods for joint analysis of biological networks and expression data. Bioinformatics 20(10): 1517-1521 (2004)

Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer: Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 20(14): 2228-2235 (2004)

Jan E. Gewehr, Niklas von Öhsen, Ralf Zimmer: Combining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition. German Conference on Bioinformatics 2004: 141-148

Michael Amberg, Jens Wehrmann, Ralf Zimmer: Factors Influencing the Design of Mobile Services. MOBIS 2004: 199-212

Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer: Microarrays: How Many Do You Need? Journal of Computational Biology 10(3/4): 653-667 (2003)

Florian Sohler, Daniel Hanisch, Ralf Zimmer: New methods for joint analysis of biological networks and expression data. German Conference on Bioinformatics 2003: 141-146

Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer: Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. Pacific Symposium on Biocomputing 2003: 252-263

Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer: Playing Biology's Name Game: Identifying Protein Names in Scientific Text. Pacific Symposium on Biocomputing 2003: 403-414

Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer: Confidence measures for protein fold recognition. Bioinformatics 18(6): 802-812 (2002)

Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: ProML - the Protein Markup Language for specification of protein sequences, structures and families. In Silico Biology 2: 29 (2002)

Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: Improving fold recognition of protein threading by experimental distance constraints. In Silico Biology 2: 30 (2002)

Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer: A hypergraph-based method for unification of existing protein structure- and sequence-families. In Silico Biology 2: 31 (2002)

Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Co-clustering of biological networks and gene expression data. ISMB 2002: 145-154

Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer: Microarrays: how many do you need? RECOMB 2002: 321-330

Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Confidence Measures for Fold Recognition. German Conference on Bioinformatics 2001: 26-33

Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: ProML - the Protein Markup Language for specification of protein sequences, structures and families. German Conference on Bioinformatics 2001: 58-67

Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: Improving Fold Recognition of Protein Threading by Experimental Distance Constraints. German Conference on Bioinformatics 2001: 68-77

Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer: A new Method for Unification of Existing Protein Structure- and Sequence-Families. German Conference on Bioinformatics 2001: 78-84

Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer: Centralization: a new method for the normalization of gene expression data. ISMB (Supplement of Bioinformatics) 2001: 323-331

Niklas von Öhsen, Ralf Zimmer: Improving Profile-Profile Alignments via Log Average Scoring. WABI 2001: 11-26

Thomas Lengauer, Ralf Zimmer: Protein Structure Prediction Methods for Drug Design. Briefings in Bioinformatics 1(3): 275-288 (2000)

Robert Küffner, Ralf Zimmer, Thomas Lengauer: Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16(9): 825-836 (2000)

Alexander Zien, Ralf Zimmer, Thomas Lengauer: A Simple Iterative Approach to Parameter Optimization. Journal of Computational Biology 7(3-4): 483-501 (2000)

Alexander Zien, Robert Küffner, Ralf Zimmer, Thomas Lengauer: Analysis of Gene Expression Data with Pathway Scores. ISMB 2000: 407-417

Alexander Zien, Ralf Zimmer, Thomas Lengauer: A simple iterative approach to parameter optimization. RECOMB 2000: 318-327

Robert Küffner, Ralf Zimmer, Thomas Lengauer: Pathway analysis in metabolic databases via differetial metabolic display (DMD). German Conference on Bioinformatics 1999: 141-147

Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Application of Parameter Optimization to Molecular Comparison Problems. Pacific Symposium on Biocomputing 1999: 482-493

Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas L. Brutlag, Janice I. Glasgow, Hans-Werner Mewes, Ralf Zimmer (Eds.): Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany. AAAI 1999, isbn 1-57735-083-9

Ralf Zimmer, Marko Wöhler, Ralf Thiele: New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics 14(3): 295-308 (1998)

Marko Wöhler, Ralf Thiele, Ralf Zimmer: New scoring Schemes for Protein fold recognition based on Voronoi contacts. German Conference on Bioinformatics 1997: 111-120

Ralf Zimmer, Thomas Lengauer: Fast and numerically stable parametric alignment of biosequences. RECOMB 1997: 344-353

Ralf Zimmer, Ralf Thiele: Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. German Conference on Bioinformatics 1996: 78-83

Ralf Zimmer, Ralf Thiele: Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. German Conference on Bioinformatics - Selected Papers 1996: 137-146

Ralf Thiele, Ralf Zimmer, Thomas Lengauer: Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. ISMB 1995: 384-392