Ralf Zimmer

Publication Activity (10 Years)

Years Active: 1995-2022
Publications (10 Years): 11

Top Topics

Biological Processes

Top Venues

Inform. Spektrum

Briefings Bioinform.

Publications

Alexandra Schubö, Armin Hadziahmetovic, Markus Joppich, Ralf Zimmer
Collecting SARS-CoV-2 Encoded miRNAs via Text Mining. IWBBIO (1) (2022)
Karel Sedlár, Ralf Zimmer
Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium. IWBBIO (2) (2022)
Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Toward a gold standard for benchmarking gene set enrichment analysis. Briefings Bioinform. 22 (1) (2021)
Vinícius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana C. A. Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, Ludwig Geistlinger
CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinform. 36 (3) (2020)
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. Bioinform. 35 (18) (2019)
Evi Berchtold, Gergely Csaba, Ralf Zimmer
YESdb: integrative analysis of environmental stress in yeast. Database J. Biol. Databases Curation 2019 (2019)
Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
Bioinformatics advances biology and medicine by turning big data troves into knowledge. Inform. Spektrum 40 (2) (2017)
Matthias Barann, Ralf Zimmer, Fabian Birzele
Manananggal - a novel viewer for alternative splicing events. BMC Bioinform. 18 (1) (2017)
Evi Berchtold, Gergely Csaba, Ralf Zimmer
RelExplain - integrating data and networks to explain biological processes. Bioinform. 33 (12) (2017)
Robert Pesch, Ralf Zimmer
Cross-species Conservation of context-specific networks. BMC Syst. Biol. 10 (2016)
Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinform. 17 (2016)
Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel
ContextMap 2: fast and accurate context-based RNA-seq mapping. BMC Bioinform. 16 (2015)
Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer, Robert Küffner
Addressing false discoveries in network inference. Bioinform. 31 (17) (2015)
Robert Maier, Ralf Zimmer, Robert Küffner
A Turing test for artificial expression data. Bioinform. 29 (20) (2013)
Florian Erhard, Lars Dölken, Ralf Zimmer
RIP-chip enrichment analysis. Bioinform. 29 (1) (2013)
Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer
Inferring gene regulatory networks by ANOVA. Bioinform. 28 (10) (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 Bioinform. 13 (S-6) (2012)
Robert Pesch, Matthias Böck, Ralf Zimmer
ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes. GCB (2012)
Tobias Petri, Evi Berchtold, Ralf Zimmer, Caroline C. Friedel
Detection and correction of probe-level artefacts on microarrays. BMC Bioinform. 13 (2012)
Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner
Rigorous assessment of gene set enrichment tests. Bioinform. 28 (11) (2012)
Tobias Petri, Robert Küffner, Ralf Zimmer
Experiment Specific Expression Patterns. RECOMB (2011)
Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinform. 27 (13) (2011)
Orland R. Gonzalez, Ralf Zimmer
Contextual analysis of RNAi-based functional screens using interaction networks. Bioinform. 27 (19) (2011)
Tobias Petri, Robert Küffner, Ralf Zimmer
Experiment Specific Expression Patterns. J. Comput. Biol. 18 (11) (2011)
Florian Erhard, Ralf Zimmer
Classification of ncRNAs using position and size information in deep sequencing data. Bioinform. 26 (18) (2010)
Orland R. Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt
. PLoS Comput. Biol. 6 (6) (2010)
Gergely Csaba, Ralf Zimmer
Vorescore - fold recognition improved by rescoring of protein structure models. Bioinform. 26 (18) (2010)
Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer
HALO - a Java framework for precise transcript half-life determination. Bioinform. 26 (9) (2010)
Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer
miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinform. 11 (2010)
Orland R. Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt
. PLoS Comput. Biol. 5 (4) (2009)
Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. J. Comput. Biol. 16 (8) (2009)
Caroline C. Friedel, Ralf Zimmer
Identifying the topology of protein complexes from affinity purification assays. Bioinform. 25 (16) (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. Inform. Spektrum 32 (4) (2009)
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 Res. 36 (Database-Issue) (2008)
Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Res. 36 (Database-Issue) (2008)
Lukas Windhager, Ralf Zimmer
Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics (2008)
Volker Heun, Ralf Zimmer
Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. GI Jahrestagung (2) (2008)
Florian Erhard, Caroline C. Friedel, Ralf Zimmer
FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinform. 9 (2008)
Caroline C. Friedel, Ralf Zimmer
Identifying the Topology of Protein Complexes from Affinity Purification Assays. German Conference on Bioinformatics (2008)
Gergely Csaba, Fabian Birzele, Ralf Zimmer
Protein structure alignment considering phenotypic plasticity. ECCB (2008)
Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB (2008)
Orland R. Gonzalez, Ralf Zimmer
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinform. 24 (10) (2008)
Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer
ProCope - protein complex prediction and evaluation. Bioinform. 24 (18) (2008)
Jan E. Gewehr, Volker Hintermair, Ralf Zimmer
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinform. 23 (10) (2007)
Katrin Fundel, Robert Küffner, Ralf Zimmer
RelEx - Relation extraction using dependency parse trees. Bioinform. 23 (3) (2007)
Jan E. Gewehr, Martin Szugat, Ralf Zimmer
BioWeka - extending the Weka framework for bioinformatics. Bioinform. 23 (5) (2007)
Caroline C. Friedel, Ralf Zimmer
Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinform. 8 (2007)
Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer
Vorolign - fast structural alignment using Voronoi contacts. Bioinform. 23 (2) (2007)
Robert Küffner, Timo Duchrow, Katrin Fundel, Ralf Zimmer
Characterization of Protein Interactions. German Conference on Bioinformatics (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. Bioinform. 22 (19) (2006)
Jan E. Gewehr, Ralf Zimmer
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinform. 22 (2) (2006)
Katrin Fundel, Ralf Zimmer
Gene and protein nomenclature in public databases. BMC Bioinform. 7 (2006)
Caroline C. Friedel, Ralf Zimmer
Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinform. 7 (2006)
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)
Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis
A simple approach for protein name identification: prospects and limits. BMC Bioinform. 6 (S-1) (2005)
Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
QUASAR - scoring and ranking of sequence-structure alignments. Bioinform. 21 (24) (2005)
Katrin Fundel, Robert Küffner, Thomas Aigner, Ralf Zimmer
Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. German Conference on Bioinformatics (2005)
Florian Sohler, Ralf Zimmer
Identifying active transcription factors and kinases from expression data using pathway queries. ECCB/JBI (2005)
Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck
ProMiner: rule-based protein and gene entity recognition. BMC Bioinform. 6 (S-1) (2005)
Martin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler, Ralf Zimmer
Web servicing the biological office. ECCB/JBI (2005)
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)
Michael Amberg, Jens Wehrmann, Ralf Zimmer
Factors Influencing the Design of Mobile Services. MOBIS (2004)
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. Bioinform. 20 (2) (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)
Florian Sohler, Daniel Hanisch, Ralf Zimmer
New methods for joint analysis of biological networks and expression data. Bioinform. 20 (10) (2004)
Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinform. 20 (14) (2004)
Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. Pacific Symposium on Biocomputing (2003)
Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
Microarrays: How Many Do You Need? J. Comput. Biol. 10 (3/4) (2003)
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)
Florian Sohler, Daniel Hanisch, Ralf Zimmer
New methods for joint analysis of biological networks and expression data. German Conference on Bioinformatics (2003)
Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer
Confidence measures for protein fold recognition. Bioinform. 18 (6) (2002)
Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer
A hypergraph-based method for unification of existing protein structure- and sequence-families. Silico Biol. 2 (3) (2002)
Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
ProML - the Protein Markup Language for specification of protein sequences, structures and families. Silico Biol. 2 (3) (2002)
Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer
Co-clustering of biological networks and gene expression data. ISMB (2002)
Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
Improving fold recognition of protein threading by experimental distance constraints. Silico Biol. 2 (3) (2002)
Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
Microarrays: how many do you need? RECOMB (2002)
Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer
Confidence Measures for Fold Recognition. German Conference on Bioinformatics (2001)
Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer
Centralization: a new method for the normalization of gene expression data. ISMB (Supplement of Bioinformatics) (2001)
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)
Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
ProML - the Protein Markup Language for specification of protein sequences, structures and families. German Conference on Bioinformatics (2001)
Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
Improving Fold Recognition of Protein Threading by Experimental Distance Constraints. German Conference on Bioinformatics (2001)
Niklas von Öhsen, Ralf Zimmer
Improving Profile-Profile Alignments via Log Average Scoring. WABI (2001)
Alexander Zien, Ralf Zimmer, Thomas Lengauer
A Simple Iterative Approach to Parameter Optimization. J. Comput. Biol. 7 (3-4) (2000)
Alexander Zien, Robert Küffner, Ralf Zimmer, Thomas Lengauer
Analysis of Gene Expression Data with Pathway Scores. ISMB (2000)
Robert Küffner, Ralf Zimmer, Thomas Lengauer
Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinform. 16 (9) (2000)
Alexander Zien, Ralf Zimmer, Thomas Lengauer
A simple iterative approach to parameter optimization. RECOMB (2000)
Thomas Lengauer, Ralf Zimmer
Protein Structure Prediction Methods for Drug Design. Briefings Bioinform. 1 (3) (2000)
Robert Küffner, Ralf Zimmer, Thomas Lengauer
Pathway analysis in metabolic databases via differetial metabolic display (DMD). German Conference on Bioinformatics (1999)
Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer
Application of Parameter Optimization to Molecular Comparison Problems. Pacific Symposium on Biocomputing (1999)
Ralf Zimmer, Marko Wöhler, Ralf Thiele
New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinform. 14 (3) (1998)
Ralf Zimmer, Thomas Lengauer
Fast and numerically stable parametric alignment of biosequences. RECOMB (1997)
Marko Wöhler, Ralf Thiele, Ralf Zimmer
New scoring Schemes for Protein fold recognition based on Voronoi contacts. German Conference on Bioinformatics (1997)
Ralf Zimmer, Ralf Thiele
Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. German Conference on Bioinformatics - Selected Papers (1996)
Ralf Zimmer, Ralf Thiele
Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. German Conference on Bioinformatics (1996)
Ralf Thiele, Ralf Zimmer, Thomas Lengauer
Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. ISMB (1995)