Zur Pragmatik eines operationalisierten λ-Kalküls als Basis für interaktive Reduktionssysteme. - Ralf Martin Zimmer (Oldenbourg, 1990)

Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. - Ralf Thiele; Ralf Zimmer; Thomas Lengauer (ISMB, 1995)

Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. - Ralf Zimmer; Ralf Thiele (German Conference on Bioinformatics - Selected Papers, 1996)

Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. - Ralf Zimmer; Ralf Thiele (German Conference on Bioinformatics, 1996)

Fast and numerically stable parametric alignment of biosequences. - Ralf Zimmer; Thomas Lengauer (RECOMB, 1997)

New scoring schemes for protein fold recognition based on Voronoi contacts. - Ralf Zimmer; Marko Wöhler; Ralf Thiele (Bioinform., 1998)

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

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

Analysis of Gene Expression Data with Pathway Scores. - Alexander Zien; Robert Küffner; Ralf Zimmer; Thomas Lengauer (ISMB, 2000)

Protein Structure Prediction Methods for Drug Design. - Thomas Lengauer; Ralf Zimmer (Briefings Bioinform., 2000)

Pathway analysis in metabolic databases via differential metabolic display (DMD). - Robert Küffner; Ralf Zimmer; Thomas Lengauer (Bioinform., 2000)

A Simple Iterative Approach to Parameter Optimization. - Alexander Zien; Ralf Zimmer; Thomas Lengauer (J. Comput. Biol., 2000)

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

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

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

Improving Profile-Profile Alignments via Log Average Scoring. - Niklas von Öhsen; Ralf Zimmer (WABI, 2001)

Co-clustering of biological networks and gene expression data. - Daniel Hanisch; Alexander Zien; Ralf Zimmer; Thomas Lengauer (ISMB, 2002)

Confidence measures for protein fold recognition. - Ingolf Sommer; Alexander Zien; Niklas von Öhsen; Ralf Zimmer; Thomas Lengauer (Bioinform., 2002)

Improving fold recognition of protein threading by experimental distance constraints. - Mario Albrecht; Daniel Hanisch; Ralf Zimmer; Thomas Lengauer (Silico Biol., 2002)

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

ProML - the Protein Markup Language for specification of protein sequences, structures and families. - Daniel Hanisch; Ralf Zimmer; Thomas Lengauer (Silico Biol., 2002)

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

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

Microarrays: How Many Do You Need? - Alexander Zien; Juliane Fluck; Ralf Zimmer; Thomas Lengauer (J. Comput. Biol., 2003)

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

Factors Influencing the Design of Mobile Services. - Michael Amberg; Jens Wehrmann; Ralf Zimmer (MOBIS, 2004)

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. - Torsten Crass; Iris Antes; Rico Basekow; Peer Bork; Christian Buning; Maik Christensen; Holger Claussen 002; Christian Ebeling; Peter Ernst; Valérie Gailus-Durner; Karl-Heinz Glatting; Rolf Gohla; et al. (Bioinform., 2004)

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. - Niklas von Öhsen; Ingolf Sommer; Ralf Zimmer; Thomas Lengauer (Bioinform., 2004)

New methods for joint analysis of biological networks and expression data. - Florian Sohler; Daniel Hanisch; Ralf Zimmer (Bioinform., 2004)

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

Identifying active transcription factors and kinases from expression data using pathway queries. - Florian Sohler; Ralf Zimmer (ECCB/JBI, 2005)

Web servicing the biological office. - Martin Szugat; Daniel Güttler; Katrin Fundel; Florian Sohler; Ralf Zimmer (ECCB/JBI, 2005)

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

QUASAR - scoring and ranking of sequence-structure alignments. - Fabian Birzele; Jan E. Gewehr; Ralf Zimmer (Bioinform., 2005)

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

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

Characterization of Protein Interactions. - Robert Küffner; Timo Duchrow; Katrin Fundel; Ralf Zimmer (German Conference on Bioinformatics, 2006)

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

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

SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. - Jan E. Gewehr; Ralf Zimmer (Bioinform., 2006)

Inferring topology from clustering coefficients in protein-protein interaction networks. - Caroline C. Friedel; Ralf Zimmer (BMC Bioinform., 2006)

Gene and protein nomenclature in public databases. - Katrin Fundel; Ralf Zimmer (BMC Bioinform., 2006)

Vorolign - fast structural alignment using Voronoi contacts. - Fabian Birzele; Jan E. Gewehr; Gergely Csaba; Ralf Zimmer (Bioinform., 2007)

RelEx - Relation extraction using dependency parse trees. - Katrin Fundel; Robert Küffner; Ralf Zimmer (Bioinform., 2007)

AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. - Jan E. Gewehr; Volker Hintermair; Ralf Zimmer (Bioinform., 2007)

BioWeka - extending the Weka framework for bioinformatics. - Jan E. Gewehr; Martin Szugat; Ralf Zimmer (Bioinform., 2007)

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

Protein structure alignment considering phenotypic plasticity. - Gergely Csaba; Fabian Birzele; Ralf Zimmer (ECCB, 2008)

Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. - Lukas Windhager; Ralf Zimmer (German Conference on Bioinformatics, 2008)

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

Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. - Orland R. Gonzalez; Ralf Zimmer (Bioinform., 2008)

ProCope - protein complex prediction and evaluation. - Jan Krumsiek; Caroline C. Friedel; Ralf Zimmer (Bioinform., 2008)

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

AutoPSI: a database for automatic structural classification of protein sequences and structures. - Fabian Birzele; Jan E. Gewehr; Ralf Zimmer (Nucleic Acids Res., 2008)

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

Identifying the topology of protein complexes from affinity purification assays. - Caroline C. Friedel; Ralf Zimmer (Bioinform., 2009)

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

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. - Caroline C. Friedel; Jan Krumsiek; Ralf Zimmer (J. Comput. Biol., 2009)

Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum. - Orland R. Gonzalez; Susanne Gronau; Friedhelm Pfeiffer; Eduardo Mendoza; Ralf Zimmer; Dieter Oesterhelt (PLoS Comput. Biol., 2009)

Vorescore - fold recognition improved by rescoring of protein structure models. - Gergely Csaba; Ralf Zimmer (Bioinform., 2010)

Classification of ncRNAs using position and size information in deep sequencing data. - Florian Erhard; Ralf Zimmer (Bioinform., 2010)

HALO - a Java framework for precise transcript half-life determination. - Caroline C. Friedel; Stefanie Kaufmann; Lars Dölken; Ralf Zimmer (Bioinform., 2010)

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

Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis. - Orland R. Gonzalez; Tanja Oberwinkler; Locedie Mansueto; Friedhelm Pfeiffer; Eduardo Mendoza; Ralf Zimmer; Dieter Oesterhelt (PLoS Comput. Biol., 2010)

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. - Ludwig Geistlinger; Gergely Csaba; Robert Küffner; Nicola J. Mulder; Ralf Zimmer (Bioinform., 2011)

Contextual analysis of RNAi-based functional screens using interaction networks. - Orland R. Gonzalez; Ralf Zimmer (Bioinform., 2011)

Experiment Specific Expression Patterns. - Tobias Petri; Robert Küffner; Ralf Zimmer (J. Comput. Biol., 2011)

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

Inferring gene regulatory networks by ANOVA. - Robert Küffner; Tobias Petri; Pegah Tavakkolkhah; Lukas Windhager; Ralf Zimmer (Bioinform., 2012)

Rigorous assessment of gene set enrichment tests. - Haroon Naeem; Ralf Zimmer; Pegah Tavakkolkhah; Robert Küffner (Bioinform., 2012)

A context-based approach to identify the most likely mapping for RNA-seq experiments. - Thomas Bonfert; Gergely Csaba; Ralf Zimmer; Caroline C. Friedel (BMC Bioinform., 2012)

Detection and correction of probe-level artefacts on microarrays. - Tobias Petri; Evi Berchtold; Ralf Zimmer; Caroline C. Friedel (BMC Bioinform., 2012)

RIP-chip enrichment analysis. - Florian Erhard; Lars Dölken; Ralf Zimmer (Bioinform., 2013)

A Turing test for artificial expression data. - Robert Maier; Ralf Zimmer; Robert Küffner (Bioinform., 2013)

Addressing false discoveries in network inference. - Tobias Petri; Stefan Altmann; Ludwig Geistlinger; Ralf Zimmer; Robert Küffner (Bioinform., 2015)

ContextMap 2: fast and accurate context-based RNA-seq mapping. - Thomas Bonfert; Evelyn Kirner; Gergely Csaba; Ralf Zimmer; Caroline C. Friedel (BMC Bioinform., 2015)

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Ralf Zimmer (BMC Bioinform., 2016)

Cross-species Conservation of context-specific networks. - Robert Pesch; Ralf Zimmer (BMC Syst. Biol., 2016)

Fuzzy Modeling. - Lukas Windhager; Florian Erhard; Ralf Zimmer (Modeling in Systems Biology, The Petri Net Approach, 2016)

Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge. - Julien Gagneur; Caroline C. Friedel; Volker Heun; Ralf Zimmer; Burkhard Rost (50 Jahre Universitäts-Informatik in München, 2017)

RelExplain - integrating data and networks to explain biological processes. - Evi Berchtold; Gergely Csaba; Ralf Zimmer (Bioinform., 2017)

Manananggal - a novel viewer for alternative splicing events. - Matthias Barann; Ralf Zimmer; Fabian Birzele (BMC Bioinform., 2017)

Bioinformatics advances biology and medicine by turning big data troves into knowledge. - Julien Gagneur; Caroline C. Friedel; Volker Heun; Ralf Zimmer; Burkhard Rost (Inform. Spektrum, 2017)

YESdb: integrative analysis of environmental stress in yeast. - Evi Berchtold; Gergely Csaba; Ralf Zimmer (Database J. Biol. Databases Curation, 2019)

Comparison of six breast cancer classifiers using qPCR. - Evi Berchtold; Martina Vetter; Melanie Gündert; Gergely Csaba; Christine Fathke; Susanne E. Ulbrich; Christoph Thomssen; Ralf Zimmer; Eva J. Kantelhardt (Bioinform., 2019)

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. - Vinícius da Silva; Marcel Ramos; Martien Groenen; Richard Crooijmans; Anna Johansson; Luciana C. A. Regitano; Luiz Coutinho; Ralf Zimmer; Levi Waldron; Ludwig Geistlinger (Bioinform., 2020)

Toward a gold standard for benchmarking gene set enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Mara Santarelli; Marcel Ramos; Lucas Schiffer; Nitesh Turaga; Charity W. Law; Sean Davis 001; Vincent J. Carey; Martin Morgan; Ralf Zimmer; Levi Waldron (Briefings Bioinform., 2021)

Collecting SARS-CoV-2 Encoded miRNAs via Text Mining. - Alexandra Schubö; Armin Hadziahmetovic; Markus Joppich; Ralf Zimmer (IWBBIO (1), 2022)

Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium. - Karel Sedlár; Ralf Zimmer (IWBBIO (2), 2022)