Prof. Dr. Ralf Zimmer

Robert Pesch. Cross-Species Network and Transcript Transfer. PhD Thesis, Ludwig-Maximilians-Universität München, 2016.

Thomas Bonfert. Context-based RNA-seq mapping. PhD Thesis, LMU München, 2016.

Ludwig Geistlinger. Network-based analysis of gene expression data. PhD Thesis, LMU München, 2016.

Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD Thesis, Ludwig-Maximilians-Universität München, April 2016.

Florian Erhard. Algorithmic Methods for Systems Biology of Herpes-viral microRNAs. PhD Thesis, LMU München, 2014.

Lukas Windhager. Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. PhD Thesis, LMU München, 2013.

Gergely Csaba. Context Based Bioinformatics. PhD Thesis, LMU München, 2013.

Haroon Naeem. Activity of microRNAs and transcription factors in Gene Regulatory Networks. PhD Thesis, LMU München, 2012.

Caroline C. Friedel. Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. PhD Thesis, LMU München, February 2009.

Fabian Birzele. Alternative Splicing and Protein Structure Evolution. PhD Thesis, LMU München, January 2009.

Orland Gonzalez. Reconstruction, Modeling and Analysis of Haloarcheal Metabolic Networks. PhD Thesis, LMU München, January 2009.

Luca Chiarabini. Program Development by Proof Transformation. PhD Thesis, LMU München, December 2009.

Simon W. Ginzinger. Bioinformatics Methods for NMR Chemical Shift Data. PhD Thesis, LMU München, February 2008.

Johannes Fischer. Data Structures for Efficient String Algorithms. PhD Thesis, LMU München, October 2007.

Katrin Fundel. Text Mining and Gene Expression Analysis - Towards Combined Interpretation of High Throughput Data. PhD Thesis, LMU München, September 2007.

Jan Gewehr. New Methods for the Prediction and Classification of Protein Domains. PhD Thesis, Ludwig-Maximilians-Universität München, October 2007.

Florian Sohler. Contextual Analysis of Gene Expression Data. PhD Thesis, LMU München, July 2006.

Niklas von Öhsen. Profile-Profile alignment for remote homology and domain detection of proteins. PhD Thesis, Ludwig-Maximilians-Universität München, 2005.

Daniel Hanisch. New Analysis Methods for Gene Expression Data via Construction and Incorporation of Biological Networks. PhD Thesis, Ludwig-Maximilians-Universität München, 2004.

Dorothee Liebich. Packungsprobleme bei Proteinen. PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2004.

Alexander Zien. Computational Methods for Gene Expression Data Analysis. PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2003.

Ralf Zimmer. Zur Pragmatik eines operationalisierten Lambda-Kalkül als Basis für interaktive Reduktionssysteme. PhD Thesis, Universität Kiel, 1990.

Robert Pesch. Cross-Species Network and Transcript Transfer. PhD Thesis, Ludwig-Maximilians-Universität München, 2016.

Thomas Bonfert. Context-based RNA-seq mapping. PhD Thesis, LMU München, 2016.

Ludwig Geistlinger. Network-based analysis of gene expression data. PhD Thesis, LMU München, 2016.

Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD Thesis, Ludwig-Maximilians-Universität München, April 2016.

Vinicius H. Silva. Metabolic pathways and meat tenderness: from CNVs to gene expression in Nelore cattle breed. Master Thesis, Escola Superior de Agricultura Luiz de Queiroz (ESALQ) / Universidade de São Paulo (USP), 2015.

Katharina Schmid. Efficient Construction of de Bruijn Graphs Using Suffix Arrays. Bachelor Thesis, LFE Bioinformatik / LMU München, September 2015.

Anna-Kathrin Kopetzki. On Closest String Problems for Different Distances and Norms. Bachelor Thesis, LFE Bioinformatik / LMU München, December 2015.

Julia Sophia Gerke. Integrated analysis of gene expression data and clinical data. Master Thesis, LFE Bioinformatik / LMU München, 2015.

Caroline C. Friedel. Bioinformatics methods for the biological interpretation of high-throughput experiments. Habilitation, Ludwig-Maximilians-Universität München, 2014.

Florian Erhard. Algorithmic Methods for Systems Biology of Herpes-viral microRNAs. PhD Thesis, LMU München, 2014.

Laura Schiller. Efficient computation of hybridization networks. Master Thesis, LFE Bioinformatik / LMU München, June 2014.

Evelyn Kirner. Detektion von zirkulären RNAs in Sequenzierdaten. Bachelor Thesis, LMU München, April 2014.

Yvonne Awaloff. Reconstruction of microbial transcripts from RNA-seq experiments. Bachelor Thesis, LMU München, September 2014.

Julia Söllner. Evaluation of RNA-seq mapping methods for newly transcribed RNA measurements. Bachelor Thesis, LMU München, September 2014.

Elisabeth Frank. Evaluation of transcript reconstruction methods for newly transcribed RNA measurements. Bachelor Thesis, LMU München, November 2014.

Matthias Danner. Implementierung und Evaluierung einer fehlertoleranten Textsuche basierend auf Suffix-Arrays. Bachelor Thesis, LFE Bioinformatik / LMU München, November 2014.

Michael Kluge. Analysis of mouse RNA-Seq data with regard to high fat diet and obesity. Master Thesis, TUM Lehrstuhl für Genomorientierte Bioinformatik, September 2014.

Lukas Windhager. Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. PhD Thesis, LMU München, 2013.

Gergely Csaba. Context Based Bioinformatics. PhD Thesis, LMU München, 2013.

Alexander Grün. Interactive Modeling of Complex Hypothesis Using Ontologies. Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.

Lars von den Driesch. Evolutionary conservation of PAR-CLIP microRNA target sites. Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.

Judith Boldt. Entwicklung eines Validierungs-Programms von Real-Time PCRs in der GVO-Analytik. Bachelor Thesis, LMU München, Oktober 2013.

Haroon Naeem. Activity of microRNAs and transcription factors in Gene Regulatory Networks. PhD Thesis, LMU München, 2012.

Evi Berchtold. RELEXplain - Relation Networks Explaining Biological Processes. Master Thesis, LFE Bioinformatik / LMU München, 2012.

Lucia Puchbauer. Analysis of High-Throughput Data in Oncology. Master Thesis, LFE Bioinformatik / LMU München, October 2012.

Johann Hawe. Prediction of disease progression in patients with Amyotrophic Lateral Sclerosis. Bachelor Thesis, Bioinformatics, LMU München, 2012.

Michael Kluge. miRNA regulation mechanisms of Herpes viruses. Bachelor Thesis, LFE Bioinformatik, LMU München, October 2011.

Philipp Angerer. Model Based Data Viewing and Analysis. Bachelor Thesis, LFE Bioinformatik, LMU München, September 2011.

Michael Bernhofer. Analysis of Virus Host Interaction Networks. Bachelor Thesis, LFE Bioinformatik, LMU München, September 2011.

Jonas Zierer. Transcript Quantification Biases in Next Generation Sequencing Data. Bachelor Thesis, LFE Bioinformatik, LMU München, September 2011.

Andreas Kolberg. Automatische Klassifizierung von Alternativen Splicing-Events in Proteinstrukturen. Bachelor Thesis, LFE Bioinformatik, LMU München, May 2011.

Uwe Altermann. Analysis of Expression Data of Tissue Mixtures. Bachelor Thesis, LFE Bioinformatik, LMU München, October 2011.

Vadim Jördens. Optimization of Homology-based Structure Models. Bachelor Thesis, LFE Bioinformatik, LMU München, December 2011.

Sebastian Ullherr. Prediction of Transcript Half-Lives. Bachelor Thesis, LFE Bioinformatik, LMU München, January 2010.

Thomas Bonfert. Phylogenetic networks from multi-labeled trees. Diploma Thesis, Eberhard Karls Universität Tübingen, 2010.

Evi Berchtold. Quality Check and Differential Expression Using Newly Synthesized RNA. Bachelor Thesis, LFE Bioinformatik, LMU München, September 2010.

Florian Goebels. Network Oriented Transfer of Experimental Data Between Organisms. Diploma Thesis, LFE Bioinformatik, LMU München, September 2010.

Bernd Streppel. Representation of Structure Variations of Protein Families by Partial Order Graphs. Bachelor Thesis, LFE Bioinformatik, LMU München, September 2010.

Ludwig Geistlinger. Gene Graph Enrichment Analysis (GGEA): Mapping of Gene Expression Data onto Networks of Biochemical Processes. Diploma Thesis, LFE Bioinformatik, LMU München, September 2010.

Markus Meier. Visualisierung von Repeats im Genom. Bachelor Thesis, LFE Bioinformatik, LMU München, November 2010.

Mark Heron. Network Oriented Analysis of CLA Expression Data. Bachelor Thesis, LFE Bioinformatik, LMU München, November 2009.

Caroline C. Friedel. Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. PhD Thesis, LMU München, February 2009.

Stefan Heinisch. Integration of Textmining Priors into Structural Inference of Bayesian Networks. Bachelor Thesis, LFE Bioinformatik / LMU München, March 2009.

Fabian Birzele. Alternative Splicing and Protein Structure Evolution. PhD Thesis, LMU München, January 2009.

Orland Gonzalez. Reconstruction, Modeling and Analysis of Haloarcheal Metabolic Networks. PhD Thesis, LMU München, January 2009.

Maximilian Miller. miRNA-Target-Networks. Bachelor Thesis, LFE Bioinformatik / LMU München, March 2009.

Nikolas Gross. Prediction of Protein Secondary Structure. Bachelor Thesis, LFE Bioinformatik / LMU München, March 2009.

Konrad Schreiber. Metabolic network reconstruction from Fourier Transform Mass Spectrometry data. Master Thesis, TUM / LMU München, 2009.

Jeremias Weihmann. Genome-Rearrangements: Sortieren mit erweiterten Transreversals. Diploma Thesis, LFE Bioinformatik / LMU München, August 2009.

Yanxiang Zhou. Small RNA Annotation and Analysis in Deep Sequencing Data. Bachelor Thesis, LFE Bioinformatik, LMU München, October 2009.

Johannes Bräuer. Optimization of 3D Protein Structure Models. Bachelor Thesis, LFE Bioinformatik, LMU München, December 2009.

Luca Chiarabini. Program Development by Proof Transformation. PhD Thesis, LMU München, December 2009.

Simon W. Ginzinger. Bioinformatics Methods for NMR Chemical Shift Data. PhD Thesis, LMU München, February 2008.

Florian Erhard. Petri Net Based System for Spatio-Temporal Simulation of Gene Regulation. Diploma Thesis, LFE Bioinformatik/LMU München, July 2008.

Marko Skocibusic. Improving CheckShift. Diploma Thesis, LFE Bioinformatik, LMU München, June 2008.

Annabelle Teresa Klarl. Konstruktion und Anwendung von Affixarrays. Bachelor Thesis, LFE Bioinformatik, LMU München, August 2008.

Theresa Niederberger. Regelbasierte Extraktion von Proteinwechselwirkungen. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, July 2008.

Simon Berger. Protonation State and Enzyme Substrate Interaction. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, August 2008.

Stefan Brandmaier. Strukturelle Analyse von alternativem Splicing. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, August 2008.

Thomas Mair. Analysis of Alternative Splicing of Proteins. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, September 2008.

Sebastian Pölsterl. Comparison of Alternative Splicing in Higher Organisms. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, October 2008.

Lukas Windhager. Vergleichende Genomanalyse eines neu sequenzierten H.pylori Stamms. Master Thesis, LFE Bioinformatik, LMU München, July 2007.

Alois Huber. OBMASS: Entwicklung eines linearen Algorithmus zur Berechnung des Bounded Maximum Average Scoring Subsequence Problems. Diploma Thesis, LFE Bioinformatik, LMU München, January 2007.

Horst Martin Stühler. Practical Performance of Preprocessing Schemes for Range Minimum Queries. Diploma Thesis, LFE Bioinformatik, LMU München, October 2007.

Johannes Fischer. Data Structures for Efficient String Algorithms. PhD Thesis, LMU München, October 2007.

Tobias Petri. Novel Graph Kernels for Biological Network Comparison. Diploma Thesis, Database and Information Systems/LMU München, 2007.

Volker Hintermair. Comparative Analysis of Bos Taurus and Homo Sapiens DNA Microarrays. Master Thesis, LMU München, September 2007.

Katrin Fundel. Text Mining and Gene Expression Analysis - Towards Combined Interpretation of High Throughput Data. PhD Thesis, LMU München, September 2007.

Jan Gewehr. New Methods for the Prediction and Classification of Protein Domains. PhD Thesis, Ludwig-Maximilians-Universität München, October 2007.

Frank Wallrapp. Empirical Scoring Functions for Protein Structure Analysis. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, February 2007.

Alex Jarasch. Similarity-Based Analysis of Medium- and High Throughput Screening Data. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, February 2007.

Robert Körner. Analyse biochemischer Reaktionen an Hand von imaginären Übergangszuständen. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, March 2007.

Alexander Pöschl. Browsing the protein space. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, May 2007.

Matthias Siebert. Voronoi contact patterns for protein function prediction. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, June 2007.

Florian Oefinger. A Database for Alternative Splicing in the Context of Protein Structures,. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, June 2007.

Anton Moll. Splice-isoform analysis using data from standard human gene DNA chips. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, July 2007.

Andreas Grimm. 3D tomographic and single-particle reconstruction using level set methods. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, August 2007.

Sebastian Dümcke. Optimization of Sequence-Structure Alignments using the Vorolign-Scoring Function. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, November 2007.

Gergely Csaba. Phenotypic Plasticity as a Measure for Protein Structural Similarity. Master Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, November 2007.

Julia Sellmeier. Analysis of Available Bioinformatic Tools for Exploration of Microarray Data using Gene Ontology and Design of a Bioinformatic Tool with a Graphical User Interface for Interactive Exploration of Gene Networks Predicted from Microarray Data. Diploma Thesis, LFE Bioinformatik, LMU München, May 2006.

Sebastian Bauer. Vergleich und Visualisierung von Algorithmen zur Konstruktion von Suffix-Arrays anhand sehr langer Texte. Bachelor Thesis, LFE Bioinformatik, LMU München, May 2006.

Fabian Gerick. Identification and Correction of Errors in NMR-Chemical Shift Data. Master Thesis, LFE Bioinformatik, LMU München, June 2006.

Gergely Csaba. Analysis of Protein Sequence-Structure Alignments. Bachelor Thesis, LMU München, December 2006.

Daniel Güttler. LiMB - Ein interaktiver Browser zur Analyse biomedizinischer Texte mit Hilfe von Textmining. Diploma Thesis, LMU München, April 2006.

Jonathan Hoser. Ein Scheduling System für netzwerkorientierte Bioinformatik Arbeitsabläufe. Bachelor Thesis, LMU München, December 2006.

Florian Sohler. Contextual Analysis of Gene Expression Data. PhD Thesis, LMU München, July 2006.

Chad A. Davis. Feature Selection Methods in Bioinformatics. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, June 2006.

Simon Tietze. Prediction of Specificity in Protein-Ligand Interactions Using Structure Based Virtual Screening. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, August 2006.

Jörn Marialke. Similarity Based Methods for the Prediction of Protein Ligand Complexes. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, November 2006.

Maximilian Karasz. A Fragment-Based Approach to Virtual Screening. Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, December 2006.

Lukas Windhager. Inference of Regulatory Networks Using Physical Models. Bachelor Thesis, LFE Bioinformatik, LMU München, September 2005.

Alexander Kohn. Quantitative Analyse von Protein-Massenspektren. Diploma Thesis, LFE Bioinformatik, LMU München, October 2005.

Caroline C. Friedel. On Abstaining Classifiers. Master Thesis, TU München, 2005.

Fabian Gerick. Ein programmierbarer Web Service zur Charakterisierung biologischer Objekte. Bachelor Thesis, LMU München, February 2005.

Martin Szugat. BioWeka: Extending the Weka framework for Bioinformatics. Bachelor Thesis, LMU München, October 2005.

Stephan Vogt. Topic Maps. Bachelor Thesis, LMU München, December 2005.

Niklas von Öhsen. Profile-Profile alignment for remote homology and domain detection of proteins. PhD Thesis, Ludwig-Maximilians-Universität München, 2005.

Daniel Hanisch. New Analysis Methods for Gene Expression Data via Construction and Incorporation of Biological Networks. PhD Thesis, Ludwig-Maximilians-Universität München, 2004.

Dorothee Liebich. Packungsprobleme bei Proteinen. PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2004.

Thomas Obkircher. Eine erweiterbare Bioinformatik Umgebung zur kriterienbasierten Protein Identifizierung. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, January 2004.

Volker Hintermair. Characterisation and Visualisation of Protein Families based on Multicriterial Clustering. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, November 2004.

Andreas Spitzmüller. JRDP - Ein Java Framework für Rekursive Dynamische Programmierung. Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, June 2004.

Caroline C. Friedel. Automatische Generierung und Verbesserung von Synonymlisten und Entwicklung eines geeigneten Benchmarksystems. Bachelor Thesis, LMU München, June 2003.

Cornelia Donner. Erkennung von Gennamen in wissenschaftlichen Texten - automatische Generierung von Synonymlisten und Präprozessierung der Texte. Bachelor Thesis, LMU München, June 2003.

Jan Gewehr. The Binding Matrix - A Statistical Learning Approach to Protein-DNA Binding Site Prediction. Diploma Thesis, University of Lübeck, 2003.

William Travis Holton. Evaluation of mapping consistency between public gene and protein databases. Bachelor Thesis, Ludwig-Maximilians-Universität München, November 2003.

Alexander Zien. Computational Methods for Gene Expression Data Analysis. PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2003.

Daniel Hanisch. ProML - the Protein Markup Language for efficient Threading and Clustering. Master Thesis, Friedrich-Wilhelms-Universität Bonn, 2000.

Alessandro Macri. Entwicklung von bioinformatischen Methoden zur Identifikation und Charakterisierung von Homeobox-Genen im Human- und Mausgenom. Master Thesis, Department of Computer Science / LMU Munich, 2000.

Florian Sohler. Promoter Prediction in E. coli: an Empirical Evaluation of Different Probabilistic Methods. Master Thesis, Department of Computer Science / University of Michigan, Wisconsin, USA, 2000.

Katrin Fundel. Entwicklung und Erprobung einer Teststrategie zur ökotoxikologischen Bewertung von Baustoffen. Master Thesis, Ecole superieure de biotechnologie, 1998.

J. Halfmann. Heuristische Verfahren zur Optimierung von Sequenz-Struktur-Alignments von Proteinen mittels empirischer Kontaktpotentiale. Master Thesis, Friedrich-Wilhelms-Universität, 1998.

Marco Wähler. Optimierung von Alignment-Bewertungssystemen mit Voronoi Zerlegungen von Proteinen}. Master Thesis, Department of Computer Science / Friedrich-Wilhelms-Universität Bonn, 1998.

Jörg Blankenburg. Parametric alignment. Master Thesis, Friedrich-Wilhelms-Universität Bonn, 1997.

Ralf Zimmer. Zur Pragmatik eines operationalisierten Lambda-Kalkül als Basis für interaktive Reduktionssysteme. PhD Thesis, Universität Kiel, 1990.

Fabian Birzele, E. Hoffmann, Gergely Csaba, Ralf Zimmer. Alternative Splicing of Protein Repeats. BMC Structural Biology, Submitted.

Fabian Birzele, Ralf Zimmer. Alternative Splicing and Proteome Complexity in Mass Spectrometry. PLoS Computational Biology, Submitted.

Gergely Csaba, Fabian Birzele, Ralf Zimmer. On the Similarity of Protein Structures. submitted, Submitted.

Volker Hintermair, R. Küffner, S. Bauersachs, Ralf Zimmer. Improving incomplete annotation of genome microarrays. submitted, Submitted.

R. Küffner, Fabian Birzele, Ralf Zimmer. PASS: Reliable detection of alternative splicing with microarrays. BMC Bioinformatics, Submitted.

Florian Erhard, Ralf Zimmer. Context-dependent rescoring of Tandem-MS spectra dramatically increases peptide identification rates. ISMB 2011, submitted, Submitted.

Gergely Csaba, Evi Berchtold, Ralf Zimmer. Explaining data via networks - Gene Set Enrichment using Significant Area Search on mined regulatory relation networks. submitted, Submitted.

Gergely Csaba, Simone Wolf, Ralf Zimmer. SynTree: a fast context specic NER method and its application on correctly identify psychiatric disorders in publications. submitted, Submitted.

Martin MacGuill, Tobias Petri, Ralf Zimmer. On Risk Stratification in Intensive Care Medicine. Journal of Intensive Care Medicine, Submitted.

Robert Pesch, Gergely Csaba, Ralf Zimmer. Isoform Structure Alignment Representation. submitted, Submitted.

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, January 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, June 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, Apr 2016.

Robert Pesch, Ralf Zimmer. Cross-Species Conservation of Context-Specific Networks. BMC Systems Biology, vol 10, no. 76, 2016.

Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer, Robert Küffner. Addressing false discoveries in network inference. Bioinformatics, vol 31, no. 17, pp. 2836-43, September 2015.

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. , Jul 8 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 Jul 16 2015.

Konrad Schreiber, Gergely Csaba, Martin Haslbeck, Ralf Zimmer. Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae. PLoS ONE, October 15 2015.

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 Mar 25 2014.

Robert Pesch, Ralf Zimmer. To be, or not to be: konservierte eukaryotische Regulationsnetzwerke?. BIOspektrum, vol 20, no. 5, pp. 514-516, 2014.

Florian Erhard, Lars Dölken, Ralf Zimmer. RIP-chip enrichment analysis. Bioinformatics, vol 29, no. 1, pp. 77--83, September 2012, Basel, Switzerland, Jan 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, May 2013.

Robert Pesch, Ralf Zimmer. Complementing the Eukaryotic Protein Interactome. PLOS One, vol 8, no. 6, pp. e66635, 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, July 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.

Ronny Kramer, Simone Wolf, Tobias Petri, vonDirk 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.

Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. Mining RNA-Seq Data for Infections and Contaminations. PloS one, vol 8, pp. e73071, Sep 2013.

Robert Maier, Ralf Zimmer, Robert Küffner. A Turing test for artificial expression data. Bioinformatics, vol 29, no. 20, pp. 2603-2609, Aug 16 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, May 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.

Lenac Roviš T, Bailer SM, Pothineni VR, Ouwendijk WJ, Šimić H, Babić M, Miklić K, Malić S, Verweij MC, Baiker A, Gonzalez O, vonBrunn 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, Jun 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 Jul 29 2013.

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.

Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner. Rigorous assessment of gene set enrichment tests. Bioinformatics, vol bts164v1-bts164, pp. 7, April 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 Jun 18 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, March 2012.

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.

Lisa Marcinowski, Michael Lidschreiber, Lukas Windhager, Martina Rieder, Jens B. Bosse, Bernd Rädle, Thomas Bonfert, Ildiko Györy, deMiranda Graaf, daOlivia Prazeres 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.

Robert Pesch, Matthias Böck, Ralf Zimmer. ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes. Proceedings of the German Conference on Bioinformatics (GCB), Open Access Series in Informatics of the Schloss Dagstuhl, vol 26, pp. 69-81, 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 Oct 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.

Tobias Petri, Robert Küffner, Ralf Zimmer. Experiment Specific Expression Patterns. Vineet Bafna, Cenk S. Sahinalp (eds.): RECOMB 2011, Research in Computational Molecular Biology, LNBI 6577, vol 15, pp. 339-354, Springer, 2011.

Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola Mulder, Ralf Zimmer. From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems. Bioinformatics, Bioinformatics, vol 27, no. 13, pp. i366-i373, July 2011.

Susanne Pfefferle, Julia Schöpf, Manfred Kögl, Caroline C. Friedel, Marcel A. Müller, Javier Carbajo-Lozoya, Thorsten Stellberger, vonEkatarina 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, 10 2011.

Orland Gonzalez, Ralf Zimmer. Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics, vol 27, pp. 2707-2713, November 2011.

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.

Florian Erhard, Caroline C. Friedel, Ralf Zimmer. FERN - Stochastic Simulation and Evaluation of Reaction Networks. Sangdun Choi (ed.): Systems Biology for Signaling Networks, Systems Biology, vol 1, Part 4, pp. 751-775, Springer, 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, May 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, April 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, September 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, Epub May 2010 2010.

Lukas Windhager, Florian Erhard, Ralf Zimmer. Fuzzy modeling. Ina Koch, Wolfgang Reisig, Falk Schreiber (eds.): Modeling in Systems Biology: The Petri Net Approach, Springer, 2010.

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.

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, 16 March 2010 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, 09 2010.

Gergely Csaba, Ralf Zimmer. Vorescore - fold recognition improved by rescoring of protein structure models. Bioinformatics, vol 26, no. 18, pp. i482-i488, September 2010.

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.

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.

Caroline C. Friedel, Ralf Zimmer. Identifying the topology of protein complexes from affinity purification assays. Bioinformatics, vol 25, no. 16, pp. 2140-2146, August 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, Sep 2009.

A.G. Moll, M.T. Lindenmeyer, M. Kretzler, P.J. Nelson, Ralf Zimmer, C.D. Cohen. Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS ONE, vol 4, no. 3, pp. e4702, Epub 2009 Mar 11 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.

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, Sep 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.

Fabian Birzele, Gergely Csaba, Ralf Zimmer. Alternative splicing and protein structure evolution. Nucleic Acids Res., vol 36, pp. 550–558, Feb 2008.

Fabian Birzele, Jan Gewehr, Ralf Zimmer. AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Res., vol 36, pp. 398–401, Jan 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), September 9-12, 2008, Dresden, Germany, Lecture Notes in Informatics, vol P-136, pp. 30-43, GI, 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, Jan 2008.

Lukas Windhager, Ralf Zimmer. Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics, September 9-12, 2008, Dresden, Germany, Lecture Notes in Informatics, vol P-136, pp. 106-115, Gesellschaft für Informatik, 2008.

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. Sorin Istrail, Pavel Pevzner, Michael Waterman (eds.): Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008, Singapore, March 30 - April 2, 2008, Lecture Notes in Computer Science, vol 4955, pp. 3-16, Springer, 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, Sep 2008.

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer. ProCope–protein complex prediction and evaluation. Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 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.

Gergely Csaba, Fabian Birzele, Ralf Zimmer. Protein structure alignment considering phenotypic plasticity. Bioinformatics, vol 24, pp. 98–104, Aug 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.

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 Gewehr, Gergely Csaba, Ralf Zimmer. Vorolign - Fast Structural Alignment using Voronoi Contacts. Bioinformatics, vol 23, no. 2, pp. e205-e211, 2007.

Jan 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.

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 Gewehr, Martin Szugat, Ralf Zimmer. BioWeka--extending the Weka framework for bioinformatics. Bioinformatics, vol 23, no. 5, pp. 651-653, 2007.

Jan 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, Jun 2006.

Caroline C. Friedel, Ralf Zimmer. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics, vol 7, pp. 519, Nov 2006.

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. Daniel Huson, Oliver Kohlbacher, Andrei Lupas, Kay Nieselt, Andreas Zell (eds.): German Conference on Bioinformatics (GCB), Tübingen, Germany, September 19-22, 2006, Lecture Notes in Informatics, vol P-83, pp. 64-73, Gesellschaft für Informatik, 2006.

Katrin Fundel, Ralf Zimmer. Gene and protein nomenclature in public databases. BMC Bioinformatics, vol 7, pp. 372, 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. R. Decker, H.-J. Lenz (eds.): Advances in Data Analysis. Proc. 30th Annual Conference of the German Classification Society (GfKl), pp. 385-594, Springer-Verlag, Heidelberg-Berlin, 2007, 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.

Katrin Fundel, R. Küffner, Thomas Aigner, Ralf Zimmer. Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. A. Torda, S. Kurtz, Matthias Rarey (eds.): German Conference on Bioinformatics (GCB) 2005, GI Lecture Notes in Informatics, vol P-71, pp. 77-91, GI, 2005.

Fabian Birzele, Jan Gewehr, Ralf Zimmer. QUASAR–scoring and ranking of sequence-structure alignments. Bioinformatics, vol 21, no. 24, pp. 4425–4426, Dec 2005.

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.

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, May 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, May 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, 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. Robert Giegerich, Jens Stoye (eds.): German Conference on Bioinformatics, GCB 2004, Bielefeld, Germany, October 4-6, 2004, Lecture Notes in Informatics, vol P-53, pp. 159-168, Gesellschaft für Informatik, 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, Jun 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, van derM. Linden, H. Luz, K. Meissner, vonC. 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 Gewehr, Niklas von Öhsen, Ralf Zimmer. Combining Secondary Structure Element Alignment and Profile Alignment for Fold Recognition. Robert Giegerich, Jens Stoye (eds.): German Conference on Bioinformatics, GCB 2004, Bielefeld, Germany, October 4-6, 2004, Lecture Notes in Informatics, vol P-53, pp. 141-148, Gesellschaft für Informatik, 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.

Ralf Zimmer, D. Hoffmann. Fluorescent Energy for Elucidating the 3D Structure of Biological Macromolecules (FETMA). Patent-No.: PCT/EP 99/01008 (Feb 10, 1999), US 6,713,256 B1 (Mar 30, 2004), Appl-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. Patent-No.: PCT/EP 00/11171, Appl-No.: PCT Patent application, European patent office 12.11.1999, 2004.

Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer. Playing biology's name game: identifying protein names in scientific text. Russ B. Altman, Keith A. Dunker, Lawrence Hunter, Teri E. Klein (eds.): Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003), 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. W. Mewes, D. Frishman, V. Heun, S. Kramer (eds.): Proceedings of the German Conference on Bioinformatics, GCB 2003, Neuherberg and Garching, Germany, October 12-14, 2003, pp. 141-146, belleville Verlag, München, 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. Russ B. Altman, Keith A. Dunker, Lawrence Hunter, Teri E. Klein (eds.): Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003), Lihue, Hawaii, USA, January 3-7, 2003, pp. 252-63, 2003.

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. H.-P. Lenhof (ed.): ECCB 2002, vol Poster, 2002.

Joannis Apostolakis, D. Güttler, Florian Sohler, Ralf Zimmer. Prediction of gene functions from biological interactions. M. Vingron (ed.): RECOMB 2002, 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?. E. Myers, etal (eds.): Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002, pp. 321-330, ACM Press, New York, 2002.

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. E. Windender, R. Hofestädt, I. Liebich (eds.): German Conference on Bioinformatics (GCB 2001), 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. E. Wingender, R. Hofestädt, I. Liebich (eds.): German Conference on Bioinformatics (GCB 2001), 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. E. Wingender, R. Hofestädt, I. Liebich (eds.): German Conference on Bioinformatics (GCB 2001), 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. E. Wingender (ed.): German Conference on Bioinformatics, pp. 26-33, 2001.

Niklas von Öhsen, Ralf Zimmer. Improving profile-profile alignments via log average scoring. O. Gascuel, B.M.E. Moret (eds.): Proceedings of the First International Workshop on Algorithms in Bioinformatics (WABI 2001), Århus, Denmark, August 28-31, 2001, Lecture Notes in Computer Science, vol 2149, pp. 11-26, Springer-Verlag, 2001.

Ralf Zimmer, Thomas Lengauer. Protein Structure Prediction. Thomas Lengauer (ed.): Bioinformatics - From Genomes to Drugs, Methods and Principles in Medicinal Chemistry, pp. 237-313, Wiley-VCH, 2001.

Ralf Zimmer. Frei programmierbares, universelles Parallel-rechnersystem zur Durchführung von allgemeinen Berechnungen. Patent-No.: EP 0 976 060 B1, Appl-No.: PCT Patent application, European patent office 15.04.1998, 2001.

Alexander Zien, R. Küffner, H. Mevissen, Ralf Zimmer, T. Lengauer. Identifikation von Drug Target Proteinen. ERCIM News, vol 43, pp. 16-17, 2000.

Alexander Zien, R. Küffner, Ralf Zimmer, Thomas Lengauer. Analysis of gene expression data with pathway scores. Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, vol 8, pp. 407-417, August 2000.

R. Küffner, Ralf Zimmer, Thomas Lengauer. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics, vol 16, no. 9, pp. 825-36, 2000.

Alexander Zien, R. Küffner, Ralf Zimmer, Thomas Lengauer. Analysis of gene expression data with pathway scores. Institute for Algorithms and Scientific Computing, vol 8, 2000.

Thomas Lengauer, Ralf Zimmer. Protein structure prediction methods for drug design. Brief Bioinform, vol 1, no. 3, pp. 275-88, 2000.

S. Springstubbe, Matthias Rarey, Ralf Zimmer. Schneller Check beim Screening. Supplement in Umweltmagazin, vol 2, pp. 26-29, 2000.

S. Springstubbe, Matthias Rarey, Ralf Zimmer. Schneller Check beim Screening. Life Science Technologien, vol 2, pp. 26-29, 2000.

S. Springstubbe, Matthias Rarey, Ralf Zimmer. Supplement in Process. Supplement in Process, vol 2, pp. 26-29, 2000.

S. Springstubbe, Matthias Rarey, Ralf Zimmer. Schneller Check beim Screening. Supplement in Laborpraxis, vol 2, pp. 26-29, 2000.

Alexander Zien, Ralf Zimmer, Thomas Lengauer. A simple iterative approach to parameter optimization. J Comput Biol, vol 7, no. 3-4, pp. 483-501, 2000.

R. Küffner, Ralf Zimmer, Thomas Lengauer. Pathway Analysis in Metabolic Databases via Differential Metabolic Display (DMD). GMD, pp. 825-836, 1999.

T. Dräge, M. Rarey, Ralf Zimmer. Proteinstrukturvorhersage und Molecular Docking. Transkript, vol 5, no. 3, pp. 24-26, 1999.

C. Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer. Application of parameter optimization to molecular comparison problems. Pac Symp Biocomput, pp. 482-493, 1999.

Thomas Lengauer, M. Rarey, Ralf Zimmer. Bioinformatik - Diagnose von Krankheiten und Entwicklung von Wirkstoffen mit Hilfe des Computers. Spektrum der Wissenschaft, vol 2, pp. 38-43, 1999.

S. Springstubbe, T. Dräge, Matthias Rarey, Ralf Zimmer. Protein Strukturvorhersage und Molekulares Docking. BIOforum, vol 10, pp. 634-636, 1999.

Ralf Thiele, Ralf Zimmer, Thomas Lengauer. Protein threading by recursive dynamic programming. J Mol Biol, vol 290, no. 3, pp. 757-79, 1999.

Ralf Zimmer. Ein universeller DNA Computer - Vom Chip zu den Erbmolekülen. GMD Spiegel, no. Okt, pp. 24-28, 1999.

Thomas Lengauer, Hans W. Mewes, R. Schneider, Ralf Zimmer. Seventh international Conference on Intelligent Systems for Molecular Biology (ISMB 1999). AAAI Press, 1999.

Ralf Zimmer, J. Halfmann. Optimizing Homology Models of Protein Structure with Potentials of Mean Force. P. Grassberger, G. Barkema, W. Nadler (eds.): Monte Carlo Approach to Biopolymers and Protein Folding, pp. 45-68, World Scientific Publishing, 1998.

Ralf Zimmer, M. Wöhler, Ralf Thiele. New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics, vol 14, no. 3, pp. 295-308, 1998.

Marco Wähler, Ralf Zimmer, Ralf Thiele. New scoring schemes for protein fold recognition based on Voronoi contacts. German Conference on Bioinformatics (GCB'97), 1997.

Ralf Zimmer, Thomas Lengauer. Fast and Numerically Stable Parametric Alignment of Biosequences. M. Waterman (ed.): First Annual International Conference on Computational Molecular Biology (RECOMB'97), pp. 344-353, ACM Press, 1997.

Ralf Zimmer, Thomas Lengauer. Fast and Numerically Stable Parametric Alignment of Biosequences. M. Waterman (ed.): First Annual International Conference on Computational Molecular Biology (RECOMB'97), pp. 344-353, ACM Press, 1997.

Ralf Zimmer, Ralf Thiele. Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. D. Schomburg, R. Hofestädt, T. Lengauer, M. Löffler (eds.): German Conference on Bioinformatics (GCB'96), LNCS, vol 1278, pp. 137-146, Springer-Verlag, 1997.

Ralf Zimmer. Frei programmierbares, universelles Parallel-Rechnersystem zur Durchführung von allgemeinen Berechnungen. Patent-No.: Internationale PCT Anmeldung, PCT/EP98/, 0976060, 1997.

Nickolai N. Alexandrov, Ruth Nussinov, Ralf Zimmer. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. Pac Symp Biocomput, pp. 53-72, 1996.

Thomas Lengauer, Ralf Thiele, Ralf Zimmer. Modellierung von Proteinstrukturen. GMD Spiegel, vol Juli/Sept, pp. 14-18, 1996.

Ralf Thiele, Ralf Zimmer, Thomas Lengauer. Recursive dynamic programming for adaptive sequence and structure alignment. Proc Int Conf Intell Syst Mol Biol, vol 3, no. 384-92, 1995.

Ralf Zimmer. On the Efficiency of Parallel Algorithms for DNA/Protein Sequence Alignment. Gaetan Hains Mullin, Lenore M.R. (eds.): ATABLE-92 Second International Workshop on Array Structures, pp. 214-234, Universit de Montreal, 1992.

Ralf Zimmer. The Efficiency of Parallel Machines and Algorithms. K.D. Reinartz (ed.): GI-Workshop, Parallelrechner und Programmiersprachen, vol 10, pp. 37-49, PARS, 1992.

Ralf Zimmer. Zur Pragmatik eines operationalisierten Lambda-Kalkül als Basis für interaktive Reduktionssysteme. PhD Thesis, Universität Kiel, 1990.