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

Florian Erhard, Lea Haarup Gregersen, Markus Landthaler, Lars Dölken, Ralf Zimmer. RIP-chip enrichment analysis. European Conference on Computational Biology (ECCB2012), September 2012, Basel, Switzerland, Submitted.

Milan Spasic, Caroline C. Friedel, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin. Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm. PLoS Genet, vol 8, no. 1, pp. e1002433, 01 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.

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.

Benjamin Albrecht, Volker Heun. Space Efficient Modifications to Structator - a Fast Index-Based Search Tool for RNA Sequence-Structure Patterns. Ralf Klasing (ed.): Proceedings of the 11th International Symposium on Experimental Algorithms (SEA 2012), Bordeaux, France, June 7-9, 2012, Lecture Notes in Computer Science, vol 7276, pp. 27-38, Springer Verlag, 2012.

Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner. Rigorous assessment of gene set enrichment tests. Bioinformatics, vol bts164v1-bts164, pp. 7, April 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. Ultra short and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Research, 2012.

Florian Erhard, Ralf Zimmer. Detecting outlier peptides in quantitative high-throughput mass spectrometry data. Journal of Proteomics, in press, 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, 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.

Herbert B. Schiller, Caroline C. Friedel, Cyril Boulegue, Reinhard Fässler. Quantitative proteomics of the integrin adhesome reveals a myosin II-dependent recruitment of LIM domain proteins. EMBO Reports, 2011.

Johannes Fischer, Volker Heun. Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays. SIAM Journal on Computing, vol 40, no. 2, pp. 465-492, 2011.

Zhen Wang, Guohui Ding, Ludwig Geistlinger, Hong Li, Lei Liu, Rong Zeng, Yoshio Tateno, Yixue Li. Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. Molecular Biology and Evolution, vol 28, no. 3, pp. 1131-40, March 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, 2011.

Dintner Sebastian, Anna Staroń, Evi Berchtold, Tobias Petri, Thorsten Mascher, Susanne Gebhard. Co-evolution of ABC-transporters and two-component regulatory systems as resistance modules against antimicrobial peptides in Firmicutes bacteria. Journal of Bacteriology, 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.

Caroline C. Friedel, Jürgen Haas. Virus-host interactomes and global models of virus-infected cells. Trends in Microbiology , vol 19, no. 10, pp. 501-8, 2011.

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

Naeem H, Küffner R, Zimmer R.. MIRTFnet: analysis of miRNA regulated transcription factors. PLoS One, pp. 6(8):e22519, August 2011.

Benjamin Albrecht, Celine Scornavacca, Alberto Cenci, Daniel H. Huson. Fast computation of minimum hybridization networks. Bioinformatics, vol 28, no. 2, pp. 191-197, 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.

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.

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.

Johannes Fischer, Volker Heun. Finding Range Minima in the Middle: Approximations and Applications. Mathematics in Computer Science, vol 3, no. 1, pp. 17-30, March 2010.

Johannes Fischer, Volker Heun. Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing. Mirka Miller, Koichi Wada (eds.): Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA'08), September 13-15, 2008, Nagoya, Japan, Texts in Algorithmics, vol 12, pp. 239-252, College Publications, January 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.

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.

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, R. 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.

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.

Caroline C. Friedel. Analysis of High-throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. Ausgezeichnete Informatikdissertationen 2009, GI-Edition Lecture Notes in Informatics, 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.

Carola Marzi, Eva Albrecht, Pirro G. Hysi, Vasiliki Lagou, Melanie Waldenberger, Anke Tönjes, Inga Prokopenko, Katharina Heim, Hannah Blackburn, Janina S. Ried, Marcus E. Kleber, Massimo Mangino, Barbara Thorand, Annette Peters, Christopher J. Hammond, Harald Grallert, Bernhard O. Boehm, Peter Kovacs, Ludwig Geistlinger, Holger Prokisch, Bernhard R. Winkelmann, Tim D. Spector, H.-Erich Wichmann, Michael Stumvoll, Nicole Soranzo, Winfried März, Wolfgang Koenig, Thomas Illig, Christian Gieger. Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A. PLoS Genetics, vol 6, no. 11, pp. e1001213, November 2010.

Benjamin Albrecht, Philip Effinger, Markus Held, Michael Kaufmann. An Automatic Layout Algorithm for BPEL Processes. SoftVis '10: Proceedings of the 5th ACM Symposium on Software visualization, New York, NY, USA, ACM, October 2010.

Benjamin Albrecht, Philip Effinger, Markus Held, Michael Kaufmann, Stephan Kottler. Visualization of Complex BPEL Models. Proc. of the 17th International Symposium on Graph Drawing (GD '09), LNCS, 2010.

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

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

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.

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.

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.

Nino Shervashidze, SVN Vishwanathan, Tobias Petri, Kurt Mehlhorn, Karsten Borgwardt. Efficient Graphlet Kernels for Large Graph Comparison. 12th International Conference on Artificial Intelligence and Statistics (AISTATS), Clearwater Beach, Fl, USA, April, 16-18, 2009, Society for Artificial Intelligence and Statistics, 2009.

Simon W. Ginzinger, Murray Coles. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database. Journal of Biomolecular NMR, vol 43, no. 3, pp. 179-185, March 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.

Simon W. Ginzinger, Marko Skocibusic, Volker Heun. CheckShift Improved: Fast Chemical Shift Reference Correction with High Accuracy. Journal of Biomolecular NMR, vol 44, no. 4, pp. 207-211, August 2009.

Caroline C. Friedel, Lars Dölken. Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Molecular BioSystems, vol 5, no. 11, pp. 1271-8, Nov 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.

Luca Chiarabini. Automatic Synthesis of an Efficient Algorithm for the Similarity of Strings Problem. H. Saidi, N. Shankar (eds.): Proceedings of the 4th Workshop on Automated Formal Methods (AFM'09), Grenoble, France, June 27, 2009, pp. 23-30, 2009.

Philippe Audebaud, Luca Chiarabini. New Development in Extracting Tail Recursive Programs from Proofs. Pre-Proceedings of the 19th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR'09), Coimbra, Portugal, September 9-11, 2009, 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.

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.

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.

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.

Volker Heun. Analysis of a Modification of Gusfield's Recursive Algorithm for Reconstructing Ultrametric Trees. Information Processing Letters, vol 108, no. 4, pp. 222-225, 2008.

Johannes Fischer, Volker Heun, Horst Martin Stühler. Practical Entropy-Bounded Schemes for O(1)-Range Minimum Queries. J.A. Storer, M.W. Marcellin (eds.): Proceedings of the 2008 Data Compression Conference (DCC'08), Snowbird, Utah, U.S.A., March 25-27, 2008, pp. 272-281, IEEE Computer Society, 2008.

Johannes Fischer, Volker Heun. Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing. Mirka Miller, Koichi Wada (eds.): Local Proceedings of the 19th International Workshop on Combinatorial Algorithms (IWOCA'08), Nagoya, Japan, September 13-15, 2008, pp. 239-252, 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.

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

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.

Robert Körner, Joannis Apostolakis. Determination of Reaction Mappings and Reaction Center Information: The Imaginary Transition State Energy approach. J. Chem. Inf. Model., vol 48, no. 6, pp. 1181–1189, 2008.

Joannis Apostolakis, Oliver Sacher, Robert Körner, Johann Gasteiger. Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database. J. Chem. Inf. Model., vol 48, no. 6, pp. 1190–1198, 2008.

Jörn Marialke, Simon Tietze, Joannis Apostolakis. Similarity based docking. J. Chem. Inf. Model., vol 48, no. 1, pp. 186–196, 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.

Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Katrin Fundel, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L. Overview of BioCreative II gene normalization.. Genome Biology, vol 9, no. Supplement 2, pp. S3, Epub 2008 Sep 1 2008.

Luca Chiarabini. Extraction of Efficient Programs from Proofs: The Case of Structural Induction over Natural Numbers. A. Beckmann, C. Dimitracopoulos, B. Löwe (eds.): Local Proceedings of the Fourth Conference on Computability in Europe: Logic and Theory of Algorithms (CiE'08), Athens, Greece, June 15-20, 2008, pp. 64-76, 2008.

Luca Chiarabini. Program Development by Proof Transformation: Recent Evolutions. 15th International Conferences on Logic for Programming, Artificial Intelligence and Reasoning (LPAR'08), Doha, Qatar, November 22-27, 2008, Short Talk, 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.

Michaela Falb, Kerstin Müller, Lisa Königsmaier, Tanja Oberwinkler, Patrick Horn, vonSusanne Gronau, Orland Gonzalez, Friedhelm Pfeiffer, Erich Bornberg-Bauer, Dieter Oesterhelt. Metabolism of halophilic archaea. Extremophiles, vol 12, no. 2, pp. 177-196, 2008.

Christian Gieger, Ludwig Geistlinger, Elisabeth Altmaier, Martin Hrabé-de-Angelis, Florian Kronenberg, Thomas Meitinger, Hans-Werner Mewes, H.-Erich Wichmann, Klaus M. Weinberger, Jerzy Adamski, Thomas Illig, Karsten Suhre. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet., vol 4, no. 11, pp. e1000282, November 2008.

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.

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

Simon W. Ginzinger, Fabian Gerick, Murray Coles, Volker Heun. CheckShift: Automatic Correction of Inconsistent Chemical Shift Referencing. Journal of Biomolecular NMR, vol 39, no. 3, pp. 223-227, September 2007.

Simon W. Ginzinger, Thomas Gräupl, Volker Heun. SimShiftDB: Chemical-Shift-Based Homology Modeling. Sepp Hochreiter, Roland Wagner (eds.): Proceedings of the First International Conference on Bioinformatics Research and Development (BIRD'07), Berlin, Germany, March 12-14, Lecture Notes in Bioinformatics, vol 4414, pp. 357-370, Springer, 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.

Johannes Fischer, Volker Heun. A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array. Bo Chen, Mike Paterson, Guochuan Zhang (eds.): Proceedings of the International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE'07), Hangzhou, China, April 7-9, 2007, Lecture Notes in Computer Science, vol 4614, pp. 459-470, Springer-Verlag, 2007.

Paolo Ferragina, Johannes Fischer. Suffix Arrays on Words. Bin Ma, Kaizhong Zhang (eds.): Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), London, Ontario, July 9-11, 2007, Lecture Notes in Computer Science, vol 4580, pp. 328-339, Springer-Verlag, 2007.

Amihood Amir, Johannes Fischer, Moshe Lewenstein. Two-Dimensional Range Minimum Queries. Bin Ma, Kaizhong Zhang (eds.): Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07),, London, Ontario, July 9-11, 2007, Lecture Notes in Computer Science, vol 4580, pp. 286-294, Springer-Verlag, 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.

K.M. Borgwardt, Tobias Petri, SVN Vishwanathan, H.P. Kriegel. An efficient sampling scheme for comparison of large graphs. Mining and Learning with Graphs, no. 1, Electronic Proceedings, 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.

Andreas Steffen, Joannis Apostolakis. On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes. Chem Cent J. , vol 1, no. 29, 2007.

Stefan Zahler, Simon Tietze, Frank Totzke, Michael Kubbutat, Laurent Meijer, Angelika M. Vollmar, Joannis Apostolakis. Inverse in silico screening of 5/6/67 substituted Halogenoindirubins reveals PDK1 as target. Chem. Biol., vol 14, no. 11, pp. 1207-1214, 2007.

Andreas Steffen, Maximilian Karasz, Carolin Thiele, Thomas Lengauer, Andreas Kämper, Gerhard Wenz, Joannis Apostolakis. Combined Similarity and QSPR Virtual Screening for Guest Molecules of β-Cyclodextrin. New Journal of Chemistry, vol 31, pp. 1941 - 1949, 2007.

Markus Böhl, Simon Tietze, Andrea Sokoll, Sineej Madathil, Frank Pfennig, Joannis Apostolakis, Karim Fahmy, Herwig O. Gutzeit. Flavonoids Affect Actin Functions in Cytoplasm and Nucleus. Biophysical Journal, vol 93, no. 8, pp. 2767-2780, 2007.

Andreas Steffen, Carolin Thiele, Simon Tietze, Christian Strassnig, Andreas Kämper, Thomas Lengauer, Gerhard Wenz, Joannis Apostolakis. Improved Cyclodextrin-Based Receptors for Camptothecin by Inverse Virtual Screening. Chemistry 2007, vol 13, no. 24, pp. 6801-6809, 2007.

Simon Tietze, Joannis Apostolakis. GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes. Journal of Chemical Information and Modelling, vol 47, no. 4, pp. 1657–1672, 2007.

Simon Tietze, Jörn Marialke, Robert Körner, Joannis Apostolakis. Graph-Based Molecular Alignment (GMA). Journal of Chemical Information and Modelling, vol 47, no. 2, pp. 591-601, 2007.

Joannis Apostolakis, Jörn Marialke, Robert Körner, Simon Tietze. Predicting activated conformations of substrates in enzyme binding sites. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 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.

Z. Fan, S. Soder, S. Oehler, Katrin Fundel, Thomas Aigner. Activation of interleukin-1 signaling cascades in normal and osteoarthritic articular cartilage. Am J Pathol, vol 171, no. 3, pp. 938-946, 2007.

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

Alexander Zien, Pia M. Gebhard, Katrin Fundel, Thomas Aigner. Phenotyping of chondrocytes in vivo and in vitro using cDNA array technology. Clin Orthop Relat Res, vol 460, pp. 226-33, 2007.

Simon W. Ginzinger, Volker Heun. SimShiftDB: Chemical-Shift-Based Homology Modeling. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria., PLoS Track Talk and Poster, 2007.

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.

Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying structural similarities from NMR chemical shifts. Bioinformatics, vol 22, no. 4, pp. 460-465, 2006.

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.

Johannes Fischer, Volker Heun. Theoretical and Practical Improvements on the RMQ-Problem with Applications to LCA and LCE. Moshe Lewenstein, Gabriel Valiente (eds.): Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM'06), Barcelona, Spain, July 5-7, 2006, Lecture Notes in Computer Science, vol 4009, pp. 36-48, Springer-Verlag, 2006.

Johannes Fischer, Volker Heun, Stefan Kramer. Optimal String Mining Under Frequency Constraints. J. Fürnkranz, T. Scheffer, M. Spiliopoulou (eds.): Proceedings of the 10th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD'06), Berlin, Germany, September 18-22, 2006, Lecture Notes in Computer Science, vol 4213, pp. 139-150, Springer-Verlag, 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.

Thomas Aigner, Pia M. Gebhard‌, R. Küffner, Hongwei Zhang‌, Wayne K. Marshall. cDNA arrays in degenerative arthritis research. Future Rheumatology, vol 11, pp. 101-109, 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.

Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer. Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies. Journal of Chemical Information and Modelling, vol 46, no. 2, pp. 903–911, 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.

Martin Szugat. Web Servicing the Office. XML and Web Services Magazin, vol 2006, no. 1, pp. 150-152, 2006.

Martin Szugat. Wikimanie. Entwicklermagazin, vol 2006, no. 1, pp. 96-99, 2006.

Peter Uetz, Yu-An Dong, Christine Zeretzke, C. Atzler, Armin Baiker, B. Berger, Seesandra V. Rajagopala, M. Roupelieva, Dietlinde Rose, Even Fossum, Jürgen Haas. Herpesviral protein networks and their interaction with the human proteome. Science, vol 311, no. 5758, pp. 239-42, 2006.

Orland Gonzalez, Christoph Küper, Kirsten Jung, Prospero Naval, Eduardo Mendoza. Parameter estimation using Simulated Annealing for S-system models of biochemical networks. Bioinformatics, vol 23, no. 4, pp. 480-486, 2006.

Martin Szugat, Jan Gewehr, Cordula Lochmann. Social Software. entwickler.press, 2006.

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.

Johannes Fischer, Volker Heun, Stefan Kramer. Fast Frequent String Mining Using Suffix Arrays. Technical Report, no. TUM-I0512, Institut für Informatik der Technischen Universität München, November 2005.

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.

Johannes Fischer, Simon W. Ginzinger. A 2-Approximation Algorithm for Sorting by Prefix Reversals. Gerth Stølting Brodal, Stefano Leonardi (eds.): Proceedings of the 13th Annual European Symposium on Algorithms (ESA'05), Mallorca, Spain, October 3-6, 2005, Lecture Notes in Computer Science, vol 3669, pp. 415-425,, Springer-Verlag, 2005.

Johannes Fischer, Volker Heun, Stefan Kramer. Fast Frequent String Mining Using Suffix Arrays. Proceedings of the 5th IEEE International Conference on Data Mining (ICDM'05), Houston, TX, USA, November 27-30, 2005, pp. 609-612, IEEE Computer Society, 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.

A. Facius, C. Englbrecht, Fabian Birzele, A. Groscurth, S. Benjamin, S. Wanka, HW Mewes. PRIME: a graphical interface for integrating genomic/proteomic databases. Proteomics, vol 5, no. 1, pp. 76-80, 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.

Joannis Apostolakis, Robert Körner, Jörn Marialke. Embedded subgraph isomorphism and its applications in cheminformatics and metabolomics. 1st German Conference in Chemoinformatics, 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.

Florian Sohler, Jan Gewehr. Inference of Developmental Transcription Factor Activities in Drosophila Melanogaster (Extended abstract of oral presentation). Proceedings of the Moscow Conference on Computational Molecular Biology (MCCMB), 2005.

Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying Structural Similarities from NMR Chemical Shifts. European Conference on Computational Biology (ECCB05) , Poster, 2005.

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.

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.

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.

Jan T. Kim, Jan Gewehr, Thomas Martinetz. Binding Matrix: A Novel Approach for Binding Site Recognition. Journal of Bioinformatics and Computational Biology, vol 2, no. 2, pp. 289-307, 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.

Peter Uetz, Seesandra V. Rajagopala, Yu-An Dong, Jürgen Haas. From ORFeomes to protein interaction maps in viruses. Genome Res, vol 14, no. 10B, pp. 2029-2033, 2004.

Niklas von Öhsen, Joannis Apostolakis, Ralf Zimmer. Dopro: Automatic Protein Domain Structure Prediction using a Stochastic Model for Analyzing Homology Search Results. CAFASP 2004, pp. extended abstract, 2004.

Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer. Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics, vol 20, no. 14, pp. 2228-35, 2004.

Daniel Hanisch. 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.

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.

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. S. Istrail, P. Pevzner, R. Shamir (eds.): Computational Molecular Biology, Topics in Discrete Mathematics, vol 12, North Holland, 2003.

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. Discrete Applied Mathematics, vol 127, no. 1, pp. 163-177, 2003.

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.

D. Hofmann, Joannis Apostolakis. Crystal structure prediction with data mining. J. Mol. Struct., vol 647, no. 1, pp. 17-39, 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.

Jan Gewehr, Jan T. Kim, Thomas Martinetz. On the Correspondence between Scoring Matrices and Binding Site Sequence Distributions. ISMB 2003, pp. Poster, Brisbane, 2003.

Jan T. Kim, Jan Gewehr, Thomas Martinetz. Binding Matrix: A Novel Approach for Binding Site Recognition. Bioinformatics 2003, pp. Poster, Bioinformatics, 2003.

Thomas Martinetz, Jan Gewehr, Jan T. Kim. Statistical Learning for Detecting Protein-DNA Binding Sites. Wunsch D.C. II, M. Hasselmo, K. Venayagamoorthy (eds.): Proc. of the International Joint Conference on Neural Networks (IJCNN), pp. 2940-2945, IEEE Press, 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.

Volker Heun. Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen. 2nd edition, Vieweg Verlag, May 2003.

Werner Mewes, Dmitrij Frishman, Volker Heun, Stefan Kramer. Proceedings of the German Conference on Bioinformatics, GCB 2003 (Neuherberg and Garching, Germany, October 12-14, 2003). belleville Verlag München, 2003.

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.

Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics, vol 46, no. 1, pp. 24-33, 2002.

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.

Thomas Martinetz, Jan Gewehr, Jan T. Kim. A Statistical Learning Approach to Predicting Protein-DNA-Binding Sites. European Conference on Computational Biology (ECCB) 2002, pp. Poster, 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.

D. Hofmann, Joannis Apostolakis, Thomas Lengauer. Derivation of a scoring function for crystal structure prediction. Acta Crystallogr A., vol 57, no. Pt4, pp. 442-50, 2001.

Joannis Apostolakis, D. Hofmann, Thomas Lengauer. Using simple learning machines to derive a new potential for molecular modelling, in Rational Approaches to Drug Design. Proc. of 13th Eur. Symp. on QSAR, Prous Science, pp. 125-134, 2001.

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.

D. Hoffmann, V. Schnaible, S. Wefing, Mario Albrecht, Daniel Hanisch. Fast solution of Protein-3D-structures. Karl-Heinz Hoffmann (ed.): Coupling of Biological and Electronic Systems, Proceedings of the 2nd caesarium, pp. 59-78, Springer-Verlag, 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.