Oliver Kohlbacher

Sven Nahnsen, Oliver Kohlbacher: In silico design of targeted SRM-based experiments. BMC Bioinformatics 13(S-16): S8 (2012)

Sandra Gesing, Richard Grunzke, Jens Krüger, Georg Birkenheuer, Martin Wewior, Patrick Schäfer, Bernd Schuller, Johannes Schuster, Sonja Herres-Pawlis, Sebastian Breuers, Ákos Balaskó, Miklos Kozlovszky, Anna Szikszay Fabri, Lars Packschies, Péter Kacsuk, Dirk Blunk, Thomas Steinke, André Brinkmann, Gregor Fels, Ralph Müller-Pfefferkorn, René Jäkel, Oliver Kohlbacher: A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics. J. Grid Comput. 10(4): 769-790 (2012)

Magdalena Feldhahn, Karin Schilbach, Pierre Dönnes, Hans-Georg Rammensee, Benjamin Schubert, Oliver Kohlbacher: miHA-match: computational detection of tissue-specific minor histocompatibility antigens. BCB 2012: 625-626

Chun-Wei Tung, Matthias Ziehm, Andreas Kamper, Oliver Kohlbacher, Shinn-Ying Ho: POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics 12: 446 (2011)

Sandra Gesing, Jano I. van Hemert, Péter Kacsuk, Oliver Kohlbacher: Special Issue: Portals for life sciences - Providing intuitive access to bioinformatic tools. Concurrency and Computation: Practice and Experience 23(3): 223-234 (2011)

Marc Röttig, Marnix H. Medema, Kai Blin, Tilmann Weber, Christian Rausch, Oliver Kohlbacher: NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Research 39(Web-Server-Issue): 362-367 (2011)

Nora C. Toussaint, Magdalena Feldhahn, Matthias Ziehm, Stefan Stevanovic, Oliver Kohlbacher: T-cell epitope prediction based on self-tolerance. BCB 2011: 584-588

Sebastian Briesemeister, Jörg Rahnenführer, Oliver Kohlbacher: Going from where to why - interpretable prediction of protein subcellular localization. Bioinformatics 26(9): 1232-1238 (2010)

Andreas Hildebrandt, Anna Katharina Dehof, Alexander Rurainski, Andreas Bertsch, Marcel Schumann, Nora C. Toussaint, Andreas Moll, Daniel Stöckel, Stefan Nickels, Sabine C. Mueller, Hans-Peter Lenhof, Oliver Kohlbacher: BALL - biochemical algorithms library 1.3. BMC Bioinformatics 11: 531 (2010)

Nora C. Toussaint, Christian Widmer, Oliver Kohlbacher, Gunnar Rätsch: Exploiting physico-chemical properties in string kernels. BMC Bioinformatics 11(S-8): S7 (2010)

Sebastian Briesemeister, Jörg Rahnenführer, Oliver Kohlbacher: YLoc - an interpretable web server for predicting subcellular localization. Nucleic Acids Research 38(Web-Server-Issue): 497-502 (2010)

Marc Röttig, Christian Rausch, Oliver Kohlbacher: Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families. PLoS Computational Biology 6(1) (2010)

Sandra Gesing, Jano I. van Hemert, Jos Koetsier, Andreas Bertsch, Oliver Kohlbacher: TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal. CCGRID 2010: 598-599

Carsten Henneges, Marc Röttig, Oliver Kohlbacher, Andreas Zell: Graphlet Data Mining of Energetical Interaction Patterns in Protein 3D Structures. IJCCI (ICFC-ICNC) 2010: 190-195

Christian Widmer, Nora C. Toussaint, Yasemin Altun, Oliver Kohlbacher, Gunnar Rätsch: Novel Machine Learning Methods for MHC Class I Binding Prediction. PRIB 2010: 98-109

Georg Birkenheuer, Sebastian Breuers, André Brinkmann, Dirk Blunk, Gregor Fels, Sandra Gesing, Sonja Herres-Pawlis, Oliver Kohlbacher, Jens Krüger, Lars Packschies: Grid-Workflows in Molecular Science. Software Engineering (Workshops) 2010: 177-184

Sebastian J. Schultheiß, Wolfgang Busch, Jan Lohmann, Oliver Kohlbacher, Gunnar Rätsch: KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics 25(16): 2126-2133 (2009)

Magdalena Feldhahn, Pierre Dönnes, Philipp Thiel, Oliver Kohlbacher: FRED - a framework for T-cell epitope detection. Bioinformatics 25(20): 2758-2759 (2009)

Andreas Keller, Christina Backes, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof: A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics 25(21): 2787-2794 (2009)

Sebastian J. Schultheiß, Wolfgang Busch, Jan Lohmann, Oliver Kohlbacher, Gunnar Rätsch: KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. BMC Bioinformatics 10(S-13): 0 (2009)

Torsten Blum, Sebastian Briesemeister, Oliver Kohlbacher: MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics 10: 274 (2009)

Nora C. Toussaint, Oliver Kohlbacher: OptiTope - a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Research 37(Web-Server-Issue): 617-622 (2009)

Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert: Integer Linear Programming in Computational Biology. Efficient Algorithms 2009: 199-218

Mario Albrecht, Andreas Kerren, Karsten Klein, Oliver Kohlbacher, Petra Mutzel, Wolfgang Paul, Falk Schreiber, Michael Wybrow: On Open Problems in Biological Network Visualization. Graph Drawing 2009: 256-267

Torsten Blum, Oliver Kohlbacher: MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 24(18): 2108-2109 (2008)

Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof: GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics 9 (2008)

Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert: LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics 9 (2008)

Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher: OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics 9 (2008)

Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, Tim W. Nattkemper: Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinformatics 9 (2008)

Torsten Blum, Oliver Kohlbacher: Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks. Journal of Computational Biology 15(6): 565-576 (2008)

Magdalena Feldhahn, Philipp Thiel, Mathias M. Schuler, Nina Hillen, Stefan Stevanovic, Hans-Georg Rammensee, Oliver Kohlbacher: EpiToolKit - a web server for computational immunomics. Nucleic Acids Research 36(Web-Server-Issue): 519-522 (2008)

Nora C. Toussaint, Pierre Dönnes, Oliver Kohlbacher: A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines. PLoS Computational Biology 4(12) (2008)

Sebastian J. Schultheiß, Wolfgang Busch, Jan Lohmann, Oliver Kohlbacher, Gunnar Rätsch: KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences. German Conference on Bioinformatics 2008: 158-167

Nico Pfeifer, Oliver Kohlbacher: Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles. WABI 2008: 210-221

Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof: Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics 23(2): 99-103 (2007)

Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm: TOPP - the OpenMS proteomics pipeline. Bioinformatics 23(2): 191-197 (2007)

Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, Oliver Kohlbacher: SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 23(11): 1410-1417 (2007)

Jan Küntzer, Christina Backes, Torsten Blum, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof: BNDB - The Biochemical Network Database. BMC Bioinformatics 8 (2007)

Nico Pfeifer, Andreas Leinenbach, Christian G. Huber, Oliver Kohlbacher: Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics. BMC Bioinformatics 8 (2007)

Torsten Blum, Oliver Kohlbacher: Finding Relevant Biotransformation Routes in Weighted Metabolic Networks. German Conference on Bioinformatics 2007: 30-44

Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. Bioinformatics 22(3): 365-366 (2006)

Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, Oliver Kohlbacher: MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics 22(10): 1158-1165 (2006)

Dirk Neumann, Oliver Kohlbacher, Christian Merkwirth, Thomas Lengauer: A Fully Computational Model for Predicting Percutaneous Drug Absorption. Journal of Chemical Information and Modeling 46(1): 424-429 (2006)

Andreas Kerzmann, Dirk Neumann, Oliver Kohlbacher: SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions. Journal of Chemical Information and Modeling 46(4): 1635-1642 (2006)

Jan Küntzer, Torsten Blum, Andreas Gerasch, Christina Backes, Andreas Hildebrandt, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof: BN++ - A Biological Information System. J. Integrative Bioinformatics 3(2) (2006)

Pierre Dönnes, Oliver Kohlbacher: SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Research 34(Web-Server-Issue): 194-197 (2006)

Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay: Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data . Pacific Symposium on Biocomputing 2006: 16-27

Eva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt: High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. Pacific Symposium on Biocomputing 2006: 243-254

Christian G. Huber, Oliver Kohlbacher, Knut Reinert (Eds.): Computational Proteomics, 20.-25. November 2005. Dagstuhl Seminar Proceedings 05471, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2006

Daniel H. Huson, Oliver Kohlbacher, Andrei N. Lupas, Kay Nieselt, Andreas Zell (Eds.): German Conference on Bioinformatics GCB 2006, 19.09. 2006 - 22.09. 2006 in Tübingen, Germany. LNI 83, GI 2006, isbn 978-3-88579-177-5

Clemens Gröpl, Eva Lange, Knut Reinert, Oliver Kohlbacher, Marc Sturm, Christian G. Huber, Bettina M. Mayr, Christoph L. Klein: Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. CompLife 2005: 151-162

Nathanaël Delmotte, Bettina M. Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph L. Klein, Christian G. Huber: Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. Computational Proteomics 2005

Christian G. Huber, Oliver Kohlbacher, Knut Reinert: 05471 Executive Summary - Computational Proteomics. Computational Proteomics 2005

Christian G. Huber, Oliver Kohlbacher, Knut Reinert: 05471 Abstract Collection - Computational Proteomics. Computational Proteomics 2005

Eva Lange, Clemens Gröpl, Oliver Kohlbacher, Andreas Hildebrandt: High-accuracy peak picking of proteomics data. Computational Proteomics 2005

Marc Sturm, Sascha Quinten, Christian G. Huber, Oliver Kohlbacher: A machine learning approach for prediction of DNA and peptide retention times. Computational Proteomics 2005

Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, Oliver Kohlbacher: Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations. German Conference on Bioinformatics 2005: 45-59

Jochen Supper, Pierre Dönnes, Oliver Kohlbacher: Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules. ICAPR (1) 2005: 446-453

Michael R. Berthold, Robert C. Glen, Kay Diederichs, Oliver Kohlbacher, Ingrid Fischer (Eds.): Computational Life Sciences, First International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005, Proceedings. Lecture Notes in Computer Science 3695, Springer 2005, isbn 3-540-29104-0

Oliver Kohlbacher, Knut Reinert: Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges). it - Information Technology 46(1): 31-38 (2004)

Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail: Epitope Prediction Algorithms for Peptide based Vaccine Design. CSB 2003: 17-26

Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller: A Combinatorial Approach to Protein Docking with Flexible Side Chains. Journal of Computational Biology 9(4): 597-612 (2002)

Marite Sirava, T. Schäfer, Markus Eiglsperger, Michael Kaufmann, Oliver Kohlbacher, Erich Bornberg-Bauer, Hans-Peter Lenhof: BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks. ECCB 2002: 219-230

Russell J. Turner, Kabir Chaturvedi, Nathan Edwards, Daniel P. Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail: Visualization challenges for a new cyberpharmaceutical computing paradigm. IEEE Symposium on Parallel and Large-Data Visualization and Graphics 2001: 7-18

Oliver Kohlbacher, Andreas Burchardt, Andreas Moll, Andreas Hildebrandt, Peter Bayer, Hans-Peter Lenhof: A NMR-spectra-based scoring function for protein docking. RECOMB 2001: 184-192

Oliver Kohlbacher, Hans-Peter Lenhof: BALL-rapid software prototyping in computational molecular biology. Bioinformatics 16(9): 815-824 (2000)

Nicolas Boghossian, Oliver Kohlbacher, Hans-Peter Lenhof: Rapid Software Prototyping in Molecular Modeling Using the Biochemical Algorithms Library (BALL). ACM Journal of Experimental Algorithmics 5: 16 (2000)

Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller: A combinatorial approach to protein docking with flexible side-chains. RECOMB 2000: 15-24

Oliver Kohlbacher, Hans-Peter Lenhof: Rapid Software Prototyping in Computational Molecular Biology. German Conference on Bioinformatics 1999: 81-92

Nicolas Boghossian, Oliver Kohlbacher, Hans-Peter Lenhof: BALL: Biochemical Algorithms Library. Algorithm Engineering 1999: 331-345