Böcker, S, Briesemeister, S, and Klau, GW (2008). Exact Algorithms for Cluster Editing: Evaluation and Experiments In: Proc. of Workshop on Experimental Algorithms (WEA 2008). Springer, pages 289–302.
Böcker, S, Briesemeister, S, Bui, QB, and Truss, A (2008). A fixed-parameter approach for Weighted Cluster Editing In: Proc. of Asia-Pacific Bioinformatics Conference (APBC 2008). Imperial College Press, pages 211–220.
Böcker, S, Briesemeister, S, Bui, QB, and Truss, A (2008). Going Weighted: Parameterized Algorithms for Cluster Editing In: Proc. of Conference on Combinatorial Optimization and Applications (COCOA 2008). To be presented.
Blum, T, and Kohlbacher, O (2008). Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks J. Comput. Biol. 15(6):565-576.
Blum, T, and Kohlbacher, O (2008). MetaRoute - fast search for relevant metabolic routes for interactive network navigation and visualization Bioinformatics((in press)).
Feldhahn, M, Thiel, P, Schuler, M, Hillen, N, Stevanovic, S, Rammensee, H, and Kohlbacher, O (2008). EpiToolKit - A web server for computational immunomics Nucl. Acids Res. (in press).
Kerzmann, A, Fuhrmann, J, Kohlbacher, O, and Neumann, D (2008). BALLDock/SLICK: A new Method for Protein-Carbohydrate Docking J. Chem. Inf. Model.:(in press).
Peifer, C, Urich, R, Schattel, V, Abdaleh, M, Röttig, M, Kohlbacher, O, and Laufer, S (2008). Implications for selectivity of 3,4-diarylquinolinones as p38aMAP kinase inhibitors Bioorg. Med. Chem. Lett. 18(4):1431-1435.
Raub, S, Steffen, A, Kämper, A, and Marian, CM (2008). AIScore - Chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes J. Chem. Inf. Model.:ASAP Article.
Reinert, K, Conrad, T, and Kohlbacher, O (2008). Bioinformatics Support for Mass Spectrometric Quality Control In: Proteomics Sample Preparation, edited by Jörg von Hagen. Wiley-VCH, Weinheim, chapter 13.1, pages 423-447.
Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, Rätsch, G, and Rätsch, G (2008). KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences In: Proc. German Conference Bioinformatikcs (GCB 2008). GI.
Seebeck, B, Reulecke, I, Kämper, A, and Rarey, M (2008). Modeling of metal interaction geometries for protein-ligand docking Proteins: Struct., Funct., Bioinf. 71(3):1237-1254.
Sturm, M, Bertsch, A, Gröpl, C, Hildebrandt, A, Hussong, R, Lange, E, Pfeifer, N, Schulz-Trieglaff, O, Zerck, A, Reinert, K, and Kohlbacher, O (2008). OpenMS - An open-source software framework for mass spectrometry BMC Bioinformatics 9:163.
Blum, T, and Kohlbacher, O (2007). Finding relevant biotransformation routes in weighted metabolic networks using atom mapping rules In: . Proceedings of the German Conference on Bioinformatics (GCB 2007).
Hildebrandt, A, Kohlbacher, O, and Lenhof, H (2007). Modeling Protein-Protein and Protein-DNA Interactions In: Bioinformatics - From Genomes to Drugs, edited by Thomas Lengauer. Wiley-VCH, chapter 17, pages 601-650.
Hildebrandt, A, Rjasanow, S, Blossey, R, Kohlbacher, O, and Lenhof, H (2007). Electrostatic potentials of proteins in water: a structured continuum approach Bioinformatics 23(2):e99-e100.
Kohlbacher, O, Reinert, K, Gröpl, C, Lange, E, Pfeifer, N, Schulz-Trieglaff, O, and Sturm, M (2007). TOPP - The OpenMS Proteomics Pipeline Bioinformatics 23(2):e191-e197.
Küntzer, J, Backes, C, Blum, T, Gerasch, A, Kaufmann, M, Kohlbacher, O, and Lenhof, H (2007). BNDB - The Biochemical Network Database BMC Bioinformatics 8:367.
Mitschke, J, Fuss, J, Blum, T, Höglund, A, Reski, R, Kohlbacher, O, and Rensing, S (2007). Prediction of dual protein targeting to plant organelles In: . Proceedings of the German Conference on Bioinformatics (GCB 2007).
Pfeifer, N, Leinenbach, A, Huber, CG, and Kohlbacher, O (2007). Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics BMC Bioinformatics 8:468.
Shatkay, H, Höglund, A, Brady, S, Blum, T, Dönnes, P, and Kohlbacher, O (2007). SherLoc : High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data. Bioinformatics 23(11):1410-1417.
Steffen, A, Karasz, M, Thiele, C, Lengauer, T, Kämper, A, Wenz, G, and Apostolakis, J (2007). Combined similarity and QSPR virtual screening for guest molecules of beta-cyclodextrin New J. Chem. 31(11):1941-1949.
Steffen, A, Thiele, C, Tietze, S, Strassnig, C, Kämper, A, Lengauer, T, Wenz, G, and Apostolakis, J (2007). Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening Chem. Eur. J. 13(24):6801-6809.
Sturm, M, Quinten, S, Huber, CG, and Kohlbacher, O (2007). A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data Nucl. Acids Res. 35(12):4195-4202.
Baldes, C, König, P, Neumann, D, Lenhof, H, Kohlbacher, O, and Lehr, C (2006). Development of a fluorescence-based assay for screening of modulators of human Organic Anion Transporter 1B3 (OATP1B3) Eur J Pharm Biopharm. 62(1):39--43.
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