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Publications from the Kohlbacher lab, sorted by year and author.
[66] 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.
[65] 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).
[64] 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.
[63] 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.
[62] 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.
[61] 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.
[60] 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.
[59] 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.
[58] Dönnes, P and Kohlbacher, O (2006). SVMHC: a server for prediction of MHC-binding peptides Nucleic Acids Res., 34:W194-W197.
[57] Huson, DH, Kohlbacher, O, Lupas, A, Nieselt, K, and Zell, A (2006). German Conference on Bioinformatics Gesellschaft für Informatik e.V., Bonner Köllen Verlag, vol. P-83.
[56] Höglund, A, Blum, T, Brady, S, Dönnes, P, Miguel, JS, Rocheford, M, Kohlbacher, O, and Shatkay, H (2006). Significantly improved prediction of subcellular localization by integrating text and protein sequence data In: Proceedings of the Pacific Symposium on Biocomputing (PSB 2006), PSB.
[55] Höglund, A, Dönnes, P, Blum, T, Adolph, H, and Kohlbacher, O (2006). MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition Bioinformatics, 22(10):1158-65.
[54] Kerzmann, A, Neumann, D, and Kohlbacher, O (2006). SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions J. Chem. Inf. Model., 46:1635-1642.
[53] Kohlbacher, O, Quinten, S, Sturm, M, Mayr, B, and Huber, C (2006). Structure-Activity Relationships in Chromatography: Retention Prediction of Oligonucleotides with Support Vector Regression Angew. Chemie Int. Ed., 45(42):7009-7012.
[52] Küntzer, J, Blum, T, Gerasch, A, Backes, C, Hildebrandt, A, Kaufmann, M, Kohlbacher, O, and Lenhof, H (2006). BN++ - A Biological Information System In: Proceedings of the 3rd International Workshop Integrative Bioinformatics, Rothamsted Research.
[51] Lange, E, Gröpl, C, Reinert, K, Kohlbacher, O, and Hildebrandt, A (2006). High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques In: Proceedings of the Pacific Symposium on Biocomputing (PSB 2006).
[50] Mayr, B, Kohlbacher, O, Reinert, K, Sturm, M, Gröpl, C, Lange, E, Klein, C, and Huber, CG (2006). Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms J. Proteome Res., 5:414–421.
[49] Moll, A, Hildebrandt, A, Lenhof, H, and Kohlbacher, O (2006). BALLView: An object-oriented molecular visualization and modeling framework J. Comput.-Aided Mol. Des., 19(11):791.
[48] Moll, A, Hildebrandt, A, Lenhof, H, and Kohlbacher, O (2006). BALLView: A tool for research and education in molecular modeling Bioinformatics, 22(3):365–366.
[47] Neumann, D, Kohlbacher, O, Merkwirth, C, and Lengauer, T (2006). A fully computational model for predicting percutaneous drug absorption J. Chem. Inf. Model., 46(1):424–429.
[46] Peifer, C, Krasowski, A, Hämmerle, N, Kohlbacher, O, Dannhardt, G, Totzke, F, Schächtele, C, and Laufer, S (2006). Profile and Molecular Modeling of 3-(Indole-3-yl)-4-(3,4,5-trimethoxyphenyl)-1 H-pyrrole-2,5-dione (1) as a Highly Selective VEGF-R2/3 Inhibitor J. Med. Chem., 49(25):7549-7553.
[45] Reinert, K, Kohlbacher, O, Gröpl, C, Lange, E, Schulz-Trieglaff, O, Sturm, M, and Pfeifer, N (2006). OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics In: Computational Proteomics, ed. by Christian G. Huber and Oliver Kohlbacher and Knut Reinert, Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, Germany.
[44] Sturm, M, Quinten, S, Huber, CG, and Kohlbacher, O (2006). A machine learning approach for prediction of DNA and peptide retention times In: Proceedings of the Dagstuhl Seminar on Computational Proteomics 2005, ed. by Christian Huber and Oliver Kohlbacher and Knut Reinert, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany.
[43] Berthold, M, Glen, R, Diederichs, K, Kohlbacher, O, and Fischer, I (2005). Computational Life Sciences Springer Lecture notes in Bioinformatics, vol. 3695.
[42] Dönnes, P and Kohlbacher, O (2005). Integrated modelling of the major events in the MHC class I antigen processing pathway Protein Sci., 14(8):2132-2140.
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