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Publications

Publications from the Kohlbacher lab, sorted by year and author.

2007

[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.

2006

[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.

2005

[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.

[41] Gröpl, C, Lange, E, Reinert, K, Kohlbacher, O, Sturm, M, Huber, C, Mayr, B, and Klein, C (2005).
Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples
In: Proceedings of the 1st Symposium on Computational Life Sciences (CLS 2005), ed. by M. Berthold, R. Glen, K. Diederichs, O. Kohlbacher, I. Fischer, pp. 151–161, Springer LNBI 3695.

[40] Höglund, A, Dönnes, P, Adolph, H, and Kohlbacher, O (2005).
From prediction of subcellular localization to functional classification: Discrimination of DNA-packing and other nuclear proteins
Online Journal of Bioinformatics, 6(1):51-64.

[39] Höglund, A, Dönnes, P, Blum, T, Adolph, H, and Kohlbacher, O (2005).
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization
In: Proceedings of the German Conference on Bioinformatics (GCB 2005), ed. by Andrew Torda, Stefan Kurtz, Matthias Rarey, pp. 45–59, GI.

[38] Klein, CL, Kohlbacher, O, Huber, C, and Reinert, K (2005).
Reference methods and materials in standardisation and quality assurance
FEBS J., 272(S1).

[37] Moll, A, Hildebrandt, A, Kerzmann, A, Lenhof, H, and Kohlbacher, O (2005).
BALLView - An Open Source Tool for Molecular Modeling and Visualization
In: Tagungsband zum doIT Software-Forschungstag 2005, ed. by D. Spath, K. Haasis, D. Klumpp, pp. 203–214, Stuttgart, MFG Stiftung.