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Publications

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

2008

[77] Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Rätsch, G (2008).
KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
In: Proc. German Conference Bioinformatikcs (GCB 2008), ed. by A. Beyer and M. Schroeder, pp. 158-167, GI.

[76] Schulz-Trieglaff, O, Pfeifer, N, Gröpl, C, Kohlbacher, O, and Reinert, K (2008).
LC-MSsim - a simulation software for Liquid ChromatographyMass Spectrometry data
BMC Bioinformatics, 9:423.

[75] 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.

[74] 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.

[73] Timm, W, Scherbart, A, Böcker, S, Kohlbacher, O, and Nattkemper, TW (2008).
Peak Intensity Prediction in MALDI-TOF Mass Spectrometry: A Machine Learning Study to Support Quantitative Proteomics
BMC Bioinformatics, 9:443.

[72] Toussaint, NC, Dönnes, P, and Kohlbacher, O (2008).
A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines
PLoS Comput. Biol., 4(12):e1000246.

[71] Zhang, F, Skoda, MW, Jacobs, RM, Zorn, S, Martin, R, Martin, C, Clark, G, Weggler, S, Hildebrandt, A, Kohlbacher, O, and Schreiber, F (2008).
Reentrant Condensation of Proteins ins Solution Induced by Multivalent Counterions
Phys. Rev. Lett., 101(14):148101.

2007

[70] 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).

[69] Hildebrandt, A, Kohlbacher, O, and Lenhof, H (2007).
Modeling Protein–Protein and Protein–DNA Docking
In: Bioinformatics - From Genomes to Drugs, ed. by Thomas Lengauer. Wiley-VCH, chap. 17, pp. 601-650.

[68] 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.

[67] 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.

[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.

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.