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Publications

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

2008

[90] 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), vol. 5, pp. 211-220, Imperial College Press. Series on Advances in Bioinformatics and Computational Biology.

[89] 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.

[88] Blum, T and Kohlbacher, O (2008).
MetaRoute - fast search for relevant metabolic routes for interactive network navigation and visualization
Bioinformatics, 24(18):2108-2109.

[87] Borgatti, S, Kobourov, S, Kohlbacher, O, and Mutzel, P (2008).
08191 Abstracts Collection – Graph Drawing with Applications to Bioinformatics and Social Sciences
In: Graph Drawing with Applications to Bioinformatics and Social Sciences, ed. by Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel, Dagstuhl, Germany, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany.

[86] Borgatti, S, Kobourov, S, Kohlbacher, O, and Mutzel, P (2008).
08191 Executive Summary – Graph Drawing with Applications to Bioinformatics and Social Sciences
In: Graph Drawing with Applications to Bioinformatics and Social Sciences, ed. by Stephen P. Borgatti and Stephen Kobourov and Oliver Kohlbacher and Petra Mutzel, Dagstuhl, Germany, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany.

[85] Feldhahn, M, Thiel, P, Schuler, M, Hillen, N, Stevanovic, S, Rammensee, H, and Kohlbacher, O (2008).
EpiToolKit - A web server for computational immunomics
Nucleic Acids Res., 36:W519-22.

[84] Keller, AC, Backes, C, Al-Awadhi, M, Gerasch, A, Küntzer, J, Kohlbacher, O, Kaufmann, M, and Lenhof, H (2008).
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments
BMC Bioinformatics, 9:552.

[83] Kerzmann, A, Fuhrmann, J, Kohlbacher, O, and Neumann, D (2008).
BALLDock/SLICK: A new Method for Protein-Carbohydrate Docking
J. Chem. Inf. Model., 48(8):1616-1625.

[82] 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.

[81] Pfeifer, N and Kohlbacher, O (2008).
Multiple Instance Learning Allows MHC Class II Epitope Predictions across Alleles
In: Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI 2008), Lecture Note in Bioinformatics vol. 5251, ed. by K. A. Crandall and J. Lagergren, pp. 210-221, Springer.

[80] 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., 48(7):1492–-1510.

[79] Reinert, K, Conrad, T, and Kohlbacher, O (2008).
Bioinformatics Support for Mass Spectrometric Quality Control
In: Proteomics Sample Preparation, ed. by Jörg von Hagen. Wiley-VCH, Weinheim, chap. 13.1, pp. 423-447.

[78] Reinert, K, Huber, C, Marcus, K, Linial, M, and Kohlbacher, O (2008).
08101 Executive Summary and Abstracts Collection - Computational Proteomics
In: Computational Proteomics, ed. by Christian Huber and Oliver Kohlbacher and Michal Linial and Katrin Marcus and Knut Reinert, Dagstuhl, Germany, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany.

[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.