Publications

298 entries « 5 of 6 »

Althaus, Ernst; Klau, Gunnar W; Kohlbacher, Oliver; Lenhof, Hans-Peter; Reinert, Knut

Integer Linear Programming in Computational Biology

Efficient Algorithms, pp. 199-218, Springer, 2009.

(Abstract | Links | BibTeX)

Briesemeister, Sebastian; Blum, Torsten; Brady, Scott; Lam, Yin; Kohlbacher, Oliver; Shatkay, Hagit

SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins

J. Proteome Res., 8 (11), pp. 5363–5366, 2009.

(Abstract | Links | BibTeX)

Ahrends, Robert; Lichtner, Björn; Bertsch, Andreas; Kohlbacher, Oliver; Trusch, Maria; Schlüter, Hartmut

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction

J. Chromatogr. A, 1217 (19), pp. 3321-9, 2009.

(Abstract | Links | BibTeX)

Toussaint, Nora; Kohlbacher, Oliver; Rätsch, Gunnar

Exploiting Physico-Chemical Properties in String-Kernels

MLCB 2009 (accepted), 2009.

(BibTeX)

Kohlbacher, Oliver; Reinert, Knut

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

Hubbard, Simon J; Jones, Andrew R (Ed.): Proteome Bioinformatics, 604 , pp. 201-11, Humana Press, 2009.

(Abstract | Links | BibTeX)

Peifer, Christian; Urich, Robert; Schattel, Verena; Abdaleh, Mohammed; Röttig, Marc; Kohlbacher, Oliver; Laufer, Stefan

Implications for selectivity of 3,4-diarylquinolinones as p38aMAP kinase inhibitors

Bioorg. Med. Chem. Lett., 18 (4), pp. 1431-1435, 2008.

(Links | BibTeX)

Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut; Kohlbacher, Oliver

OpenMS - An open-source software framework for mass spectrometry

BMC Bioinformatics, 9 , pp. 163, 2008.

(Links | BibTeX)

Feldhahn, Magdalena; Thiel, Philipp; Schuler, Mathias; Hillen, Nina; Stevanovic, Stefan; Rammensee, Hans-Georg; Kohlbacher, Oliver

EpiToolKit - A web server for computational immunomics

Nucleic Acids Res., 36 , pp. W519-22, 2008.

(Abstract | Links | BibTeX)

Blum, Torsten; Kohlbacher, Oliver

Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks

J. Comput. Biol., 15 (6), pp. 565-576, 2008.

(Links | BibTeX)

Kerzmann, Andreas; Fuhrmann, Jan; Kohlbacher, Oliver; Neumann, Dirk

BALLDock/SLICK: A new Method for Protein-Carbohydrate Docking

J. Chem. Inf. Model., 48 (8), pp. 1616-1625, 2008.

(Links | BibTeX)

Schultheiss, Sebastian J; Busch, Wolfgang; Lohmann, Jan U; Kohlbacher, Oliver; Rätsch, Gunnar

KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences

Beyer, A; Schroeder, M (Ed.): Proc. German Conference Bioinformatikcs (GCB 2008), pp. 158-167, GI, 2008.

(Links | BibTeX)

Borgatti, Stephen; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra

08191 Abstracts Collection -- Graph Drawing with Applications to Bioinformatics and Social Sciences

Borgatti, Stephen P; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra (Ed.): Graph Drawing with Applications to Bioinformatics and Social Sciences, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Borgatti, Stephen; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra

08191 Executive Summary -- Graph Drawing with Applications to Bioinformatics and Social Sciences

Borgatti, Stephen P; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra (Ed.): Graph Drawing with Applications to Bioinformatics and Social Sciences, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Albrecht, Mario; Estrella-Balderrama, Alejandro; Geyer, Markus; Gutwenger, Carsten; Klein, Karsten; Kohlbacher, Oliver; Schulz, Michael

08191 Working Group Summary -- Visually Comparing a Set of Graphs

Borgatti, Stephen P; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra (Ed.): Graph Drawing with Applications to Bioinformatics and Social Sciences, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Pfeifer, Nico; Kohlbacher, Oliver

Multiple Instance Learning Allows MHC Class II Epitope Predictions across Alleles

Crandall, K A; Lagergren, J (Ed.): Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI 2008), Lecture Note in Bioinformatics vol. 5251, pp. 210-221, Springer, 2008.

(Links | BibTeX)

Zhang, Fajun; Skoda, Maximilian W A; Jacobs, Robert M J; Zorn, S; Martin, R A; Martin, C M; Clark, G F; Weggler, Sophie; Hildebrandt, Andreas; Kohlbacher, Oliver; Schreiber, Frank

Reentrant Condensation of Proteins ins Solution Induced by Multivalent Counterions

Phys. Rev. Lett., 101 (14), pp. 148101, 2008.

(Links | BibTeX)

Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut

LC-MSsim - a simulation software for Liquid ChromatographyMass Spectrometry data

BMC Bioinformatics, 9 , pp. 423, 2008.

(Abstract | Links | BibTeX)

Toussaint, Nora C; Dönnes, Pierre; Kohlbacher, Oliver

A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines

PLoS Comput. Biol., 4 (12), pp. e1000246, 2008.

(Links | BibTeX)

Keller, Andreas C; Backes, Christina; Al-Awadhi, Maher; Gerasch, Andreas; Küntzer, Jan; Kohlbacher, Oliver; Kaufmann, Michael; Lenhof, Hans-Peter

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

BMC Bioinformatics, 9 , pp. 552, 2008.

(Links | BibTeX)

Reinert, Knut; Huber, Christian; Marcus, Kathrin; Linial, Michal; Kohlbacher, Oliver

08101 Executive Summary and Abstracts Collection - Computational Proteomics

Huber, Christian; Kohlbacher, Oliver; Linial, Michal; Marcus, Katrin; Reinert, Knut (Ed.): Computational Proteomics, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Timm, Wiebke; Scherbart, Alexandra; Böcker, Sebastian; Kohlbacher, Oliver; Nattkemper, Tim W

Peak Intensity Prediction in MALDI-TOF Mass Spectrometry: A Machine Learning Study to Support Quantitative Proteomics

BMC Bioinformatics, 9 , pp. 443, 2008.

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Reinert, Knut; Conrad, Tim; Kohlbacher, Oliver

Bioinformatics Support for Mass Spectrometric Quality Control

von Hagen, Jörg (Ed.): Proteomics Sample Preparation, Chapter 13.1, pp. 423-447, Wiley-VCH, Weinheim, 2008, (ISBN 978-3-527-31796-7).

(Links | BibTeX)

Blum, Torsten; Kohlbacher, Oliver

MetaRoute - fast search for relevant metabolic routes for interactive network navigation and visualization

Bioinformatics, 24 (18), pp. 2108-2109, 2008.

(Links | BibTeX)

Böcker, Sebastian; Briesemeister, Sebastian; Klau, Gunnar W

Exact Algorithms for Cluster Editing: Evaluation and Experiments

Proc. of Workshop on Experimental Algorithms (WEA 2008), pp. 289–302, Springer, 2008.

(Abstract | Links | BibTeX)

Böcker, Sebastian; Briesemeister, Sebastian; Bui, Quang BaoAnh; Truss, Anke

Going Weighted: Parameterized Algorithms for Cluster Editing

Proc. of Conference on Combinatorial Optimization and Applications (COCOA 2008), pp. 1-12, Springer, 2008.

(Abstract | Links | BibTeX)

Böcker, Sebastian; Briesemeister, Sebastian; Bui, Quang BaoAnh; Truss, Anke

A fixed-parameter approach for Weighted Cluster Editing

Proc. of Asia-Pacific Bioinformatics Conference (APBC 2008), pp. 211-220, Imperial College Press, 2008.

(Abstract | BibTeX)

Seebeck, Birte; Reulecke, Ingo; Kämper, Andreas; Rarey, Matthias

Modeling of metal interaction geometries for protein-ligand docking

Proteins: Struct., Funct., Bioinf., 71 (3), pp. 1237-1254, 2008.

(Abstract | Links | BibTeX)

Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M

AIScore - Chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes

J. Chem. Inf. Model., 48 (7), pp. 1492–-1510, 2008.

(Abstract | Links | BibTeX)

Hildebrandt, Andreas; Kohlbacher, Oliver; Lenhof, Hans-Peter

Modeling Protein–Protein and Protein–DNA Docking

Lengauer, Thomas (Ed.): Bioinformatics - From Genomes to Drugs, Chapter 17, pp. 601-650, Wiley-VCH, 2007.

(Links | BibTeX)

Hildebrandt, Andreas; Rjasanow, Sergej; Blossey, Ralf; Kohlbacher, Oliver; Lenhof, Hans-Peter

Electrostatic potentials of proteins in water: a structured continuum approach

Bioinformatics, 23 (2), pp. e99-e100, 2007.

(Links | BibTeX)

Kohlbacher, Oliver; Reinert, Knut; Gröpl, Clemens; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Sturm, Marc

TOPP - The OpenMS Proteomics Pipeline

Bioinformatics, 23 (2), pp. e191-e197, 2007.

(Abstract | Links | BibTeX)

Shatkay, Hagit; Höglund, Annette; Brady, Scott; Blum, Torsten; Dönnes, Pierre; Kohlbacher, Oliver

SherLoc : High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data.

Bioinformatics, 23 (11), pp. 1410-1417, 2007.

(Abstract | Links | BibTeX)

Sturm, Marc; Quinten, Sascha; Huber, Christian G; Kohlbacher, Oliver

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

Nucl. Acids Res., 35 (12), pp. 4195-4202, 2007.

(Abstract | Links | BibTeX)

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

BNDB - The Biochemical Network Database

BMC Bioinformatics, 8 , pp. 367, 2007.

(Abstract | Links | BibTeX)

Pfeifer, Nico; Leinenbach, Andreas; Huber, Christian G; Kohlbacher, Oliver

Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics

BMC Bioinformatics, 8 , pp. 468, 2007.

(Abstract | Links | BibTeX)

Blum, Torsten; Kohlbacher, Oliver

Finding relevant biotransformation routes in weighted metabolic networks using atom mapping rules

Proceedings of the German Conference on Bioinformatics (GCB 2007), 2007.

(BibTeX)

Mitschke, Jan; Fuss, Janina; Blum, Torsten; Höglund, Annette; Reski, Ralf; Kohlbacher, Oliver; Rensing, Stefan

Prediction of dual protein targeting to plant organelles

Proceedings of the German Conference on Bioinformatics (GCB 2007), 2007.

(BibTeX)

Steffen, Andreas; Thiele, Carolin; Tietze, Simon; Strassnig, Christian; Kämper, Andreas; Lengauer, Thomas; Wenz, Gerhard; Apostolakis, Joannis

Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening

Chem. Eur. J., 13 (24), pp. 6801-6809, 2007.

(Abstract | Links | BibTeX)

Steffen, Andreas; Karasz, Maximilian; Thiele, Carolin; Lengauer, Thomas; Kämper, Andreas; Wenz, Gerhard; Apostolakis, Joannis

Combined similarity and QSPR virtual screening for guest molecules of beta-cyclodextrin

New J. Chem., 31 (11), pp. 1941-1949, 2007.

(Abstract | Links | BibTeX)

Neumann, Dirk; Kohlbacher, Oliver; Merkwirth, Christian; Lengauer, Thomas

A fully computational model for predicting percutaneous drug absorption

J. Chem. Inf. Model., 46 (1), pp. 424–429, 2006.

(Links | BibTeX)

Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver

BALLView: A tool for research and education in molecular modeling

Bioinformatics, 22 (3), pp. 365–366, 2006.

(Links | BibTeX)

Baldes, Christiane; König, Petra; Neumann, Dirk; Lenhof, Hans-Peter; Kohlbacher, Oliver; Lehr, Claus-Michael

Development of a fluorescence-based assay for screening of modulators of human Organic Anion Transporter 1B3 (OATP1B3)

Eur J Pharm Biopharm., 62 (1), pp. 39–43, 2006.

(Links | BibTeX)

Lange, Eva; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; Hildebrandt, Andreas

High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques

Proceedings of the Pacific Symposium on Biocomputing (PSB 2006), 2006.

(Links | BibTeX)

Mayr, Bettina; Kohlbacher, Oliver; Reinert, Knut; Sturm, Marc; Gröpl, Clemens; Lange, Eva; Klein, Christoph; Huber, Christian G

Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms

J. Proteome Res., 5 , pp. 414–421, 2006.

(Abstract | Links | BibTeX)

Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver

BALLView: An object-oriented molecular visualization and modeling framework

J. Comput.-Aided Mol. Des., 19 (11), pp. 791, 2006.

(Links | BibTeX)

Sturm, Marc; Quinten, Sascha; Huber, Christian G; Kohlbacher, Oliver

A machine learning approach for prediction of DNA and peptide retention times

Huber, Christian; Kohlbacher, Oliver; Reinert, Knut (Ed.): Proceedings of the Dagstuhl Seminar on Computational Proteomics 2005, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany, 2006.

(Links | BibTeX)

Kerzmann, Andreas; Neumann, Dirk; Kohlbacher, Oliver

SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions

J. Chem. Inf. Model., 46 , pp. 1635-1642, 2006.

(Links | BibTeX)

Küntzer, Jan; Blum, Torsten; Gerasch, Andreas; Backes, Christina; Hildebrandt, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

BN++ - A Biological Information System

Proceedings of the 3rd International Workshop Integrative Bioinformatics, Rothamsted Research, 2006.

(Links | BibTeX)

Huson, Daniel H; Kohlbacher, Oliver; Lupas, Andrei; Nieselt, Kay; Zell, Andreas

German Conference on Bioinformatics

Gesellschaft für Informatik e.V., Bonner Köllen Verlag, 2006.

(Links | BibTeX)

Kohlbacher, Oliver; Quinten, Sascha; Sturm, Marc; Mayr, Bettina; Huber, Christian

Structure-Activity Relationships in Chromatography: Retention Prediction of Oligonucleotides with Support Vector Regression

Angew. Chemie Int. Ed., 45 (42), pp. 7009-7012, 2006.

(Abstract | Links | BibTeX)

298 entries « 5 of 6 »

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