Publications

325 entries « 6 of 7 »

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)

Peifer, Christian; Krasowski, Agata; Hämmerle, Nina; Kohlbacher, Oliver; Dannhardt, Gerd; Totzke, Frank; Schächtele, Christoph; Laufer, Stefan

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), pp. 7549-7553, 2006.

(Links | BibTeX)

Höglund, Annette; Blum, Torsten; Brady, Scott; Dönnes, Pierre; Miguel, John San; Rocheford, Matthew; Kohlbacher, Oliver; Shatkay, Hagit

Significantly improved prediction of subcellular localization by integrating text and protein sequence data

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

(Links | BibTeX)

Höglund, Annette; Dönnes, Pierre; Blum, Torsten; Adolph, Hans-Werner; Kohlbacher, Oliver

MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition

Bioinformatics, 22 (10), pp. 1158-65, 2006.

(Links | BibTeX)

Dönnes, Pierre; Kohlbacher, Oliver

SVMHC: a server for prediction of MHC-binding peptides

Nucleic Acids Res., 34 , pp. W194-W197, 2006.

(Links | BibTeX)

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

OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics

Huber, Christian G; Kohlbacher, Oliver; Reinert, Knut (Ed.): Computational Proteomics, Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, Germany, 2006.

(Links | BibTeX)

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

Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples

Glen, Diederichs Kohlbacher Fischer Berthold K O I M R (Ed.): Proceedings of the 1st Symposium on Computational Life Sciences (CLS 2005), pp. 151–161, Springer LNBI 3695, 2005.

(Links | BibTeX)

Höglund, Annette; Dönnes, Pierre; Blum, Torsten; Adolph, Hans-Werner; Kohlbacher, Oliver

Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization

Kurtz, Matthias Rarey Andrew Torda Stefan (Ed.): Proceedings of the German Conference on Bioinformatics (GCB 2005), pp. 45–59, GI, 2005.

(Links | BibTeX)

Klein, Christoph L; Kohlbacher, Oliver; Huber, Christian; Reinert, Knut

Reference methods and materials in standardisation and quality assurance

FEBS J., 272 (S1), 2005, (in press).

(BibTeX)

Rausch, Christian; Weber, Tilmann; Kohlbacher, Oliver; Wohlleben, Wolfgang; Huson, Daniel

Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using Transductive Support Vector Machines (TSVM)

Nucl. Acids Res., 33 (18), pp. 5799-5808, 2005.

(Links | BibTeX)

Berthold, Michael; Glen, Robert; Diederichs, Kay; Kohlbacher, Oliver; Fischer, Ingrid

Computational Life Sciences

Springer Lecture notes in Bioinformatics, 2005.

(Links | BibTeX)

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

BALLView - An Open Source Tool for Molecular Modeling and Visualization

Haasis, Klumpp Spath D D K (Ed.): Tagungsband zum doIT Software-Forschungstag 2005, pp. 203–214, MFG Stiftung, Stuttgart, 2005.

(BibTeX)

Höglund, A; Dönnes, P; Adolph, HW; Kohlbacher, O

From prediction of subcellular localization to functional classification: Discrimination of DNA-packing and other nuclear proteins

Online Journal of Bioinformatics, 6 (1), pp. 51-64, 2005.

(Links | BibTeX)

Supper, Jochen; Dönnes, Pierre; Kohlbacher, Oliver

Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules

Springer Lecture Notes in Computer Science (LNCS), 3686 , pp. 446-453, 2005.

(Links | BibTeX)

Dönnes, Pierre; Kohlbacher, Oliver

Integrated modelling of the major events in the MHC class I antigen processing pathway

Protein Sci., 14 (8), pp. 2132-2140, 2005.

(Links | BibTeX)

Schuler, Mathias M; Dönnes, Pierre; Nastke, Maria-Dorothea; Kohlbacher, Oliver; Rammensee, Hans-Georg; Stevanovic, Stefan

SNEP: SNP-derived Epitope Prediction program for minor H antigens.

Immunogenetics, 57 (11), pp. 816-820, 2005.

(Links | BibTeX)

Schuler, Mathias; Dönnes, Pierre; Nastke, Maria; Kohlbacher, Oliver; Rammensee, H-G; Stevanovic, Stefan

SNEP: SNP-derived Epitope Prediction program for minor H antigens

Kabelitz, Dietrich (Ed.): Joint Annual Meeting of the German and Scandinavian Societies of Immunology, 21-24 September 2005, Kiel, Germany, pp. 361-622, Immunobiology 210(6-8), 2005.

(BibTeX)

Neumann, Dirk; Lehr, Claus-Michael; Lenhof, Hans-Peter; Kohlbacher, Oliver

Computational modeling of the sugar–lectin interaction

Advanced Drug Delivery Reviews, 56 (4), pp. 437-457, 2004.

(Links | BibTeX)

Kohlbacher, Oliver; Reinert, Knut

Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen

IT - Information Technology, 46 (1), pp. 31-38, 2004, (article in German).

(Links | BibTeX)

Höglund, Annette; Kohlbacher, Oliver

From sequence to structure and back again: approaches for predicting protein-DNA binding

Proteome Science, 2 , pp. 3, 2004.

(Links | BibTeX)

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

Novel formulation of nonlocal electrostatics

Phys. Rev. Lett., 93 , pp. 108104, 2004.

(Links | BibTeX)

Istrail, Sorin; Florea, Liliana; Halldorsson, Bjarni V; Kohlbacher, Oliver; Schwartz, Russell S; Yap, Von Bing; Yewdell, Jonathan W; Hoffman, Stephen L

Comparative Immuno-Peptidomics of Humans and their Pathogens

Proc. Natl. Acad. Sci. USA, 101 (36), pp. 13268, 2004.

(Links | BibTeX)

Dönnes, Pierre; Höglund, Annette; Sturm, Marc; Comtesse, Nicole; Backes, Christina; Meese, Eckart; Kohlbacher, Oliver; Lenhof, Hans-Peter

Integrative analysis of cancer-related data using CAP

FASEB Journal, 18 (12), pp. 1465-1467, 2004.

(Links | BibTeX)

Dönnes, Pierre; Höglund, Annette

Predicting Protein Subcellular Localization: Past, Present, and Future

Genomics Proteomics Bioinformatics, 2 (4), pp. 209–215, 2004.

(Abstract | Links | BibTeX)

Kerzmann, Andreas; Neumann, Dirk; Kohlbacher, Oliver

High-Accuracy Prediction of Protein-Carbohydrate Interactions

Trends in Glycoscience and Glycotechnology, 16 , pp. S26, 2004.

(BibTeX)

Florea, Liliana; Halldórsson, Bjarni; Kohlbacher, Oliver; Schwartz, Russell; Hoffman, Stephen; Istrail, Sorin

Epitope Prediction Algorithms for Peptide based Vaccine Design

Proceedings of the 2nd IEEE Computer Society Conference on Bioinformatics, pp. 17-26, IEEE Computer Society, 2003, (PMID: 16826643).

(Links | BibTeX)

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

Using nonlocal electrostatics for solvation free energy computations: ions and small molecules

2003.

(Links | BibTeX)

Sandelin, Albin; Höglund, Annette; Lenhard, Boris; Wasserman, Wyeth

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes

Funct Integr Genomics, 3 (3), pp. 125-134, 2003.

(BibTeX)

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans Peter; Müller, Peter

A Combinatorial Approach to Protein Docking with Flexible Side-Chains

J. Comput. Biol., 9 (4), pp. 597-612, 2002.

(Abstract | Links | BibTeX)

Neumann, Dirk; Kohlbacher, Oliver; Lenhof, Hans-Peter; Lehr, Claus-Michael

Protein-sugar interactions: Calculated versus experimental binding energies

Eur. J. Biochem., 269 (5), pp. 1518-1524, 2002.

(Links | BibTeX)

Neumann, Dirk; Kerzmann, Andreas; Kohlbacher, Oliver

Modelling the sugar-lectin interaction by computer simulated docking

Abstracts of the 20th Interlec Meeting, pp. 116, University of Copenhagen, Copenhagen, Denmark, 2002.

(BibTeX)

325 entries « 6 of 7 »

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