Publications

310 entries « 6 of 7 »

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.

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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.

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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.

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Kerzmann, Andreas; Neumann, Dirk; Kohlbacher, Oliver

SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions

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

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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.

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

German Conference on Bioinformatics

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

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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.

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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.

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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.

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Dönnes, Pierre; Kohlbacher, Oliver

SVMHC: a server for prediction of MHC-binding peptides

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

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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.

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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.

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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.

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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.

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

Computational Life Sciences

Springer Lecture notes in Bioinformatics, 2005.

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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.

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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.

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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.

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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.

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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.

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Kohlbacher, Oliver; Reinert, Knut

Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen

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

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Höglund, Annette; Kohlbacher, Oliver

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

Proteome Science, 2 , pp. 3, 2004.

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

Novel formulation of nonlocal electrostatics

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

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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.

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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)

Sirava, Marite; Schäfer, Thomas; Eiglsperger, Markus; Kaufmann, Michael; Kohlbacher, Oliver; Bornberg-Bauer, Erich; Lenhof, Hans-Peter

BioMiner - modeling, analysing, and visualizing biochemical pathways and networks

Bioinformatics, 19 (10), pp. S219-230, 2002.

(Links | BibTeX)

Dönnes, Pierre; Elofsson, Arne

Prediction of MHC class I binding peptides, using SVMHC

BMC Bioinformatics, 3 (25), 2002.

(Links | BibTeX)

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

Structure prediction of protein complexes by a NMR-based protein docking algorithm

J. Biomol. NMR, 20 , pp. 15-21, 2001.

(Abstract | Links | BibTeX)

Turner, Russell J; Chaturvedi, Kabir; Edwards, Nathan J; Fasulo, Daniel; Halpern, Aaron L; Huson, Daniel H; Remington, Karin A; Schwartz, Russell; Walenz, Brian; Yooseph, Shibu; Istrail, Sorin

Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm

Proceedings of the IEEE Symposium on Parallel and Large-Data Visualization and Graphics (PVG2001), pp. 7–18, San Diego, USA,, 2001.

(BibTeX)

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

A NMR-spectra-based scoring function for protein docking

Sankoff, David; Lengauer, Thomas (Ed.): RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, pp. 169-177, ACM press, 2001.

(Links | BibTeX)

Kohlbacher, Oliver

BALL - A Framework for Rapid Application Development in Molecular Modeling

Beiträge zum Heinz-Billing-Preis 2000, pp. 13-28, Gesellschaft für wissenschaftliche Datenverarbeitung mbH, Göttingen, 2001.

(Links | BibTeX)

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

Modeling the Sugar Lectin Interaction by Computational Chemistry Relevant to Drug Design

Proc. 3rd World Meeting on Pharmaceutics, Biopharmaceutics and Pharmaceutical Technology, pp. 233, 2000.

(BibTeX)

Kohlbacher, Oliver; Lenhof, Hans-Peter

BALL - Rapid Software Prototyping in Computational Molecular Biology

Bioinformatics, 16 (9,), pp. 815–824, 2000.

(Abstract | Links | BibTeX)

Boghossian, N P; Kohlbacher, O; Lenhof, H P

Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL)

J. Exp. Algorithmics, 5 , pp. 16, 2000.

(BibTeX)

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

A Combinatorial Approach to Protein Docking with Flexible Side-Chains

Shamir, Ron; Miyano, Satoru; Istrail, Sorin; Pevzner, Pavel; Waterman, Michael (Ed.): RECOMB 2000 -- Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, pp. 15–24, ACM press, 2000.

(BibTeX)

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

A branch and cut algorithm for the optimal solution of the side-chain placement problem

Max-Planck-Institute für Informatik Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany, (MPI-I-2000-1-001), 2000.

(Links | BibTeX)

310 entries « 6 of 7 »

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