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Publications

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

2005

[37] Moll, A, Hildebrandt, A, Kerzmann, A, Lenhof, H, and Kohlbacher, O (2005).
BALLView - An Open Source Tool for Molecular Modeling and Visualization
In: Tagungsband zum doIT Software-Forschungstag 2005, ed. by D. Spath, K. Haasis, D. Klumpp, pp. 203–214, Stuttgart, MFG Stiftung.

[36] Mück, A, Nilse, L, Pilaftsis, A, and Rückl, R (2005).
Quantization and High Energy Unitarity of 5D Orbifold Theories with Brane Kinetic Terms
Phys. Rev., D71(6):066004.

[35] Nilse, L (2005).
Quantization and High Energy Unitarity in Orbifold Theories
Doktorarbeit, University of Manchester.

[34] Rausch, C, Weber, T, Kohlbacher, O, Wohlleben, W, and Huson, D (2005).
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using Transductive Support Vector Machines (TSVM)
Nucl. Acids Res., 33(18):5799-5808.

[33] Schuler, M, Dönnes, P, Nastke, M, Kohlbacher, O, Rammensee, H, and Stevanovic, S (2005).
SNEP: SNP-derived Epitope Prediction program for minor H antigens
In: Joint Annual Meeting of the German and Scandinavian Societies of Immunology, 21-24 September 2005, Kiel, Germany, ed. by Dietrich Kabelitz, pp. 361-622, Immunobiology 210(6-8).

[32] Schuler, MM, Dönnes, P, Nastke, M, Kohlbacher, O, Rammensee, H, and Stevanovic, S (2005).
SNEP: SNP-derived Epitope Prediction program for minor H antigens.
Immunogenetics, 57(11):816-820.

[31] Supper, J, Dönnes, P, and Kohlbacher, O (2005).
Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules
Springer Lecture Notes in Computer Science (LNCS), 3686:446-453.

2004

[30] Dönnes, P and Höglund, A (2004).
Predicting Protein Subcellular Localization: Past, Present, and Future
Genomics Proteomics Bioinformatics, 2(4):209–215.

[29] Dönnes, P, Höglund, A, Sturm, M, Comtesse, N, Backes, C, Meese, E, Kohlbacher, O, and Lenhof, H (2004).
Integrative analysis of cancer-related data using CAP
FASEB Journal, 18(12):1465-1467.

[28] Hildebrandt, A, Blossey, R, Rjasanow, S, Kohlbacher, O, and Lenhof, H (2004).
Novel formulation of nonlocal electrostatics
Phys. Rev. Lett., 93:108104.

[27] Höglund, A and Kohlbacher, O (2004).
From sequence to structure and back again: approaches for predicting protein-DNA binding
Proteome Science, 2:3.

[26] Istrail, S, Florea, L, Halldorsson, BV, Kohlbacher, O, Schwartz, RS, Yap, VB, Yewdell, JW, and Hoffman, SL (2004).
Comparative Immuno-Peptidomics of Humans and their Pathogens
Proc. Natl. Acad. Sci. USA, 101(36):13268.

[25] Kerzmann, A, Neumann, D, and Kohlbacher, O (2004).
High-Accuracy Prediction of Protein-Carbohydrate Interactions
Trends in Glycoscience and Glycotechnology, 16:S26.

[24] Kohlbacher, O and Reinert, K (2004).
Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen
IT - Information Technology, 46(1):31-38.

[23] Neumann, D, Lehr, C, Lenhof, H, and Kohlbacher, O (2004).
Computational modeling of the sugar–lectin interaction
Advanced Drug Delivery Reviews, 56(4):437-457.

2003

[22] Florea, L, Halldórsson, B, Kohlbacher, O, Schwartz, R, Hoffman, S, and Istrail, S (2003).
Epitope Prediction Algorithms for Peptide based Vaccine Design
In: Proceedings of the 2nd IEEE Computer Society Conference on Bioinformatics, pp. 17-26, IEEE Computer Society.

[21] Hildebrandt, A, Kohlbacher, O, Blossey, R, and Lenhof, H (2003).
Using nonlocal electrostatics for solvation free energy computations: ions and small molecules
Preprint at ArXiv.

[20] Sandelin, A, Höglund, A, Lenhard, B, and Wasserman, W (2003).
Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes
Funct Integr Genomics, 3(3):125-134.

2002

[19] Althaus, E, Kohlbacher, O, Lenhof, HP, and Müller, P (2002).
A Combinatorial Approach to Protein Docking with Flexible Side-Chains
J. Comput. Biol., 9(4):597-612.

[18] Dönnes, P and Elofsson, A (2002).
Prediction of MHC class I binding peptides, using SVMHC
BMC Bioinformatics, 3(25).

[17] Neumann, D, Kerzmann, A, and Kohlbacher, O (2002).
Modelling the sugar-lectin interaction by computer simulated docking
In: Abstracts of the 20th Interlec Meeting, ed. by Bog-Hansen, Torkhild, pp. 116, University of Copenhagen, Copenhagen, Denmark.

[16] Neumann, D, Kohlbacher, O, Lenhof, H, and Lehr, C (2002).
Protein-sugar interactions: Calculated versus experimental binding energies
Eur. J. Biochem., 269(5):1518-1524.

[15] Sirava, M, Schäfer, T, Eiglsperger, M, Kaufmann, M, Kohlbacher, O, Bornberg-Bauer, E, and Lenhof, H (2002).
BioMiner - modeling, analysing, and visualizing biochemical pathways and networks
Bioinformatics, 19(10):S219-230.

2001

[14] Kohlbacher, O (2001).
BALL - A Framework for Rapid Application Development in Molecular Modeling
In: Beiträge zum Heinz-Billing-Preis 2000, pp. 13-28, Gesellschaft für wissenschaftliche Datenverarbeitung mbH, Göttingen.

[13] Kohlbacher, O, Burchardt, A, Hildebrandt, A, Moll, A, Bayer, P, and Lenhof, H (2001).
A NMR-spectra-based scoring function for protein docking
In: RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, ed. by David Sankoff and Thomas Lengauer, pp. 169-177, ACM press.