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Publications from the Kohlbacher lab, sorted by year and author.
[116] Kohlbacher, O and Reinert, K (2010). OpenMS and TOPP: Open Source Software for LC-MS Data Analysis In: Proteome Bioinformatics, ed. by Simon J. Hubbard and Andrew R. Jones, vol. 604, chap. 14, Humana Press. Methods in Molecular Biology.
[115] Ahrends, R, Lichtner, B, Bertsch, A, Kohlbacher, O, Trusch, M, and Schlüter, H (2009). Application of displacement chromatography for the proteome analysis of a human plasma protein fraction J. Chromatogr. A, [epub ahead of print].
[114] Albrecht, M, Kerren, A, Klein, K, Kohlbacher, O, Mutzel, P, Paul, W, Schreiber, F, and Wybrow, M (2009). On open problems in biological network visualization Springer. Lecture Notes in Computer Science.
[113] Althaus, E, Klau, GW, Kohlbacher, O, Lenhof, H, and Reinert, K (2009). Integer Linear Programming in Computational Biology In: Efficient Algorithms, vol. 5760, pp. 199-218, Springer. Lecture Notes in Computer Science.
[112] Böcker, S, Briesemeister, S, and Klau, GW (2009). On Optimal Comparability Editing with Applications to Molecular Diagnostics BMC Bioinformatics, 10(Suppl 1):S61.
[111] Böcker, S, Briesemeister, S, and Klau, GW (2009). Exact Algorithms for Cluster Editing: Evaluation and Experiments Algorithmica, (published online).
[110] Bertsch, A, Leinenbach, A, Pervukhin, A, Lubeck, M, Hartmer, R, Baessmann, C, Elnakady, YA, Müller, R, Böcker, S, Huber, CG, and Kohlbacher, O (2009). De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation Electrophoresis, 30(21):3736-3747.
[109] Blum, T, Briesemeister, S, and Kohlbacher, O (2009). MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction BMC Bioinformatics, 10:274.
[108] Briesemeister, S, Blum, T, Brady, S, Lam, Y, Kohlbacher, O, and Shatkay, H (2009). SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins J. Proteome Res., 8(11):5363–5366.
[107] Böcker, S, Briesemeister, S, Bui, QB, and Truss, A (2009). Going Weighted: Parameterized Algorithms for Cluster Editing Theoretical Computer Science, 410(52):5467-5480.
[106] Dräger, A, Kronfeld, M, Ziller, MJ, Supper, J, Planatscher, H, Magnus, JB, Oldiges, M, Kohlbacher, O, and Zell, A (2009). Modeling Metabolic Networks in C. glutamicum: A Comparison of Rate Laws in Combination with Various Parameter Optimization Strategies BMC Systems Biology, 3:5.
[105] Feldhahn, M, Dönnes, P, Thiel, P, and Kohlbacher, O (2009). FRED - A Framework for T-cell Epitope Detection Bioinformatics, 25(20):2758-9.
[104] Keller, A, Backes, C, Gerasch, A, Kaufmann, M, Kohlbacher, O, and Lenhof, H (2009). A novel algorithm for detecting differentially regulated paths based on Gene Set Enrichment Analysis Bioinformatics, 25(21):2787-94.
[103] Malisi, C, Kohlbacher, O, and Höcker, B (2009). Automated scaffold selection for enzyme design PROTEINS: Structure, Function, and Bioinformatics, 77(1):74-83.
[102] Mitschke, J, Fuss, J, Blum, T, Höglund, A, Reski, R, Kohlbacher, O, and Rensing, S (2009). Prediction of dual protein targeting to plant organelles New Phytologist, 183(1):224-236.
[101] Nahnsen, S, Nordheim, A, and Kohlbacher, O (2009). A geometric matching approach improves throughput and accurary in DIGE based proteomics In: Proceedings of the sixth International Workshop on Computational Systems Biology (WCSB 2009), pp. 123-126, Tampere International Center for Signal Processing, WCSB 2009. #48.
[100] Pfeifer, N, Leinenbach, A, Huber, CG, and Kohlbacher, O (2009). Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach J. Proteome Res., 8(8):4109-15.
[99] Schneeberger, K, Hagmann, J, Ossowski, S, Warthmann, N, Gesing, S, Kohlbacher, O, and Weigel, D (2009). Simultaneous alignment of short reads against multiple genomes Genome Biology, 10(9):R98.
[98] Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Rätsch, G (2009). KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences Bioinformatics, 25(16):2126-33.
[97] Sturm, M and Kohlbacher, O (2009). TOPPView: An Open-Source Viewer for Mass Spectrometry Data J. Proteome Res., 8(7):3760-3.
[96] Toussaint, N, Kohlbacher, O, and Rätsch, G (2009). Exploiting Physico-Chemical Properties in String-Kernels In: MLCB 2009 (accepted).
[95] Toussaint, NC and Kohlbacher, O (2009). OptiTope - A Web Server for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines Nucl. Acids Res., 37:W617-22.
[94] Toussaint, NC and Kohlbacher, O (2009). Towards in silico design of epitope-based vaccines Expert Opinion on Drug Discovery, 4(10):1047-1060.
[93] Albrecht, M, Estrella-Balderrama, A, Geyer, M, Gutwenger, C, Klein, K, Kohlbacher, O, and Schulz, M (2008). 08191 Working Group Summary – Visually Comparing a Set of Graphs 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.
[92] Böcker, S, Briesemeister, S, and Klau, GW (2008). Exact Algorithms for Cluster Editing: Evaluation and Experiments In: Proc. of Workshop on Experimental Algorithms (WEA 2008), vol. 5038, pp. 289–302, Springer. Lect. Notes Comput. Sc..
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