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


[140] Toussaint, NC, Feldhahn, M, Ziehm, M, Stevanovic, S, and Kohlbacher, O (2011).
T-Cell Epitope Prediction Based on Self-Tolerance
In: Proc. ICIW 2011.

[139] Toussaint, NC, Maman, Y, Kohlbacher, O, and Louzoun, Y (2011).
Universal peptide vaccines – optimal peptide vaccine based on viral sequence conservation
Vaccine, 29(47):8745-8753.

[138] Tung, C, Ziehm, M, Kämper, A, Kohlbacher, O, and Ho, S (2011).
POPISK: T-cell reactivity prediction using support vector machines and string kernels
BMC Bioinformatics, 12:246.

[137] Wörmann, K, Lucio, M, Forcisi, S, Schmitt-Kopplin, P, Kenar, E, Kohlbacher, O, Franken, H, Rosenbaum, L, Zell, A, Lehmann, R, and Häring, H (2011).
Verbund "BIOMARKERS" - Metabolomics im BMBF Kompetenznetz Diabetes
Diabetes, Stoffwechsel und Herz, 20(3):178-184.

[136] Zhang, G, Ansari, H, Bradley, P, Cawley, G, Hertz, T, Hu, X, Jojic, N, Kim, Y, Kohlbacher, O, Lund, O, Lundegaard, C, Magaret, C, Nielsen, M, Papadopoulos, H, Raghava, G, Tal, V, Xue, L, Yanover, C, Zhu, S, Rock, M, Crowe, JJ, Polycarpou, M, Duch, W, and Brusic, V (2011).
Machine learning competition in immunology - Prediction of HLA class I molecules
J. Immunol. Meth., 375(1-2):1-4.


[135] Albrecht, M, Kerren, A, Klein, K, Kohlbacher, O, Mutzel, P, Paul, W, Schreiber, F, and Wybrow, M (2010).
On open problems in biological network visualization
Springer, vol. 5849(256-267). Lecture Notes in Computer Science.

[134] Bertsch, A, Jung, S, Zerck, A, Pfeifer, N, Nahnsen, S, Henneges, C, Nordheim, A, and Kohlbacher, O (2010).
Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics
J. Proteome Res., 9(5):2696-704.

[133] Birkenheuer, G, Breuers, S, Brinkmann, A, Blunk, D, Fels, G, Gesing, S, Herres-Pawlis, S, Kohlbacher, O, Krüger, J, and Packschies, L (2010).
Grid-Workflows in Molecular Science
In: Lecture Notes in Informatics, pp. 177-184, GI-Edition ed. Software-Engineering 2010.

[132] Briesemeister, S, Rahnenführer, J, and Kohlbacher, O (2010).
Going from where to why - interpretable prediction of protein subcellular localization
Bioinformatics, 26(9):1232-1238.

[131] Briesemeister, S, Rahnenführer, J, and Kohlbacher, O (2010).
YLoc – an interpretable web server for predicting subcellular localization
Nucl. Acids Res., 38:W497-W502.

[130] Gehlenborg, N, O'Donoghue, SI, Baliga, NS, Goesmann, A, Hibbs, MA, Kitano, H, Kohlbacher, O, Neuweger, H, Schneider, R, Tenenbaum, D, and Gavin, A (2010).
Visualization of omics data for systems biology
Nat. Methods, 7:S56-68.

[129] Gesing, S, Marton, I, Birkenheuer, G, Schuller, B, Grunzke, R, Krüger, J, Breuers, S, Blunk, D, Fels, G, Packschies, L, Brinkmann, A, Kohlbacher, O, and Kozlovszky, M (2010).
Workflow Interoperability in a Grid Portal for Molecular Simulations
In: Proceedings of the International Worshop on Science Gateways (IWSG2010), ed. by R. Barbera, G. Andronico and G. La Rocca, pp. 44-48, Consorzio COMETA.

[128] Gesing, S, van Hemert, J, Koetsier, J, Bertsch, A, and Kohlbacher, O (2010).
TOPP goes Rapid—The OpenMS Proteomics Pipeline in a Grid-enabled Web Portal
In: 10th IEEE/ACM Internactional Conference on Cluster, Cloud, and Grid Computing (ccgrid 2010), pp. 598-599, IEEE/ACM, ACM.

[127] Henneges, C, Röttig, M, Kohlbacher, O, and Zell, A (2010).
Graphlet Data Mining of Energetical Interaction Patterns in Protein 3D Structures
In: Proceedings of the International Conference on Fuzzy Computation and 2nd International Conference on Neural Computation, pp. 190-195, SciTePress.

[126] Hildebrandt, A, Dehof, AK, Rurainski, A, Bertsch, A, Schumann, M, Toussaint, NC, Moll, A, Stöckel, D, Nickels, S, Mueller, SC, Lenhof, H, and Kohlbacher, O (2010).
BALL - Biochemical Algorithms Library 1.3
BMC Bioinformatics, 11:531.

[125] Kirchler, T, Briesemeister, S, Singer, M, Schütze, K, Keinath, M, Kohlbacher, O, Vicente-Carbajosa, J, Teige, M, Harter, K, and Chaban, C (2010).
The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors
Eur. J. Cell Biol., 89(2-3):175-183.

[124] Neumann, D and Kohlbacher, O (2010).
Structural Glycomics – Molecular Details of Protein-Carbohydrate Interactions and their Prediction
In: Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics, ed. by Martin G. Hicks and Carsten Kettner, Beilstein-Institut, Frankfurt, Germany.

[123] Röttig, M, Rausch, C, and Kohlbacher, O (2010).
Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families
PLoS Comput. Biol., 6(1):e1000636.

[122] Toussaint, NC, Widmer, C, Kohlbacher, O, and Rätsch, G (2010).
Exploiting Physico-Chemical Properties in String Kernels
BMC Bioinformatics, 11(Suppl 8):S7.

[121] Trusch, A, Ehlert, S, Bertsch, A, Kohlbacher, O, Hildebrand, D, Schlüter, H, and Tallarek, U (2010).
Improved particle-packed HPLC/MS microchips for proteomic analysis
J. Pep. Sci, 33(21):3283-91.

[120] Trusch, M, Böhlick, A, Hildebrand, D, Lichtner, B, Bertsch, A, Kohlbacher, O, Bachmann, S, and Schlüter, H (2010).
Application of displacement chromatography for the analysis of a lipid raft proteome
J. Chromatogr. B, 878(3-4):309-314.

[119] Wewior, M, Packschies, L, Blunk, D, Wickeroth, D, Warzecha, K, Herres-Pawlis, S, Gesing, S, Breuers, S, Krüger, J, Birkenheuer, G, and Lang, U (2010).
The MoSGrid Gaussian portlet -- Technologies for Implementation of Portlets for Molecular Simulations
In: Proceedings of the International Worshop on Science Gateways (IWSG2010), ed. by R. Barbera, G. Andronico and G. La Rocca, pp. 39-43, Consorzio COMETA.

[118] Widmer, C, Altun, Y, Toussaint, NC, and Rätsch, G (2010).
Inferring Latent Task Structure for Multi-Task Learning via Multiple Kernel Learning
BMC Bioinformatics, 11(Suppl 8):S5.

[117] Widmer, C, Toussaint, NC, Altun, Y, Kohlbacher, O, and Rätsch, G (2010).
Novel Machine Learning Methods for MHC Class I Binding Prediction
In: Pattern Recognition in Bioinformatics 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings, ed. by Tjeerd M.H. Dijkstra, Evgeni Tsivtsivadze, Elena Marchiori and Tom Heskes, vol. 6282, pp. 98-109, Springer. Lecture Notes in Computer Sciences.

[116] Zhang, F, Weggler, S, Ziller, MJ, Ianeselli, L, Heck, BS, Hildebrandt, A, Kohlbacher, O, Skoda, MWA, Jacobs, RMJ, and Schreiber, F (2010).
On the Universality of Protein Reentrant Condensation in Solution Induced by Multivalent Metal Ions
PROTEINS: Structure, Function, Bioinformatics, 78(16):3450–3457.