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


[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.


[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, 1217(19):3321-9.

[114] 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.

[113] Böcker, S, Briesemeister, S, and Klau, GW (2009).
On Optimal Comparability Editing with Applications to Molecular Diagnostics
BMC Bioinformatics, 10(Suppl 1):S61.

[112] 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.

[111] Blum, T, Briesemeister, S, and Kohlbacher, O (2009).
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
BMC Bioinformatics, 10:274.

[110] 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.

[109] Böcker, S, Briesemeister, S, Bui, QB, and Truss, A (2009).
Going Weighted: Parameterized Algorithms for Cluster Editing
Theoretical Computer Science, 410(52):5467-5480.

[108] 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.

[107] Feldhahn, M, Dönnes, P, Thiel, P, and Kohlbacher, O (2009).
FRED - A Framework for T-cell Epitope Detection
Bioinformatics, 25(20):2758-9.

[106] 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.