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Publications

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

2011

[152] Bertsch, A, Gröpl, C, Reinert, K, and Kohlbacher, O (2011).
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
Methods Mol. Biol., 696:353-67.

[151] Bielow, C, Gröpl, C, Kohlbacher, O, and Reinert, K (2011).
Bioinformatics for Qualitative and Quantitative Proteomics
In: Bioinformatics for Omics Data: Methods and Protocols, ed. by Bernd Mayer. Springer, chap. 15, pp. 1-19.

[150] Birkenheuer, G, Blunk, D, Breuers, S, Brinkmann, A, dos Santos Vieira, I, Fels, G, Gesing, S, Grunzke, R, Herres-Pawlis, S, Kohlbacher, O, Krüger, J, Lang, U, Packschies, L, Müller-Pfefferkorn, R, Schäfer, P, Schmalz, H, Steinke, T, Warzecha, K, and Wewior, M (2011).
A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science
In: Journal of Cheminformatics 2011, vol. 3(Suppl 1). P14.

[149] Canzar, S, Toussaint, NC, and Klau, GW (2011).
An exact algorithm for side-chain placement in protein design
Optimization Letters:1-14.

[148] Feldhahn, M, Menzel, M, Weide, B, Bauer, P, Meckbach, D, Garbe, C, Kohlbacher, O, and Bauer, J (2011).
No evidence of viral genomes in whole-transcriptome sequencings of three melanoma metastases
Exp. Dermatol., 20(9):766-768 .

[147] Gesing, S, Grunzke, R, Balasko, A, Birkenheuer, G, Blunk, D, Breuers, S, Brinkmann, A, Fels, G, Herres-Pawlis, S, Kacsuk, P, Kozlovszky, M, Krüger, J, Packschies, L, Schäfer, P, Schuller, B, Schuster, J, Steinke, T, Szikszay Fabri, A, Wewior, M, Müller-Pfefferkorn, R, and Kohlbacher, O (2011).
Granular Security for a Science Gateway in Structural Bioinformatics
In: Proc. IWSG-Life 2011.

[146] Gesing, S, Kacsuk, P, Kozlovszky, M, Birkenheuer, G, Blunk, D, Breuers, S, Brinkmann, A, Fels, G, Grunzke, R, Herres-Pawlis, S, Krüger, J, Packschies, L, Müller-Pfefferkorn, R, Schäfer, P, Steinke, T, Szikszay Fabri, A, Warzecha, K, Wewior, M, and Kohlbacher, O (2011).
A Science Gateway for Molecular Simulations
In: EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts, pp. 94–95, ISBN 978 90 816927 1 7.

[145] Gesing, S, van Hemert, J, Kacsuk, P, and Kohlbacher, O (2011).
Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools
Concurrency and Computation: Practice and Experience, 23(3):223–234.

[144] Martens, L, Chambers, M, Sturm, M, Kessner, D, Levander, F, Shofstahl, J, Tang, WH, Römpp, A, Neumann, S, Pizarro, AD, Montecchi-Palazzi, L, Tasman, N, Coleman, M, Reisinger, F, Souda, P, Hermjakob, H, Binz, P, and Deutsch, EW (2011).
mzML – a Community Standard for Mass Spectrometry Data
Mol. Cell. Prot., 10(1):R110.000133.

[143] Nahnsen, S, Bertsch, A, Rahnenführer, J, Nordheim, A, and Kohlbacher, O (2011).
Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification
J. Proteome Res., 10(8):3332-3343.

[142] Röttig, M, Medema, M, Blin, K, Weber, T, Rausch, C, and Kohlbacher, O (2011).
NRPSpredictor2 - a webserver for predicting NRPS adenylation domain specificity
Nucl. Acids Res., 39(webserver issue):W362-W367.

[141] Schaerfe, C (2011).
A Critical Assessment of the Impact of Computational Methods on the Productivity in Pharmaceutical Research and Development
Master Thesis, University of Warwick.

[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.

2010

[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.