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Publications

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

2012

[165] Gesing, S, Herres-Pawlis, S, Birkenheuer, G, Brinkmann, A, Grunzke, R, Kacsuk, P, Kohlbacher, O, Kozlovszky, M, Krüger, J, Müller-Pfefferkorn, R, Schäfer, P, and Steinke, T (2012).
A Science Gateway Getting Ready for Serving the International Molecular Simulation Community
Proceedings of Science, PoS(EGICF12-EMITC2)050.

[164] Herres-Pawlis, S, Birkenheuer, G, Brinkmann, A, Gesing, S, Grunzke, R, Jäkel, R, Kohlbacher, O, Krüger, J, and dos Santos Vieira, I (2012).
Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway
In: HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences , vol. 175, pp. 142-151, IOS Press. Studies in Health Technology and Informatics, PubMed ID: 22942005 .

[163] Jones, AR, Eisenacher, M, Mayer, G, Kohlbacher, O, Siepen, J, Hubbard, SJ, Selley, JN, Searle, BC, Shofstahl, J, Seymour, SL, Julian, R, Binz, P, Deutsch, EW, Hermjakob, H, Reisinger, F, Griss, J, Vizcaino, JA, Chambers, M, Pizarro, A, and Creasy, D (2012).
The mzIdentML data standard for mass spectrometry-based proteomics results
Mol. Cell. Prot., 11(7):M111.014381.

[162] Junker, J, Bielow, C, Bertsch, A, Sturm, M, Reinert, K, and Kohlbacher, O (2012).
TOPPAS: A graphical workflow editor for the analysis of high-throughput proteomics data
J. Proteome Res., 11(7):3914-20.

[161] Kenar, E, Franken, H, Rosenbaum, L, Lehmann, R, Forcisi, S, Wörmann, K, Lucio, M, König, A, Rahnenführer, J, Schmidt-Kopplin, P, Haering, H, Zell, A, and Kohlbacher, O (2012).
Mit Bioinformatik zu Biomarkern
Med. Welt, 63(5):245-50.

[160] Malisi, CU, Toussaint, NC, Kohlbacher, O, and Höcker, B (2012).
Binding pocket optimization by computational protein design
PLoS One, 7(12):e52505.

[159] Michta, E, Schad, K, Blin, K, Ort-Winklbauer, R, Röttig, M, Kohlbacher, O, Wohlleben, W, Schinko, E, and Mast, Y (2012).
The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494
Env. Microbiol. .

[158] Nahnsen, S and Kohlbacher, O (2012).
In silico design of targeted SRM-based experiments
BMC Bioinformatics, 13:S8.

[157] Röglin, L, Thiel, P, Kohlbacher, O, and Ottmann, C (2012).
Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins
Proc. Natl. Acad. Sci. USA, 109(18):E1051-3.

[156] Schlemmer, T, Grunzke, R, Gesing, S, Krüger, J, Birkenheuer, G, Müller-Pfefferkorn, R, and Kohlbacher, O (2012).
Generic User Management for Science Gateways via Virtual Organizations
In: EGI Technical Forum 2012.

[155] Trusch, M, Tillack, K, Kwiatkowski, M, Bertsch, A, Ahrends, R, Kohlbacher, O, Martin, R, Sospedra, M, and Schlüter, H (2012).
Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample—The proteome of neutrophils
J. Chromatogr. A, 1232:288-94.

[154] Wörman, K, Lucio, M, Forcisi, S, Heinzmann, SS, Kenar, E, Franken, H, Rosenbaum, L, Schmitt-Kopplin, P, Kohlbacher, O, Zell, A, Häring, H, and Lehmann, R (2012).
„Metabolomics“ in der Diabetesforschung
Der Diabetologe(1):42-48.

2011

[153] Böcker, S, Briesemeister, S, and Klau, GW (2011).
Exact Algorithms for Cluster Editing: Evaluation and Experiments
Algorithmica, 60(2):316-334.

[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.