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Publications

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

2013

[175] Weisser, H, Nahnsen, S, Grossmann, J, Nilse, L, Quandt, A, Brauer, H, Sturm, M, Kenar, E, Kohlbacher, O, Aebersold, R, and Malmström, L (2013).
An automated pipeline for high-throughput label-free quantitative proteomics
J. Proteome Res., 12(4):1824-1644.

[174] Ziller, MJ, Gu, H, Müller, F, Donaghey, J, Kohlbacher, O, Bernstein, BE, Gnirke, A, and Meissner, A (2013).
Charting a dynamic DNA methylation landscape of the human genome
Nature, 500:477–481.

2012

[173] Ahrends, R, Lichtner, B, Buck, F, Hildebrand, D, Kotasinska, M, Kohlbacher, O, Kwiatkowski, M, Wagner, M, Trusch, M, and Schlüter, H (2012).
Comparison of displacement versus gradient mode for separation of a complex protein mixture by anion-exchange chromatography
J. Chromatogr. B, 901:34-40.

[172] 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, Steinke, T, Warzecha, K, and Wewior, M (2012).
MoSGrid: Efficient Data Management and a Standardized Data Exchange Format for Molecular Simulations in a Grid Environment
Journal of Cheminformatics, 4(Suppl 1):P21.

[171] Birkenheuer, G, Blunk, D, Breuers, S, Brinkmann, A, Fels, G, Gesing, S, Grunzke, R, Herres-Pawlis, S, Kohlbacher, O, Krüger, J, Lang, U, Packschies, L, Müller-Pfefferkorn, R, Schäfer, P, Schuster, J, Steinke, T, Warzecha, K, and Wewior, M (2012).
MoSGrid: Progress of Workflow driven Chemical Simulations
In: Proc. of Grid Workflow Workshop 2011, Cologne, Germany, vol. 826, CEUR Workshop Proceedings.

[170] Briesemeister, S, Rahnenführer, J, and Kohlbacher, O (2012).
No longer confidential: Estimating the Confidence of Individual Regression Predictions
PLoS One, 7(11):e48723.

[169] Feldhahn, M, Dönne, P, Schubert, B, Schilbach, K, Rammensee, H, and Kohlbacher, O (2012).
miHA-Match: computational detection of tissue-specific minor histocompatibility antigens
J. Immunol. Meth., 386(1-2):94-100.

[168] Gesing, S, Glatard, T, Krüger, J, Delgado Olabarriaga, S, Solomonides, T, Silverstein, J, Montagnat, J, Gaignard, A, and Krefting, D (2012).
HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences
IOS Press, vol. 175. Studies in Health Technology and Informatics.

[167] Gesing, S, Grunzke, R, Krüger, J, Birkenheuer, G, Wewior, M, Schäfer, P, Schuller, B, Schuster, J, Herres-Pawlis, S, Breuers, S, Balasko, A, Kozlovszky, M, Szikszay Fabri, A, Packschies, L, Kacsuk, P, Blunk, D, Steinke, T, Brinkmann, A, Fels, G, Müller-Pfefferkorn, R, Jäkel, R, and Kohlbacher, O (2012).
A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics
Journal of Grid Computing, 10(4):769-790..

[166] Gesing, S, Herres-Pawlis, S, Birkenheuer, G, Brinkmann, A, Grunzke, R, Kacsuk, P, Kohlbacher, O, Kozlovszky, M, Krüger, J, Müller-Pfe fferkorn, R, Schäfer, P, and Steinke, T (2012).
The MoSGrid Community – From National to International Scale
In: EGI Community Forum 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.