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Publications

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

2013

[189] de la Garza, L, Krüger, J, Schärfe, C, Röttig, M, Aiche, S, Reinert, K, and Kohlbacher, O (2013).
From the desktop to the grid: conversion of KNIME Workflows to gUSE
In: Proc. IWSG 2013, vol. 993, pp. 9. CEUR-WS.

[188] Gifford, CA, Ziller, MJ, Gu, H, Trapnell, C, Donaghey, J, Tsankov, A, Shalek, AK, Shishkin, AA, Issner, R, Zhang, X, Fostel, JL, Holmes, L, Meldrim, J, Guttman, M, Epstein, C, Park, H, Kohlbacher, O, Rinn, J, Gnirke, A, Lander, ES, Bernstein, BE, and Meissner, A (2013).
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
Cell, 153(5):1149-1163.

[187] Kyzirakos, C, Pflueckhahn, U, Sturm, M, Schroeder, C, Bauer, P, Walter, M, Feldhahn, M, Walzer, M, Mohr, C, Szolek, A, Bonin, M, Kohlbacher, O, Ebinger, M, Handgretinger, R, Rammensee, H, and Lang, P (2013).
iVacALL: utilizing next-generation sequencing for the establishment of an individual peptide vaccination approach for paediatric acute lymphoblastic leukaemia
Bone Marrow Transplant., 48(3):S401.

[186] Nahnsen, S, Bielow, C, Reinert, K, and Kohlbacher, O (2013).
Tools for label-free peptide quantification
Mol. Cell. Prot., 12(3):549-56.

[185] Nahnsen, S, Sachsenberg, T, and Kohlbacher, O (2013).
PTMeta: Increasing Identification Rates of Modified Peptides Using Modification Pre-scanning and Meta-analysis
Proteomics, 13(6):1042-51.

[184] Novak, J, Sachsenberg, T, Hoksza, D, Skopal, T, and Kohlbacher, O (2013).
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications
J. Integrative Bioinformatics, 10(3):228.

[183] Novák, J, Sachsenberg, T, Hoksza, D, Skopal, T, and Kohlbacher, O (2013).
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools
In: 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, pp. 101–109, Springer.

[182] Perez-Riverol, Y, Hermjakob, H, Kohlbacher, O, Martens, L, Creasy, D, Cox, J, Leprevost, F, Shan, BP, Cabrera, G, Guillen, G, Padron, G, Xavier Gonzalez, L, and Besada, V (2013).
Computational Proteomics Pitfalls and Challenges: HavanaBioinfo 2012 Workshop Report
J. Proteomics, 87:134-8.

[181] Roosen-Runge, F, Heck, B, Zhang, F, Kohlbacher, O, and Schreiber, F (2013).
Interplay of pH and Binding of Multivalent Metal Ions: Charge Inversion and Reentrant Condensation in Protein Solutions
J. Phys. Chem. B, 117(18):5777-87.

[180] Schubert, B, Lund, O, and Nielsen, M (2013).
Evaluation of peptide selection approaches for epitope-based vaccine design
Tissue Antigens, 82(4):243--251.

[179] Sturm, T, Leinders-Zufall, T, Maček, B, Walzer, M, Jung, S, Pömmerl, B, Stevanović, S, Zufall, F, Overath, P, and Rammensee, H (2013).
Mouse urinary peptides provide a molecular basis for genotype discrimination by nasal sensory neurons.
Nat. Commun., 19(4):1616.

[178] Thiel, P, Röglin, L, Meissner, N, Hennig, S, Kohlbacher, O, and Ottmann, C (2013).
Virtual Screening and Experimental Validation Reveal Novel Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions
Chem. Commun., 49(76):8468-70.

[177] Walzer, M, Qi, D, Mayer, G, Uszkoreit, J, Eisenacher, M, Sachsenberg, T, Gonzalez-Galarza, FF, Fan, J, Bessant, C, Deutsch, EW, Reisinger, F, Vizcaíno, JA, Medina-Aunon, JA, Albar, JP, Kohlbacher, O, and Jones, AR (2013).
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics
Mol. Cell. Prot., 12(8):2332-40.

[176] Wanke, D, Brand, LH, Fischer, NM, Peschke, F, Kilian, J, and Berendzen, K (2013).
Implications of DNA-nanostructures by Hoogsteen-dinucleotides on transcription factor binding
In: Quantum Bio-Informatics V: From Quantum Information to Bio-Informatics, ed. by uigi Accardi, Wolfgang Freudenberg, Masanori Ohya. World Scientific, chap. 30, pp. 351-362.

[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.