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


[206] Gerasch, A, Kaufmann, M, and Kohlbacher, O (2014).
Rebuilding KEGG Maps - An integrative approach for visual analytics of metabolic networks
In: Pacific Visualization Symposium (PacificVis), 2014 IEEE, pp. 97-104, IEEE.

[205] Griss, J, Jones, AR, Sachsenberg, T, Walzer, M, Gatto, L, Hartler, J, Thallinger, GG, Salek, RM, Steinbeck, C, Neuhauser, N, Cox, J, Neumann, S, Fan, J, Reisinger, F, Xu, Q, Bandeira, N, Xenarios, I, Kohlbacher, O, Vizcaino, JA, and Hermjakob, H (2014).
The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience
Mol. Cell. Prot.:mcp.O113.036681.

[204] Hopf, TA, Schärfe, CPI, Rodrigues, JP, Green, AG, Kohlbacher, O, Sander, C, Bonvin, AM, and Marks, DS (2014).
Sequence co-evolution gives 3D contacts and structures of protein complexes

[203] Jordan, E, Roosen-Runge, F, Leibfarth, S, Zhang, F, Sztucki, M, Hildebrandt, A, Kohlbacher, O, and Schreiber, F (2014).
Competing Salt Effects on Phase Behavior of Protein Solutions: Tailoring of Protein Interaction by the Binding of Multivalent Ions and Charge Screening
J. Phys. Chem. B, 118(38):11365-74.

[202] Kenar, E, Franken, H, Forcisi, S, Wörmann, K, Häring, H, Lehmann, R, Schmitt-Kopplin, P, Zell, A, and Kohlbacher, O (2014).
Automated Label-Free Quantification of Metabolites from LC-MS Data
Mol. Cell. Prot., 13(1):348-59.

[201] Kohlbacher, O, Schreiber, F, and Ward, MO (2014).
Multivariate Networks in the Life Sciences
In: Multivariate Network Visualization 2013, ed. by Andreas Kerren et al.. Springer, chap. 4, pp. 61-73.

[200] Kramer, K, Sachsenberg, T, Beckmann, BM, Qamar, S, Boon, K, Hentze, MW, Kohlbacher, O, and Urlaub, H (2014).
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
Nat. Methods, 11(10):1064-70.

[199] Krüger, J, Grunzke, R, Gesing, S, Breuers, S, Brinkmann, A, de la Garza, L, Kohlbacher, O, Kruse, M, Nagel, W, Packschies, L, Müller-Pfefferkorn, R, Schärfe, C, Steinke, T, Schlemmer, T, Warzecha, K, Zink, A, and Herres-Pawlis, S (2014).
The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations
J. Chem. Theor. Comput., 10(6):2232-2245.

[198] Krüger, J, Grunzke, R, Herres-Pawlies, S, de la Garza, L, Kohlbacher, O, Nagel, WE, and Gesing, S (2014).
Performance Studies on Distributed Virtual Screening
Biomed Res Int, 2014:624024.

[197] Menzel, M, Meckbach, D, Weide, B, Toussaint, NC, Schilbach, K, Noor, S, Eigentler, T, Ikenberg, K, Busch, C, Qunitanilla-Martinez, L, Göke, A, Göke, F, Handgretinger, R, Ottmann, C, Bastian, B, Garbe, C, Röcken, M, Perner, S, Kohlbacher, O, and Bauer, J (2014).
In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival
Pigment Cell Melanoma Res., 23(3):E45.

[196] Roberts, JC, Yang, J, Kohlbacher, O, Ward, MO, and Zhou, MX (2014).
Novel Visual Metaphors for Multivariate Networks
In: Multivariate Network Visualization 2013, ed. by Andreas Kerren et al.. Springer, chap. 7, pp. 127-147.

[195] Römer, M, Backert, L, Eichner, J, and Zell, A (2014).
ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
International Journal of Molecular Sciences, 15(10):19037–19055.

[194] Szolek, A, Schubert, B, Mohr, C, Sturm, M, Feldhahn, M, and Kohlbacher, O (2014).
OptiType: precision HLA typing from next-generation sequencing data
Bioinformatics, 30(23):3310-6.

[193] Thiel, P, Sach-Peltason, L, Ottmann, C, and Kohlbacher, O (2014).
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces
J. Chem. Inf. Model., 54(9):2395-401.

[192] Wagner, R, Li, J, Kenar, E, Kohlbacher, O, Machicao, F, Häring, H, Fritsche, A, Xu, G, and Lehmann, R (2014).
Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146
Sci. Rep., 4:5296.

[191] Walzer, M, Pernas, LE, Nasso, S, Bittremieux, W, Nahnsen, S, Kelchtermans, P, Pichler, P, van den Toorn, HW, Staes, A, Vandenbussche, J, Mazanek, M, Taus, T, Scheltema, RA, Kelstrup, CD, Gatto, L, van Breukelen, B, Aiche, S, Valkenborg, D, Laukens, K, Lilley, KS, Olsen, JV, Heck, AJ, Mechtler, K, Aebersold, R, Gevaert, K, Vizcaino, JA, Hermjakob, H, Kohlbacher, O, and Martens, L (2014).
qcML: an exchange format for quality control metrics from mass spectrometry experiments
Mol. Cell. Prot., 13(8):1905-13.


[190] Brand, L, Fischer, N, Harter, K, Kohlbacher, O, and Wanke, D (2013).
Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays
Nucl. Acids Res., 41(21):9764-78.

[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.