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Publications

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

2014

[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.

2013

[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.

[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.