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Publications

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

2016

[252] Gatto, L, Hansen, K, Hoopmann, M, Hermjakob, H, Kohlbacher, O, and Beyer, A (2016).
Testing and validation of computational methods for mass spectrometry
J. Proteome Res., 15(3):809-14.

[251] Griss, J, Perez-Riverol, Y, Lewis, S, Tabb, DL, Dianes, JA, del-Toro, N, Rurik, M, Walzer, MM, Kohlbacher, O, Hermjakob, H, Wang, R, and Vizcaíno, JA (2016).
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
Nat. Methods, 13(8):651-656.

[250] Hong, HS, Koch, SD, Scheel, B, Gnad-Vogt, U, Schröder, A, Kallen, K, Wiegand, V, Backert, L, Kohlbacher, O, Hoerr, I, Fotin-Mleczek, M, and Billingsley, JM (2016).
Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy
Oncoimmunol., 5(12):e1249560..

[249] Junker, J, Sachsenberg, T, Chernev, A, Aicheler, F, Urlaub, H, and Kohlbacher, O (2016).
LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer
J. Proteome Res., 15(9):3441-8..

[248] Kohlbacher, O, Vitek, O, and Weintraub, ST (2016).
Challenges in Large-Scale Computational Mass Spectrometry and Multiomics
J. Proteome Res., 15(3):681-2.

[247] Krüger, J and Kohlbacher, O (2016).
Containerization and wrapping of a mass spectra prediction workflow
Preprint.

[246] Krüger, J, Thiel, P, Merelli, I, Grunzke, R, and Gesing, S (2016).
Portals and Web-based Resources for Virtual Screening.
Curr Drug Targets.

[245] Löffler, M, Chandra, AP, Laske, K, Schroeder, C, Bonzheim, I, Hilke, FJ, Kowalewski, DJ, Trautwein, N, Schuster, H, Gründer, M, Walzer, M, Mohr, C, Nguyen, H, Riess, O, Bauer, P, Nahnsen, S, Königsrainer, A, Nadalina, S, Zieker, D, Glatzle, J, Thiel, K, Clasen, S, Bösmüller, H, Fend, F, Kohlbacher, O, Gouttefangeas, C, Stevanovic, S, and Rammensee, H (2016).
Personalized peptide vaccine induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient
J. Hepatol., 65(4):849-55.

[244] Mohr, C, Friedrich, A, Wojnar, D, Kenar, E, Polatkan, AC, Codrea, MC, Czemmel, S, Kohlbacher, O, and Nahnsen, S (2016).
qPortal – A Science Gateway for Biomedical Applications
Proc. Int. Workshop Science Gateways (IWSG 2016).

[243] Müller, SC, Backes, C, Gress, A, Baumgarten, N, Kalinina, OV, Moll, A, Kohlbacher, O, Meese, E, and Keller, A (2016).
BALL-SNPgp – from genetic variants towards computational diagnostics
Bioinformatics.

[242] Nicoludis, JM, Vogt, BE, Green, AG, Schärfe, CP, Marks, DS, and Gaudet, R (2016).
Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4
eLife, 5:e18449.

[241] Perez-Riverol, Y, Gatto, L, Wang, R, Sachsenberg, T, Uszkoreit, J, Leprevost, F, Fufezan, C, Ternent, T, Eglen, SJ, Katz, DS, Pollard, TJ, Konovalov, A, Flight, RM, Blin, K, and Vizcaino, JA (2016).
Ten Simple Rules for Taking Advantage of git and GitHub
bioRxiv.

[240] Ranninger, C, Schmidt, LE, Rurik, M, Limonciel, A, Jennings, P, Kohlbacher, O, and Huber, CG (2016).
Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry
Anal. Chim. Acta, 930:13-22.

[239] Röst, HL, Sachsenberg, T, Aiche, S, Bielow, C, Weisser, H, Aicheler, F, Andreotti, S, Ehrlich, H, Gutenbrunner, P, Kenar, E, Liang, X, Nahnsen, S, Nilse, L, Pfeuffer, J, Rosenberger, G, Rurik, M, Schmitt, U, Veit, J, Walzer, M, Wojnar, D, Wolski, WE, Schilling, O, Choudhary, JS, Malmström, L, Aebersold, R, Reinert, K, and Kohlbacher, O (2016).
OpenMS: A flexible open-source software platform for mass spectrometry data analysis
Nat. Methods, 13(9):741-748.

[238] Schneider, L, Stöckel, D, Kehl, T, Gerasch, A, Ludwig, N, Leidinger, P, Huwer, H, Tenzer, S, Kohlbacher, O, Hildebrandt, A, Kaufmann, M, Gessler, M, Keller, A, Meese, E, Graf, N, and Lenhof, H (2016).
DrugTargetInspector: An assistance tool for patient treatment stratification
Int. J. Cancer, 138(7):1765-76.

[237] Schubert, B and Kohlbacher, O (2016).
Designing string-of-beads vaccines with optimal spacers
Genome Med., 8(1):9.

[236] Schubert, B, Walzer, M, Brachvogel, H, Szolek, A, Mohr, C, and Kohlbacher, O (2016).
FRED 2 – An Immunoinformatics Framework for Python
Bioinformatics, 32(13):2044-6.

[235] Stickel, J, Kowalewski, D, Walz, S, Backert, L, Schuster, H, Kohlbacher, O, Weisel, K, Rittig, S, Kanz, L, Salih, H, Rammensee, H, and Stevanovic, S (2016).
Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini
Blood Cancer J., 6:e411.

2015

[234] Aiche, S, Sachsenberg, T, Kenar, E, Walzer, M, Wiswedel, B, Kristl, T, Boyles, M, Duschl, A, Huber, C, Berthold, M, Reinert, K, and Kohlbacher, O (2015).
Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry
Proteomics, 15(8):1443-7.

[233] Aicheler, F, Li, J, Lehmann, R, Xu, G, and Kohlbacher, O (2015).
Retention Time Prediction Improves Identification in Non-Targeted Lipidomics Approaches
Anal. Chem., 87(15):7698-704.

[232] Backert, L and Kohlbacher, O (2015).
Immunoinformatics and epitope prediction in the age of genomic medicine
Genome Med., 7(1):119.

[231] Bier, D, Thiel, P, Briels, J, and Ottmann, C (2015).
Stabilization of Protein-Protein Interactions in chemical biology and drug discovery.
Prog Biophys Mol Biol, 119(1):10-9.

[230] Breckels, LM, Holden, S, Wojnar, D, Mulvey, CM, Christoforou, A, Groen, AJ, Kohlbacher, O, Lilley, KS, and Gatto, L (2015).
Learning from heterogeneous data sources: an application in spatial proteomics
bioRxiv.

[229] de Lange, O, Wolf, C, Thiel, P, Krüger, J, Kleusch, C, Kohlbacher, O, and Lahaye, T (2015).
DNA-binding proteins from marine bacteria expand the sequence diversity of known TALE-like repeats
Nucl. Acids Res, 43(20):10065-80.

[228] Friedrich, A, Kenar, E, Kohlbacher, O, and Nahnsen, S (2015).
Intuitive Web-based Experimental Design for High-throughput Biomedical Data
BioMed Res Int, 2015:958302.