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


[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

[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

[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

[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.


[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

[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.

[227] Gerasch, A, Küntzer, J, Niermann, P, Stöckel, D, Kohlbacher, O, and Lenhof, H (2015).
Network-based interactive navigation and analysis of large biological datasets
it - Information Technology, 57(1):37-48.

[226] Hildebrandt, AK, Stöckel, D, Fischer, N, de la Garza Trevino, L, Krüger, J, Nickels, S, Röttig, M, Schärfe, C, Schumann, M, Thiel, P, Lenhof, H, Kohlbacher, O, and Hildebrandt, A (2015).
ballaxy: web services for structural bioinformatics
Bioinformatics, 31(1):121-2.

[225] Kowalewski, DJ, Schuster, H, Backert, L, Berlin, C, Kahn, S, Kanz, L, Salih, HR, Rammensee, H, Stevanovic, S, and Stickel, JS (2015).
HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)
Proceedings of the National Academy of Sciences of the United States of America, 112(2):E166–E175.

[224] Martens, L, Kohlbacher, O, and Weintraub, ST (2015).
Managing Expectations when Publishing Tools and Methods for Computational Proteomics
J. Proteome Res., 14(5):2002-4.