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Publications

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

2016

[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.

[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.

[223] Nicoludis, J, Lau, S, Schärfe, C, Marks, D, Weihofen, W, and Gaudet, R (2015).
Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity
Structure , 23(11):2087 - 2098.

[222] Proikas-Cezanne, T, Takacs, Z, Dönnes, P, and Kohlbacher, O (2015).
WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome
J. Cell Sci., 128(2):207-217.

[221] Ranninger, C, Rurik, M, Limonciel, A, Ruzek, S, Reischl, R, Wilmes, A, Jennings, P, Hewitt, P, Dekant, W, Kohlbacher, O, and Huber, CG (2015).
Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High-Performance Liquid Chromatography-Mass Spectrometry-Based Experimental and Computational Pipeline
J. Biol. Chem., 290(31):19121-32.

[220] Sachsenberg, T, Herbst, F, Taubert, M, Kermer, R, Jehmlich, N, von Bergen, M, Seifert, J, and Kohlbacher, O (2015).
MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics
J. Proteome Res., 14(2):619-27.

[219] Schubert, B, Brachvogel, H, Jürges, C, and Kohlbacher, O (2015).
EpiToolKit – A Web-based Workbench for Vaccine Design
Bioinformatics, 31(13):2211-3.

[218] Sharma, K, Hrle, A, Kramer, K, Sachsenberg, T, Staals, RH, Randau, L, Marchfelder, A, van der Oost, J, Kohlbacher, O, Conti, E, and Urlaub, H (2015).
Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry
Methods: S1046-2023(15)00246-7.