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Publications

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

2017

[265] Schuster, H, Peper, JK, Bösmüller, H, Röhle, K, Backert, L, Bilich, T, Ney, B, Löffler, MW, Kowalewski, DJ, Trautwein, N, Rabsteyn, A, Engler, T, Braun, S, Haen, SP, Walz, JS, Schmid-Horch, B, Brucker, S, Wallwiener, D, Kohlbacher, O, Fend, F, Rammensee, H, Stevanovic, S, Staebler, A, and Wagner, P (2017).
The immunopeptidomic landscape of ovarian carcinomas
Proc. Natl. Acad. Sci. USA, 114(46):E9942-E9951.

[264] Schärfe, CPI, Tremmel, R, Schwab, M, Kohlbacher, O, and Marks, DS (2017).
Genetic variation in human drug-related genes
Genome Med., 9:117.

[263] Schärfe, CPI, Tremmel, R, Schwab, M, Kohlbacher, O, and Marks, DS (2017).
Genetic variation in human drug-related genes
Preprint at arXiv.

[262] van Rijswijk, M, Beirnaert, C, Caron, C, Cascante, M, Dominguez, V, Dunn, W, Ebbels, T, Giacomoni, F, Gonzalez-Beltran, A, Hankemeier, T, Haug, K, Izquierdo-Garcia, J, Jimenez, R, Jourdan, F, Kale, N, Klapa, M, Kohlbacher, O, Koort, K, Kultima, K, Le Corguillé, G, Moschonas, N, Neumann, S, O?Donovan, C, Reczko, M, Rocca-Serra, P, Rosato, A, Salek, R, Sansone, S, Satagopam, V, Schober, D, Shimmo, R, Spicer, R, Spjuth, O, Thévenot, E, Viant, M, Weber, R, Willighagen, E, Zanetti, G, and Steinbeck, C (2017).
The future of metabolomics in ELIXIR [version 1; referees: awaiting peer review]
F1000Research, 6(1649).

[261] Vizcaino, JA, Mayer, G, Perkins, SR, Barnsnes, H, Vaudel, M, Perez-Riverol, Y, Ternent, T, Uszkoreit, J, Eisenacher, M, Fischer, L, Rappsilber, J, Netz, E, Walzer, M, Kohlbacher, O, Leitner, A, Chalkley, RJ, Ghali, F, Martínez-Bartolomé, S, Deutsch, EW, and Jones, AR (2017).
The mzIdentML data standard version 1.2, supporting advances in proteome informatics
Mol. Cell. Prot., 16(7):1275-1285.

[260] Vizcaíno, JA, Walzer, M, Jiménez, RC, Bittremieux, W, Bouyssie, D, Carapito, C, Corrales, F, Ferro, M, Heck, AJR, Horvatovich, P, Hubalek, M, Lane, L, Laukens, K, Levander, F, Lisacek, F, Novak, P, Palmblad, M, Piovesan, D, Pühler, A, Schwämmle, V, Valkenborg, D, van Rijswijk, M, Vondrasek, J, Eisenacher, M, Martens, L, and Kohlbacher, O (2017).
A community proposal to integrate proteomics activities in ELIXIR
F1000Research, 6:875.

2016

[259] Aebersold, R, Kohlbacher, O, and Vitek, O (2016).
Computational Mass Spectrometry (Dagstuhl Seminar 15351)
Dagstuhl Reports, 5(8):9–33.

[258] Boyles, M, Ranninger, C, Reischl, R, Rurik, M, Tessadri, R, Kohlbacher, O, Duschl, A, and Huber, C (2016).
Copper oxide nanoparticle toxicity profiling using untargeted metabolomics
Part. Fiber Toxicol., 13:49.

[257] Breckels, LM, Holden, S, Wojnar, D, Mulvey, CM, Christoforou, A, Groen, A, Kohlbacher, O, Lilley, KS, and Gatto, L (2016).
Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics
PLoS Comput. Biol., 12(5):e1004920.

[256] Dammeier, S, Nahnsen, S, Veit, J, Wehner, F, Ueffing, M, and Kohlbacher, O (2016).
Mass Spectrometry-based Proteomics Reveals Organspecific Expression Patterns To Be Used as Forensic Evidence
J. Proteome Res., 15(1):182-92.

[255] de la Garza, L, Aicheler, F, and Kohlbacher, O (2016).
From the Desktop to the Grid and Cloud: Conversion of KNIME Workflows to gUSE
Proc. Int. Workshop Science Gateways (IWSG 2016).

[254] de la Garza, L, Veit, J, Szolek, A, Röttig, M, Aiche, S, Gesing, S, Reinert, K, and Kohlbacher, O (2016).
From the Desktop to the Grid: scalable Bioinformatics via Workflow Conversion
BMC Bioinformatics, 17(1):127.

[253] Dietsche, T, Mebrhatu, MT, Brunner, MJ, Abrusci, P, Yan, J, Franz-Wachtel, M, Schärfe, C, Zilkenat, S, Grin, I, Galán, JE, Kohlbacher, O, Lea, S, Macek, B, Marlovits, TC, Robinson, C, and Wagner, S (2016).
Structural and functional characterization of the bacterial type III secretion export apparatus
PLoS Pathogens, 12(12):e1006071. .

[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.