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Publications

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

accepted

[285] Kahles, A, Lehmann, K, Toussaint, NC, Hüser, M, Stark, S, Sachsenberg, T, Stegle, O, Kohlbacher, O, Sander, C, TCGA PanCanAtlas Network, G, and Rätsch (accepted).
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
Cancer Cell.

[284] Löffler, MW, Kowalewski, DJ, Backert, L, Bernhardt, J, Adam, P, Schuster, H, Dengler, F, Backes, D, Kopp, H, Beckert, S, Wagner, S, Königsrainer, I, Kohlbacher, O, Kanz, L, Königsrainer, A, Rammensee, H, Stevanovic, S, and Haen, SP (accepted).
Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Cancer Res..

2018

[283] Choobdar, S, Ahsen, ME, Crawford, J, Tomasoni, M, Lamparter, D, Lin, J, Hescott, B, Hu, X, Mercer, J, Natoli, T, Narayan, R, , Subramanian, A, Stolovitzky, G, Kutalik, Z, Lage, K, Slonim, DK, Saez-Rodriguez, J, Cowen, LJ, Bergmann, S, and Marbach, D (2018).
Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
bioRxiv.

[282] Lederer, S, Dijkstra, TM, and Heskes, T (2018).
Additive Dose Response Models: Explicit Formulation and the Loewe Additivity Consistency Condition
Frontiers in Pharmacology, 9(31).

[281] Mohr, C, Friedrich, A, Wojnar, D, Kenar, E, Polatkan, A, Codrea, MC, Czemmel, S, Kohlbacher, O, and Nahnsen, S (2018).
qPortal: A platform for data-driven biomedical research
PLoS ONE, 13(1):e0191603.

[280] Rehm, M, Apweiler, R, Beissbarth, T, Berthold, M, Blüthgen, N, Burmeister, Y, Dammann, O, Deutsch, A, Feuerhake, F, Franke, A, Hasenauer, J, Hoffmann, S, Höfer, T, Jansen, P, Kaderali, L, Klingmüller, U, Koch, I, Kohlbacher, O, Kuepfer, L, Lammert, F, Maier, D, Pfeifer, N, Radde, N, Roeder, I, Saez-Rodriguez, J, Sax, U, Schmeck, B, Schuppert, A, Seilheimer, B, Theis, F, Vera-Gonzáles, J, and Wolkenhauer, O (2018).
Whither Systems Medicine?
Exp. Mol. Med., 50(3):e453.

[279] Schubert, B, Schärfe, C, Dönnes, P, Hopf, T, Marks, D, and Kohlbacher, O (2018).
Population-specific design of de-immunized protein biotherapeutics
PLoS Comput Biol, 14(3):(3):e1005983.

[278] Thijssen, B, Dijkstra, TM, Heskes, T, and Wessels, LF (2018).
Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates
Bioinformatics, 34(5):803-811.

2017

[277] Alberer, M, Gnad-Vogt, U, Hong, HS, Mehr, KT, Backert, L, Finak, G, Gottardo, R, Bica, MA, Garofano, A, Koch, SD, Fotin-Mleczek, M, Hoerr, I, Clemens, R, and von Sonnenburg, F (2017).
Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial
The Lancet, 390(10101):1511-1520.

[276] Audain, E, Uszkoreit, J, Sachsenberg, T, Pfeuffer, J, Liang, X, Hermjakob, H, Sanchez, A, Eisenacher, M, Reinert, K, Tabb, DL, Kohlbacher, O, and Perez-Riverol, Y (2017).
In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
J. Proteomics, 150:170–182.

[275] Backert, L, Kowalewski, D, Walz, S, Schuster, H, Berlin, C, Neidert, M, Schemionek, M, Brümmendorf, TH, Vicinic, V, Niederwieser, D, Kanz, L, Salih, HR, Kohlbacher, O, Weisel, K, Rammensee, H, Stevanovic, S, and Walz, JS (2017).
A meta-analysis of HLA peptidome composition in different hematological entities: Entity-specific dividing lines and "pan-leukemia" antigens
Oncotarget, 8(27):43915-43924..

[274] Chevrette, MG, Aicheler, F, Kohlbacher, O, Currie, CR, and Medema, MH (2017).
SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria
Bioinformatics, 33(20):3202-3210.

[273] Di Marco, M, Schuster, H, Backert, L, Ghosh, M, Rammensee, H, and Stevanovic, S (2017).
Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices
J. Immunol., 199(8):2639-2651.

[272] Flett, FJ, Sachsenberg, T, Kohlbacher, O, Mackay, CL, and Interthal, H (2017).
Differential Enzymatic 16O/18O Labelling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates
Anal. Chem., 89(21):11208-11213.

[271] Haen, SP, Groh, C, Schumm, M, Backert, L, Löffler, MW, Federmann, B, Faul, C, Dörfel, D, Vogel, W, Handgretinger, R, Kanz, L, and Bethge, WA (2017).
Haploidentical hematopoietic cell transplantation using in vitro T cell depleted grafts as salvage therapy in patients with disease relapse after prior allogeneic transplantation
Annals of Hematology:1-11.

[270] Heimgärtner, F, Hettich, S, Kohlbacher, O, and Menth, M (2017).
Scaling Home Automation to Public Buildings: A Distributed Multiuser Setup for OpenHAB 2
In: Global Internet of Things Summit (GIoTS) 2017.

[269] Nelde, A, Kowalewski, DJ, Backert, L, Schuster, H, Werner, J, Klein, R, Kohlbacher, O, Kanz, L, Salih, HR, Rammensee, H, Stevanović, S, and Stickel, JS (2017).
HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell based immunotherapy
OncoImmunol., 5(12):e1249560.

[268] Pfeuffer, JU, Sachsenberg, T, Alka, O, Walzer, M, Fillbrunn, A, Nilse, L, Schilling, O, Reinert, K, and Kohlbacher, O (2017).
OpenMS - A platform for reproducible analysis of mass spectrometry data
J. Biotechnol.:S0168-1656(17)30251-1.

[267] Schubert, B, de la Garza, L, Mohr, C, Walzer, M, and Kohlbacher, O (2017).
ImmunoNodes - Graphical Development of Complex Immunoinformatics Workflows
BMC Bioinformatics, 18(1):242.

[266] Schubert, B, Schärfe, C, Dönnes, P, Hopf, T, Marks, D, and Kohlbacher, O (2017).
Population-specific design of de-immunized protein biotherapeutics
Preprint at arXiv.

[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.