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Publications

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

accepted

[297] Ali, M, Foldvari, Z, Giannakopoulou, E, Böschen, M, Strønen, E, Yang, W, Toebes, M, Schubert, B, Kohlbacher, O, Schumacher, TN, and Olweus, J (accepted).
Induction Of Neoantigen Reactive T Cells From Healthy Donors
Nat Protocols.

[296] Bilich, T, Nelde, A, LB, Roerden, M, Salih, HR, Kowalewski, DJ, Schuster, H, Tsou, C, Marcu, A, Neidert, MC, Lübke, M, Rieth, J, Schemionek, M, Brümmendorf, TH, Vucinic, V, Niederwieser, D, Bauer, J, Märklin, M, Peper, JK, Klein, R, Kanz, L, Rammensee, H, Stevanovic, S, and Walz, JS (accepted).
The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy
Blood.

[295] Creydt, M, Hudzik, D, Rurik, M, Kohlbacher, O, and Fischer, M (accepted).
Food Authentication: Small Molecule Profiling as a Tool for the Geographic Discrimination of German White Asparagus
J. Agric. Food Chem..

2018

[294] 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.

[293] Deutsch, E, Perez-Riverol, Y, Chalkley, R, Wilhelm, M, Tate, S, Sachsenberg, T, Walzer, M, Käll, L, Delanghe, B, Böcker, S, Schymanski, E, Wilmes, P, Dorfer, V, Kuster, B, Volders, P, Jehmlich, N, Vissers, J, Wolan, D, Wang, A, Mendoza, L, Shofstahl, J, Dowsey, A, Griss, J, Salek, R, Neumann, S, Binz, P, Lam, H, Vizcaíno, J, Bandeira, N, and Röst, H (2018).
Expanding the use of spectral libraries in proteomics
Journal of Proteome Research.

[292] Domingo-Calap, P, Schubert, B, Joly, M, Solis, M, Untrau, M, Carapito, R, Georgel, P, Caillard, S, Fafi-Kremer, S, Paul, N, Kohlbacher, O, González-Candelas, F, and Bahram, S (2018).
An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
PLoS Pathogens, 14(10):e1007368.

[291] Friedrich, A, de la Garza, L, Kohlbacher, O, and Nahnsen, S (2018).
Interactive Visualization for Large-Scale Multi-factorial Research Designs
In: DILS 2018: Data Integration in the Life Sciences, ed. by Sören Auer, Maria-Esther Vidal, vol. 11371, pp. 75-84. Lecture Notes in Computer Science.

[290] Fröhlich, H, Balling, R, Beerenwinkel, N, Kohlbacher, O, Kumar, S, Lengauer, T, Maathuis, M, Moreau, Y, Murphy, S, Przytycka, T, Röst, H, Rebhan, M, Schuppert, A, Schwab, M, Spang, R, Stekhoven, D, Sun, J, Ziemek, D, and Zupan, B (2018).
From Hype to Reality: Data Science enabling Personalized Medicine
BMC Medicine, 16:150.

[289] Gleim, LC, Karim, MR, Zimmermann, L, Stenzhorn, H, Decker, S, and Beyan, O (2018).
Schema Extraction for Privacy Preserving Processing of Sensitive Data
In: MEPDaW-SeWeBMeDA-SWeTI 2018 Joint Proceedings of MEPDaW, SeWeBMeDA and SWeTI 2018, vol. 2112, pp. 36-47. CEUR Workshop Proceedings.

[288] Halfmann, M, Stenzhorn, H, Gerjets, P, Kohlbacher, O, and Oestermeier, U (2018).
User-Driven Development of a Novel Molecular Tumor Board Support Tool
In: DILS 2018: Data Integration in the Life Sciences, ed. by Sören AuerMaria-Esther Vidal, vol. 11371, pp. 195-199, Springer. Lecture Notes in Computer Science.

[287] Kahles, A, Lehmann, K, Toussaint, NC, Hüser, M, Stark, S, Sachsenberg, T, Stegle, O, Kohlbacher, O, Sander, C, TCGA PanCanAtlas Network, G, and Rätsch (2018).
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
Cancer Cell, 34(2):211-224.

[286] Karim, MR, Nguyen, B, Zimmermann, L, Kirsten, T, Löbe, M, Meineke, F, Stenzhorn, H, Kohlbacher, O, Decker, S, and Beyan, O (2018).
A Distributed Analytics Platform to Execute FHIR based Phenotyping Algorithms
. 11th International Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS'2018).

[285] 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).

[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 (2018).
Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Cancer Res., 78(16):4627-4641.

[283] 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.

[282] Prasser, F, Kohlbacher, O, Mansmann, U, Bauer, B, and Kuhn, KA (2018).
Data Integration for Future Medicine (DIFUTURE) - An Architectural and Methodological Overview
Methods Inf Med, 57(S01):e57-r65.

[281] 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.

[280] 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.

[279] 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.

[278] Wein, S, Andrews, B, Sachsenberg, T, Santos-Rosa, H, Kohlbacher, O, Kouzarides, T, Garcia, BA, and Weisser, H (2018).
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry
bioRxiv.

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.