Publications of O Kohlbacher

van Rijswijk, M.; Beirnaert, C.; Caron, C.; Cascante, M.; Dominguez, V.; Dunn, W.; Ebbels, T.; Giocomoni, F.; Gonzalez-Beltran, A.; Hankemeier , T. et al.; Haug, K.; Izquierdo-Garcia, J.; Jimenez, R.; Jourdan, F.; Kale, N.; Klapa, M.; Kohlbacher, O.; Koort, K.; Kultima, K.; Le Corguillé, G.; Moreno, P.; Moschonas, N.; Neumann, S.; O'Donovan, C.; Reczko, M.; Rocca-Serra, P.; Rosato, A.; Salek, R.; Sansone, S.-A.; Satagopam, V.; Schober, D.; Shimmo, R.; Spicer, R.; Spjuth, O.; Thévenot, E.; Viant, M.; Weber, R.; Willighagen, E.; Zanetti, G.; Steinbeck, C.: The future of metabolomics in ELIXIR. F1000Research 6, ELIXIR-1649 (2017)

Backert, L.; Kowalewski, D.; Walz, S.; Schuster, H.; Berlin, C.; Neidert, M.; Schemionek, M.; Brümmendorf, T.; Vucinic, V.; Niederwieser, D. et al.; Kanz, L.; Salih, H.; Kohlbacher, O.; Weisel, K.; Rammensee, H.-G.; Stevanovic, S.; Walz, J.: A meta-analysis of HLA peptidome composition in different hematological entities: entity-specific dividing lines and "panleukemia" antigens. Oncotarget 8 (27), pp. 43915 - 43924 (2017)

Vizcaino, J.; Mayer, G.; Perkins, S.; Barsnes, H.; Vaudel, M.; Perez-Riverol, Y.; Ternent, T.; Uszkoreit, J.; Eisenacher, M.; Fischer, L. et al.; Rappsilber, J.; Netz, E.; Walzer, M.; Kohlbacher, O.; Leitner, A.; Chalkley, R.; Ghali, F.; Martinez-Bartolome, S.; Deutsch, E.; Jones, A.: The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Molecular and Cellular Proteomics 16 (7), pp. 1275 - 1285 (2017)

Vizcaíno, J.; Walzer, M.; Jiménez, R.; Bittremieux, W.; Bouyssié, D.; Carapito, C.; Corrales, F.; Ferro, M.; Heck, A.; Horvatovich, P. et al.; 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.; Kohlbacher, O.: A community proposal to integrate proteomics activities in ELIXIR. F1000Research 6, ELIXIR-875 (2017)

Schubert, B.; de la Garza, L.; Mohr, C.; Walzer, M.; Kohlbacher, O.: ImmunoNodes: graphical development of complex immunoinformatics workflows. BMC Bioinformatics 18, 242 (2017)

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

Löffler, M.; Chandran, P.; Laske, K.; Schroeder, C.; Bonzheim, I.; Hilke, F.; Trautwein, N.; Kowalewski, D.; Schuster, H.; Günder, M. et al.; Carcamo Yañez, V.; Mohr, C.; Sturm, M.; Nguyen, H.-P.; Riess, O.; Bauer, P.; Nahnsen, S.; Nadalin, S.; Zieker, D.; Glatzle, J.; Thiel, K.; Schneiderhan-Marra, N.; Clasen, S.; Bösmüller, H.; Fend, F.; Kohlbacher, O.; Gouttefangeas, C.; Stevanović, S.; Königsrainer, A.; Rammensee, H.-G.: Erratum to "Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient". Journal of Hepatology 66 (1), pp. 252 - 253 (2017)

Dietsche, T.; Mebrhatu, M.; Brunner, M.; Abrusci, P.; Yan, J.; Franz-Wachtel, M.; Schärfe, C.; Zilkenat, S.; Grin, I.; Galán, J. et al.; Kohlbacher, O.; Lea, S.; Macek, B.; Marlovits, T.; Robinson, C.; Wagner, S.: Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus. PLoS Pathogens 12 (12), e1006071 (2016)

Hong, H.; Koch, S.; Scheel, B.; Gnad-Vogt, U.; Schröder, A.; Kallen, K.-J.; Wiegand, V.; Backert, L.; Kohlbacher, O.; Hoerr, I. et al.; Fotin-Mleczek, M.; Billingsley, J.: Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy. Oncoimmunology 5 (12), e1249560 (2016)

Löffler, M.; Chandran, P.; Laske, K.; Schroeder, C.; Bonzheim, I.; Hilke, F.; Trautwein, N.; Kowalewski, D.; Schuster, H.; Günder, M. et al.; Carcamo Yañez, V.; Mohr, C.; Sturm, M.; Nguyen, H.-P.; Riess, O.; Bauer, P.; Nahnsen, S.; Nadalin, S.; Zieker, D.; Glatzle, J.; Thiel, K.; Schneiderhan-Marra, N.; Clasen, S.; Bösmüller, H.; Fend, F.; Kohlbacher, O.; Gouttefangeas, C.; Stevanović, S.; Königsrainer, A.; Rammensee, H.-G.: Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient. Journal of Hepatology 65 (4), pp. 849 - 855 (2016)

Boyles, M.; Ranninger, C.; Reischl, R.; Rurik, M.; Tessadri, R.; Kohlbacher, O.; Duschl, H.; Huber, C.: Copper oxide nanoparticle toxicity profiling using untargeted metabolomics. Particle and Fibre Toxicology 13, 49 (2016)

Veit, J.; Sachsenberg, T.; Chernev, A.; Aicheler, F.; Urlaub, H.; Kohlbacher, O.: LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer. Journal of Proteome Research 15 (9), pp. 3441 - 3448 (2016)

Griss, J.; Perez-Riverol, Y.; Lewis, S.; Tabb, D.; Dianes, J.; Del-Toro, N.; Rurik, M.; Walzer, M.; Kohlbacher, O.; Hermjakob, H. et al.; Wang, R.; Vizcaíno, J.: Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nature Methods 13 (8), pp. 651 - 656 (2016)

Röst, H.; Sachsenberg, T.; Aiche, S.; Bielow, C.; Weisser, H.; Aicheler, F.; Andreotti, S.; Ehrlich, H.-C.; Gutenbrunner, P.; Kenar, E. et al.; Liang, X.; Nahnsen, S.; Nilse, L.; Pfeuffer, J.; Rosenberger, G.; Rurik, M.; Schmitt, U.; Veit, J.; Walzer, M.; Woijnar, D.; Wolski, W.; Schilling, O.; Choudhary, J.; Malmström, L.; Aebersold, R.; Reinert, K.; Kohlbacher, O.: OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods 13 (9), pp. 741 - 748 (2016)

Schubert, B.; Walzer, M.; Brachvogel, H.-B.; Szolek, A.; Mohr , C.; Kohlbacher, O.: FRED 2: an immunoinformatics framework for Python. Bioinformatics 32 (13), pp. 2044 - 2046 (2016)

Mueller, S.; Backes, C.; Gress, A.; Baumgarten, N.; Kalinina, O.; Moll, A.; Kohlbacher, O.; Meese, E.; Keller, A.: BALL-SNPgp-from genetic variants toward computational diagnostics. Bioinformatics 32 (12), pp. 1888 - 1890 (2016)

Breckels, L.; Holden, S.; Wojnar, D.; Mulvey, C.; Christoforou, A.; Groen, A.; Trotter, M.; Kohlbacher, O.; Lilley, K.; Gatto, L.: Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PLoS Computational Biology 12 (5), e1004920 (2016)

Kowalewski, D.; Walz, S.; Backert, L.; Schuster, H.; Kohlbacher, O.; Weisel, K.; Rittig, S.; Kanz, L.; Salih, H.; Rammensee, H.-G. et al.; Stevanović , S.; Stickel, J.: Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini. Blood Cancer Journal 6 (4), e411 (2016)

Schneider, L.; Stöckel, D.; Kehl, T.; Gerasch, A.; Ludwig, N.; Leidinger, P.; Huwer, H.; Tenzer, S.; Kohlbacher, O.; Hildebrandt, A. et al.; Kaufmann, M.; Gessler, M.; Keller, A.; Meese, E.; Graf, N.; Lenhof, H.-P.: DrugTargetInspector: An assistance tool for patient treatment stratification. International Journal of Cancer 138 (7), pp. 1765 - 1776 (2016)

Gatto, L.; Hansen, K.; Hoopmann, M.; Hermjakob, H.; Kohlbacher, O.: Testing and Validation of Computational Methods for Mass Spectrometry. Journal of Proteome Research 15 (3), pp. 809 - 814 (2016)