Publications of O Kohlbacher

Netz, E.; Dijkstra, T.; Sachsenberg, T.; Zimmermann, L.; Walzer, M.; Monecke, T.; Ficner, R.; Dybkiv, O.; Urlaub, H.; Kohlbacher, O.: OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS. Molecular and Cellular Proteomics 19 (12), pp. 2157 - 2168 (2020)

Leitner, A.; Bonvin, A.; Borchers, C.; Chalkley, R.; Chamot-Rooke, J.; Combe, C.; Cox, J.; Dong, M.-Q.; Fischer, L.; Götze, M. et al.; Gozzo, F.; Heck, A.; Hoopmann, M.; Huang, L.; Ishihama, Y.; Jones, A.; Kalisman, N.; Kohlbacher, O.; Mechtler, K.; Moritz, R.; Netz, E.; Novak, P.; Petrotchenko, E.; Sali, A.; Scheltema, R.; Schmidt, C.; Schriemer, D.; Sinz, A.; Sobott, F.; Stengel, F.; Thalassinos, K.; Urlaub, H.; Viner, R.; Vizcaíno, J.; Wilkins, M.; Rappsilber, J.: Toward increased reliability, transparency, and accessibility in cross-linking mass spectrometry. Structure 28 (11), pp. 1259 - 1268 (2020)

Stützer, A.; Welp, L.; Raabe, M.; Sachsenberg, T.; Kappert, C.; Wulf, A.; Lau, A.; David, S.-S.; Chernev, A.; Kramer, K. et al.; Politis, A.; Kohlbacher, O.; Fischle, W.; Urlaub, H.: Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications 11, 5250, p. 1 (2020)

Hentrich, T.; Koch, A.; Weber, N.; Kilzheimer, A.; Maia, A.; Burkhardt, S.; Rall, K.; Casadei, N.; Kohlbacher, O.; Riess, O. et al.; Schulze-Hentrich, J.; Brucker, S.: The Endometrial Transcription Landscape of MRKH Syndrome. Frontiers in Cell and Developmental Biology 8, 572281 (2020)

Nothias, L.-F.; Petras, D.; Schmid, R.; Dührkop, K.; Rainer, J.; Sarvepalli, A.; Protsyuk, I.; Ernst, M.; Tsugawa, H.; Fleischauer, M. et al.; Aicheler, F.; Aksenov, A.; Alka, O.; Allard, P.-M.; Barsch, A.; Cachet, X.; Caraballo-Rodriguez, A.; Da Silva, R.; Dang, T.; Garg, N.; Gauglitz, J.; Gurevich, A.; Isaac, G.; Jarmusch, A.; Kameník, Z.; Kang, K.; Kessler, N.; Koester, I.; Korf, A.; Le Gouellec, A.; Ludwig, M.; Martin, C.; McCall, L.-I.; McSayles, I.; Meyer, S.; Mohimani, H.; Morsy, M.; Moyne, O.; Neumann, S.; Neuweger, H.; Nguyen, N.; Nothias-Esposito, M.; Paolini, J.; Phelan, V.; Pluskal, T.; Quinn, R.; Rogers, S.; Shrestha, B.; Tripathi, A.; van der Hooft, J.; Vargas, F.; Weldon, K.; Witting, M.; Yang, H.; Zhang, Z.; Zubeil, F.; Kohlbacher, O.; Böcker, S.; Alexandrov, T.; Bandeira, N.; Wang, M.; Dorrestein, P.: Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17 (9), pp. 905 - 908 (2020)

Gleim, L.; Karim, M.; Zimmermann, L.; Kohlbacher, O.; Stenzhorn, H.; Decker, S.; Beyan, O.: Enabling ad-hoc reuse of private data repositories through schema extraction. Journal of Biomedical Semantics 11, 6 (2020)

Starke, R.; Oliphant, K.; Jehmlich, N.; Schäpe, S.; Sachsenberg, T.; Kohlbacher, O.; Allen-Vercoe, E.; von Bergen, M.: Corrigendum to Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics 224, 103829 (2020)

Samonig, L.; Loipetzberger, A.; Blöchl, C.; Rurik, M.; Kohlbacher, O.; Aberger, F.; Huber, C.: Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells. Cells 9 (6), 1397 (2020)

Scheidt, T.; Alka, O.; Gonczarowska-Jorge, H.; Gruber, W.; Rathje, F.; Dell'Aica , M.; Rurik, M.; Kohlbacher, O.; Zahedi, R.; Aberger, F. et al.; Huber, C.: Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Communication and Signaling 18 (1), 99 (2020)

Starke, R.; Oliphant, K.; Jehmlich, N.; Schäpe, S.; Sachsenberg, T.; Kohlbacher, O.; Allen-Vercoe, E.; von Bergen, M.: Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics 222, 103791 (2020)

Lübke, M.; Spalt, S.; Kowalewski, D.; Zimmermann, C.; Bauersfeld, L.; Nelde, A.; Bichmann, L.; Marcu, A.; Peper, J.; Kohlbacher, O. et al.; Walz, J.; Le-Trilling, V.; Hengel, H.; Rammensee, H.-G.; Stevanović, S.; Halenius, A.: Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models. The Journal of Experimental Biology 217 (3), jem.20191164 (2020)

Pfeuffer, J.; Sachsenberg, T.; Dijkstra, T.; Serang, O.; Reinert, K.; Kohlbacher, O.: EPIFANY: A Method for Efficient High-Confidence Protein Inference. Journal of Proteome Research 19 (3), pp. 1060 - 1072 (2020)

Jeong, K.; Kim, J.; Gaikwad, M.; Hidayah, S.; Heikaus, L.; Schlüter, H.; Kohlbacher, O.: FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. Cell Systems 10 (2), pp. 213 - 218 (2020)

Wein, S.; Andrews, B.; Sachsenberg, T.; Santos-Rosa, H.; Kohlbacher, O.; Kouzarides, T.; Garcia, B.; Weisser, H.: A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nature Communications 11, 926 (2020)

Winkler, I.; Bitter, C.; Winkler, S.; Weichenhan, D.; Thavamani, A.; Hengstler, J.; Borkham-Kamphorst, E.; Kohlbacher, O.; Plass, C.; Geffers, R. et al.; Weiskirchen, R.; Nordheim, A.: Identification of Ppar γ-modulated miRNA hubs that target the fibrotic tumor microenvironment. Proceedings of the National Academy of Sciences of the United States of America 117 (1), pp. 454 - 463 (2020)

Schneider, L.; Kehl, T.; Thedinga, K.; Grammes, N.; Backes, C.; Mohr, C.; Schubert, B.; Lenhof, K.; Gerstner, N.; Hartkopf, A. et al.; Wallwiener, M.; Kohlbacher, O.; Keller, A.; Meese, E.; Graf, N.; Lenhof, H.-P.: ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. Bioinformatics 35 (24), pp. 5171 - 5181 (2019)

Zhang, L.; Winkler, S.; Schlottmann, F.; Kohlbacher, O.; Elias, J.; Skotheim, J.; Ewald, J.: Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast. Frontiers in Cell and Developmental Biology 7, 338 (2019)

Bichmann, L.; Nelde, A.; Ghosh, M.; Heumos, L.; Mohr, C.; Peltzer, A.; Kuchenbecker, L.; Sachsenberg, T.; Walz, J.; Stevanović, S. et al.; Rammensee, H.-G.; Kohlbacher, O.: MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. Journal of Proteome Research 18 (11), pp. 3876 - 3884 (2019)

Cain, N.; Alka, O.; Segelke, T.; von Wuthenau; Kohlbacher, O.; Fischer, M.: Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS. Food Chemistry 298, 125013 (2019)

Wibberg, D.; Batut, B.; Belman, P.; Blom, J.; Glöckner, F.; Grüning, B.; Hoffmann, N.; Kleinbölting, N.; Rahn, R.; Rey, M. et al.; Scholz, U.; Sharan, M.; Tauch, A.; Trojahn, U.; Usadel, B.; Kohlbacher, O.: The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 8 (ELIXIR), 1877 (2019)