Publikationen von Jürgen Cox

Rudolph, J. D.; Cox, J.: A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. Journal of Proteome Research 18 (5), S. 2052 - 2064 (2019)

Tiwary, S.; Levy, R.; Gutenbrunner, P.; Salinas Soto, F.; Palaniappan, K. K.; Deming, L.; Berndl, M.; Brant, A.; Cimermancic, P.; Cox, J.: High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis. Nature methods 16 (6), S. 519 - 525 (2019)

Welker, F.; Ramos-Madrigal, J.; Kuhlwilm, M.; Liao, W.; Gutenbrunner, P.; de Manuel, M.; Samodova, D.; Mackie, M.; Allentoft, M. E.; Bacon, A.-M. et al.; Collins, M. J.; Cox, J.; Lalueza-Fox, C.; Olsen, J. V.; Demeter, F.; Wang, W.; Marques-Bonet, T.; Cappellini, E.: Enamel proteome shows that Gigantopithecus was an early diverging pongine. NATURE 576 (7786), S. 262 - 265 (2019)

Wichmann, C.; Meier, F.; Virreira Winter, S.; Brunner, A.-D.; Cox, J.; Mann, M.: MaxQuant. Live Enables Global Targeting of More Than 25,000 Peptides. Molecular and Cellular Proteomics 18 (5), S. 982 - 994 (2019)

Meier, F.; Brunner, A.-D.; Koch, S.; Koch, H.; Lubeck, M.; Krause, M.; Goedecke, N.; Decker, J.; Kosinski, T.; Park, M. A. et al.; Bache, N.; Hoerning, O.; Cox, J.; Raether, O.; Mann, M.: Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped on mobility mass spectrometer. Molecular and Cellular Proteomics 17 (12), UNSP TIR118.000900, S. 2533 - 2545 (2018)

Sinitcyn, P.; Rudolph, J. D.; Cox, J.: Computational Methods for Understanding Mass Spectrometry-Based Shotgun Proteomics Data. Annual Review of Biomedical Data Science 1 (1), S. 207 - 234 (2018)

Cappellini, E.; Prohaska, A.; Racimo, F.; Welker, F.; Pedersen, M. W.; Allentoft, M. E.; Damgaard, P. d. B.; Gutenbrunner, P.; Dunne, J.; Hammann, S. et al.; Roffet-Salque, M.; Ilardo, M.; Moreno-Mayar, J. V.; Wang, Y.; Sikora, M.; Vinner, L.; Cox, J.; Evershed, R. P.; Willerslev, E.: Ancient biomolecules and evolutionary inference. Annual Review of Biochemistry 87, S. 1029 - 1060 (2018)

Overmyer, K. A.; Tyanova, S.; Hebert, A. S.; Westphall, M. S.; Cox, J.; Coon, J. J.: Multiplexed proteome analysis with neutron-encoded stable isotope labeling in cells and mice. Nature Protocols 13 (2), S. 293 - 306 (2018)

Iglesias-Gato, D.; Thysell, E.; Tyanova, S.; Crnalic, S.; Santos, A.; Lima, T. S.; Geiger, T.; Cox, J.; Widmark, A.; Bergh, A. et al.; Mann, M.; Flores-Morales, A.; Wikstrom, P.: The Proteome of Prostate Cancer Bone Metastasis Reveals Heterogeneity with Prognostic Implications. Clinical Cancer Research 24 (21), S. 5433 - 5444 (2018)

Krahmer, N.; Najafi, B.; Schueder, F.; Quagliarini, F.; Steger, M.; Seitz, S.; Kasper, R.; Salinas, F.; Cox, J.; Uhlenhaut, N. H. et al.; Walther, T. C.; Jungmann, R.; Zeigerer, A.; Borner, G. H. H.; Mann, M.: Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis. Developmental Cell 47 (2), S. 205 - 221.e7 (2018)

Meier, F.; Geyer, P. E.; Winter, S. V.; Cox, J.; Mann, M.: BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes. Nature methods 15 (6), S. 440 - 448 (2018)

Shurtleff, M. J.; Itzhak, D. N.; Hussmann, J. A.; Oakdale, N. T. S.; Costa, E. A.; Jonikas, M.; Weibezahn, J.; Popova, K. D.; Jan, C. H.; Sinitcyn, P. et al.; Vembar, S. S.; Hernandez, H.; Cox, J.; Burlingame, A. L.; Brodsky, J.; Frost, A.; Borner, G. H. H.; Weissman, J. S.: The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. eLife 7, e37018 (2018)

Sinitcyn, P.; Tiwary, S.; Rudolph, J.; Gutenbrunner, P.; Wichmann, C.; Yilmaz, S.; Hamzeiy, H.; Salinas, F.; Cox, J.: MaxQuant goes Linux. Nature methods 15 (6), S. 401 - 401 (2018)

Virreira Winter, S.; Meier, F.; Wichmann, C.; Cox, J.; Mann, M.; Meissner, F.: EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification. Nature methods 15 (7), S. 527 - 530 (2018)

Hosp, F.; Gutiérrez-Ángel, S.; Schaefer, M. H.; Cox, J.; Meissner, F.; Hipp, M. S.; Hartl, F. U.; Klein, R.; Dudanova, I.; Mann, M.: Spatiotemporal Proteomic Profiling of Huntington’s Disease Inclusions Reveals Widespread Loss of Protein Function. Cell Reports 21 (8), S. 2291 - 2303 (2017)

Hartl, M.; Fuessl, M.; Boersema, P. J.; Jost, J.-O.; Kramer, K.; Bakirbas, A.; Sindlinger, J.; Ploechinger, M.; Leister, D.; Uhrig, G. et al.; Moorhead, G. B. G.; Cox, J.; Salvucci, M. E.; Schwarzer, D.; Mann, M.; Mann, M.; Finkemeier, I.: Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis. Molecular Systems Biology 13 (10), 949 (2017)

Hamzeiy, H.; Cox, J.: What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics. Current Opinion in Biotechnology 43, S. 141 - 146 (2017)

Hughes, M. E.; Abruzzi, K. C.; Allada, R.; Anafi, R.; Arpat, A. B.; Asher, G.; Baldi, P.; de Bekker, C.; Bell-Pedersen, D.; Blau, J. et al.; Brown, S.; Ceriani, M. F.; Chen, Z.; Chiu, J. C.; Cox, J.; Crowell, A. M.; DeBruyne, J. P.; Dijk, D.-J.; DiTacchio, L.; Doyle, F. J.; Duffield, G. E.; Dunlap, J. C.; Eckel-Mahan, K.; Esser, K. A.; FitzGerald, G. A.; Forger, D. B.; Francey, L. J.; Fu, Y.-H.; Gachon, F.; Gatfield, D.; de Goede, P.; Golden, S. S.; Green, C.; Harer, J.; Harmer, S.; Haspel, J.; Hastings, M. H.; Herzel, H.; Herzog, E. D.; Hoffmann, C.; Hong, C.; Hughey, J. J.; Hurley, J. M.; de la Iglesia, H. O.; Johnson, C.; Kay, S. A.; Koike, N.; Kornacker, K.; Kramer, A.; Lamia, K.; Leise, T.; Lewis, S. A.; Li, J.; Li, X.; Liu, A. C.; Loros, J. J.; Martino, T. A.; Menet, J. S.; Merrow, M.; Millar, A. J.; Mockler, T.; Naef, F.; Nagoshi, E.; Nitabach, M. N.; Olmedo, M.; Nusinow, D. A.; Ptacek, L. J.; Rand, D.; Reddy, A. B.; Robles, M. S.; Roenneberg, T.; Rosbash, M.; Ruben, M. D.; Rund, S. S. C.; Sancar, A.; Sassone-Corsi, P.; Sehgal, A.; Sherrill-Mix, S.; Skene, D. J.; Storch, K.-F.; Takahashi, J. S.; Ueda, H. R.; Wang, H.; Weitz, C.; Westermark, P. O.; Wijnen, H.; Xu, Y.; Wu, G.; Yoo, S.-H.; Young, M.; Zhang, E. E.; Zielinski, T.; Hogenesch, J. B.: Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms 32 (5), S. 380 - 393 (2017)

Itzhak, D. N.; Davies, C.; Tyanova, S.; Mishra, A.; Williamson, J.; Antrobus, R.; Cox, J.; Weekes, M. P.; Borner, G. H. H.: A Mass Spectrometry-Based Approach for Mapping Protein Subcellular Localization Reveals the Spatial Proteome of Mouse Primary Neurons. Cell Reports 20 (11), S. 2706 - 2718 (2017)

Bassani-Sternberg, M.; Braunlein, E.; Klar, R.; Engleitner, T.; Sinitcyn, P.; Audehm, S.; Straub, M.; Weber, J.; Slotta-Huspenina, J.; Specht, K. et al.; Martignoni, M. E.; Werner, A.; Hein, R.; Busch, D. H.; Peschel, C.; Rad, R.; Cox, J.; Mann, M.; Krackhardt, A. M.: Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nature Communications 7, 13404 (2016)