Publications of Jürgen Cox

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, pp. 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), pp. 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), pp. 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)

Sacco, F.; Humphrey, S. J.; Cox, J.; Mischnik, M.; Schulte, A.; Klabunde, T.; Schaefer, M.; Mann, M.: Glucose-regulated and drug-perturbed phosphoproteome reveals molecular mechanisms controlling insulin secretion. Nature Communications 7, 13250 (2016)

Chen, Z. A.; Fischer, L.; Cox, J.; Rappsilber, J.: Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant. Molecular and Cellular Proteomics 15 (8), pp. 2769 - 2778 (2016)

Itzhak, D. N.; Tyanova, S.; Cox, J.; Borner, G. H. H.: Global, quantitative and dynamic mapping of protein subcellular localization. eLife 5, e16950 (2016)

Grassl, N.; Kulak, N. A.; Pichler, G.; Geyer, P. E.; Jung, J.; Schubert, S.; Sinitcyn, P.; Cox, J.; Mann, M.: Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. GENOME MEDICINE 8, 44 (2016)

Iglesias-Gato, D.; Wikström, P.; Tyanova, S.; Lavallee, C.; Thysell, E.; Carlsson, J.; Hägglöf, C.; Cox, J.; Andren, O.; Stattin, P. et al.; Egevad, L.; Widmark, A.; Bjartell, A.; Collins, C. C.; Bergh, A.; Geiger, T.; Mann, M.; Flores-Morales, A.: The Proteome of Primary Prostate Cancer. EUROPEAN UROLOGY 69 (5), pp. 942 - 952 (2016)

Mischnik, M.; Sacco, F.; Cox, J.; Schneider, H.-C.; Schäfer, M.; Hendlich, M.; Crowther, D.; Mann, M.; Klabunde, T.: IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data. BIOINFORMATICS 32 (3), pp. 424 - 431 (2016)

Temu, T.; Mann, M.; Räschle, M.; Cox, J.: Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. Bioinformatics 32 (9), pp. 1417 - 1419 (2016)

Tyanova, S.; Albrechtsen, R.; Kronqvist, P.; Cox, J.; Mann, M.; Geiger, T.: Proteomic maps of breast cancer subtypes. NATURE COMMUNICATIONS 7, 10259 (2016)

Tyanova, S.; Temu, T.; Cox, J.: The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nature Protocols 11 (12), pp. 2301 - 2319 (2016)

Tyanova, S.; Temu, T.; Sinitcyn, P.; Carlson, A.; Hein, M. Y.; Geiger, T.; Mann, M.; Cox, J.: The Perseus computational platform for comprehensive analysis of (prote)omics data. Nature methods 13 (9), pp. 731 - 740 (2016)

Beck, S.; Michalski, A.; Raether, O.; Lubeck, M.; Kaspar, S.; Goedecke, N.; Baessmann, C.; Hornburg, D.; Meier, F.; Paron, I. et al.; Kulak, N. A.; Cox, J.; Mann, M.: The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics. MOLECULAR & CELLULAR PROTEOMICS 14 (7), pp. 2014 - 2029 (2015)

Deeb, S. J.; Tyanova, S.; Hummel, M.; Schmidt-Supprian, M.; Cox, J.; Mann, M.: Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles. MOLECULAR & CELLULAR PROTEOMICS 14 (11), pp. 2947 - 2960 (2015)

Deshmukh, A. S.; Cox, J.; Jensen , L. J.; Meissner, F.; Mann, M.: Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow. JOURNAL OF PROTEOME RESEARCH 14 (11), pp. 4885 - 4895 (2015)

Deshmukh, A. S.; Murgia, M.; Nagaraj, N.; Treebak, J. T.; Cox, J.; Mann, M.: Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors. MOLECULAR & CELLULAR PROTEOMICS 14 (4), pp. 841 - 853 (2015)

Hein, M. Y.; Hubner, N. C.; Poser, I.; Cox, J.; Nagaraj, N.; Toyoda, Y.; Gak, I. A.; Weisswange, I.; Mansfeld, J.; Buchholz, F. et al.; Hyman, A. A.; Mann, M.: A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances. CELL 163 (3), pp. 712 - 723 (2015)