Publications of Jürgen Cox

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)

Räschle, M.; Smeenk, G.; Hansen, R. K.; Temu, T.; Oka, Y.; Hein, M. Y.; Nagaraj, N.; Long, D. T.; Walter, J. C.; Hofmann, K. et al.; Storchova, Z.; Cox, J.; Bekker-Jensen, S.; Mailand, N.; Mann, M.: Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. SCIENCE 348 (6234), 1253671 (2015)

Schölz, C.; Weinert, B. T.; Wagner, S. A.; Beli, P.; Miyake, Y.; Qi, J.; Jensen, L. J.; Streicher, W.; McCarthy, A. R.; Westwood, N. J. et al.; Lain, S.; Cox, J.; Matthias, P.; Mann, M.; Bradner, J. E.; Choudhary, C.: Acetylation site specificities of lysine deacetylase inhibitors in human cells. NATURE BIOTECHNOLOGY 33 (4), pp. 415 - 423 (2015)

Tyanova, S.; Temu, T.; Carlson, A.; Sinitcyn, P.; Mann, M.; Cox, J.: Visualization of LC-MS/MS proteomics data in MaxQuant. PROTEOMICS 15 (8), pp. 1453 - 1456 (2015)

Griss, J.; Jones, A. R.; Sachsenberg, T.; Walzer, M.; Gatto, L.; Hartler, J.; Thallinger, G. G.; Salek, R. M.; Steinbeck, C.; Neuhauser, N. et al.; Cox, J.; Neumann, S.; Fan, J.; Reisinger, F.; Xu, Q.-W.; del Toro, N.; Perez-Riverol, Y.; Ghali, F.; Bandeira, N.; Xenarios, I.; Kohlbacher, O.; Vizcaino, J. A.; Hermjakob, H.: The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience. MOLECULAR & CELLULAR PROTEOMICS 13 (10), pp. 2765 - 2775 (2014)

Cox, J.; Hein, M. Y.; Luber, C. A.; Paron, I.; Nagaraj, N.; Mann, M.: Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ. MOLECULAR & CELLULAR PROTEOMICS 13 (9), pp. 2513 - 2526 (2014)

Azimifar, S. B.; Nagaraj, N.; Cox, J.; Mann, M.: Cell-type-resolved quantitative proteomics of murine liver. Cell metabolism 20 (6), pp. 1076 - 1087 (2014)

Deeb, S. J.; Cox, J.; Schmidt-Supprian, M.; Mann, M.: N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes. MOLECULAR & CELLULAR PROTEOMICS 13 (1), pp. 240 - 251 (2014)

Robles, M. S.; Cox, J.; Mann, M.: In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism. PLOS GENETICS 10 (1), e1004047 (2014)

Sharma, K.; D'Souza, R. C. J.; Tyanova, S.; Schaab, C.; Wisniewski, J. R.; Cox, J.; Mann, M.: Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling. CELL REPORTS 8 (5), pp. 1583 - 1594 (2014)

Wisniewski, J. R.; Hein, M. Y.; Cox, J.; Mann, M.: A "Proteomic Ruler" for Protein Copy Number and Concentration Estimation without Spike-in Standards. Molecular & cellular proteomics: MCP 13 (12), pp. 3497 - 3506 (2014)

Oppermann, F. S.; Klammer, M.; Bobe, C.; Cox, J.; Schaab, C.; Tebbe, A.; Daub, H.: Comparison of SILAC and mTRAQ Quantification for Phosphoproteomics on a Quadrupole Orbitrap Mass Spectrometer. JOURNAL OF PROTEOME RESEARCH 12 (9), pp. 4089 - 4100 (2013)

Geiger, T.; Velic, A.; Macek, B.; Lundberg, E.; Kampf, C.; Nagaraj, N.; Uhlen, M.; Cox, J.; Mann, M.: Initial Quantitative Proteomic Map of 28 Mouse Tissues Using the SILAC Mouse. MOLECULAR & CELLULAR PROTEOMICS 12 (6), pp. 1709 - 1722 (2013)

Marx, H.; Lemeer, S.; Schliep, J. E.; Matheron, L.; Mohammed, S.; Cox, J.; Mann, M.; Heck, A. J. R.; Kuster, B.: A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. NATURE BIOTECHNOLOGY 31 (6), pp. 557 - 564 (2013)

Neuhauser, N.; Nagaraj, N.; McHardy, P.; Zanivan, S.; Scheltema, R.; Cox, J.; Mann, M.: High Performance Computational Analysis of Large-scale Proteome Data Sets to Assess Incremental Contribution to Coverage of the Human Genome. JOURNAL OF PROTEOME RESEARCH 12 (6), pp. 2858 - 2868 (2013)