Publications of Jürgen Cox

Perez-Riverol, Y.; Hermjakob, H.; Kohlbacher, O.; Martens, L.; Creasy, D.; Cox, J.; Leprevost, F.; Shan, B. P.; Perez-Nueno, V. I.; Blazejczyk, M. et al.; Punta, M.; Vierlinger, K.; Valienten, P. A.; Leon, K.; Chinea, G.; Guirola, O.; Bringas, R.; Cabrera, G.; Guillen, G.; Padron, G.; Javier Gonzalez, L.; Besada, V.: Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report. JOURNAL OF PROTEOMICS 87, pp. 134 - 138 (2013)

Tyanova, S.; Cox, J.; Olsen, J.; Mann, M.; Frishman, D.: Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins. PLOS COMPUTATIONAL BIOLOGY 9 (1), e1002842 (2013)

Cox, J.; Mann, M.: 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC BIOINFORMATICS 13 (Suppl. 16), S12 (2012)

Michalski, A.; Neuhauser, N.; Cox, J.; Mann, M.: A Systematic Investigation into the Nature of Tryptic HCD Spectra. JOURNAL OF PROTEOME RESEARCH 11 (11), pp. 5479 - 5491 (2012)

Neuhauser, N.; Michalski, A.; Cox, J.; Mann, M.: Expert System for Computer-assisted Annotation of MS/MS Spectra. MOLECULAR & CELLULAR PROTEOMICS 11 (11), pp. 1500 - 1509 (2012)

Stingele, S.; Stoehr, G.; Peplowska, K.; Cox, J.; Mann, M.; Storchova, Z.: Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Molecular Systems Biology 8, 608, pp. [1] - [12] (2012)

Bennetzen, M. V.; Cox, J.; Mann, M.; Andersen, J. S.: PhosphoSiteAnalyzer: A Bioinformatic Platform for Deciphering Phospho Proteomes Using Kinase Predictions Retrieved from NetworKIN. Journal of Proteome Research 11 (6), pp. 3480 - 3486 (2012)

Nagaraj, N.; D'Souza, R. C. J.; Cox, J.; Olsen, J. V.; Mann, M.: Correction to Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation (vol 9, pg 6786, 2010). JOURNAL OF PROTEOME RESEARCH 11 (6), pp. 3506 - 3508 (2012)

Deeb, S. J.; D'Souza, R. C. J.; Cox, J.; Schmidt-Supprian, M.; Mann, M.: Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles. MOLECULAR & CELLULAR PROTEOMICS 11 (5), pp. 77 - 89 (2012)

Geiger, T.; Madden, S. F.; Gallagher, W. M.; Cox, J.; Mann, M.: Proteomic Portrait of Human Breast Cancer Progression Identifies Novel Prognostic Markers. Cancer Research 72 (9), pp. 2428 - 2439 (2012)

Geiger, T.; Wehner, A.; Schaab, C.; Cox, J.; Mann, M.: Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins. Special Issue: Prospects in Space and Time, M111.014050, pp. [1] - [11] (2012)

Schaab, C.; Geiger, T.; Stoehr, G.; Cox, J.; Mann, M.: Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database. Special Issue: Prospects in Space and Time, M111.014068, pp. [1] - [10] (2012)

Sharma, K.; Vabulas, R. M.; Macek, B.; Pinkert, S.; Cox, J.; Mann, M.; Hartl, F. U.: Quantitative Proteomics Reveals That Hsp90 Inhibition Preferentially Targets Kinases and the DNA Damage Response. Special Issue: Prospects in Space and Time, M111.014654, pp. [1] - [12] (2011)

Michalski, A.; Damoc, E.; Lange, O.; Denisov, E.; Nolting, D.; Mueller, M.; Viner, R.; Schwartz, J.; Remes, P.; Belford, M. et al.; Dunyach, J. J.; Cox, J.; Horning, S.; Mann, M.; Makarov, A.: Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes. Special Issue: Prospects in Space and Time, O111.013698, pp. [1] - [11] (2011)

Graumann, J.; Scheltema, R. A.; Zhang, Y.; Cox, J.; Mann, M.: A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics. Special Issue: Prospects in Space and Time, M111.013185, pp. [1] - [11] (2011)

Cox, J.; Heeren, R. M. A.; James, P.; Jorrin-Novo, J. V.; Kolker, E.; Levander, F.; Morrice, N.; Picotti, P.; Righetti, P. G.; Sanchez, J. C. et al.; Turck, C. W.; Zubarev, R.; Alexandre, B. M.; Corrales, F. J.; Marko-Varga, G.; O'Donovan, S.; O'Neil, S.; Prechl, J.; Simoes, T.; Weckwerth, W.; Penque, D.: Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010. Journal of Proteomics 75 (1 Sp. Iss.), pp. 4 - 17 (2011)

Nagaraj, N.; Wisniewski, J. R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Pääbo, S.; Mann, M.: Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology 7, 548, pp. [1] - [8] (2011)

Nagaraj, N.; Kulak, N. A.; Cox, J.; Neuhauser, N.; Mayr, K.; Hoerning, O.; Vorm, O.; Mann, M.: System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap. Molecular & Cellular Proteomics (Special Issue: Prospects in Space and Time) 11 (3), M111.013722, pp. [1] - [11] (2011)

Wagner, S. A.; Beli, P.; Weinert, B. T.; Nielsen, M. L.; Cox, J.; Mann, M.; Choudhary, C.: A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles. Molecular & Cellular Proteomics 10 (10), M111.013284, pp. [1] - [13] (2011)

Michalski, A.; Damoc, E.; Hauschild, J. P.; Lange, O.; Wieghaus, A.; Makarov, A.; Nagaraj, N.; Cox, J.; Mann, M.; Horning, S.: Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer. Molecular & Cellular Proteomics 10 (9), M111.011015, pp. [1] - [11] (2011)