Publications of Jürgen Cox

Welker, F.; Ramos-Madrigal, J.; Gutenbrunner, P.; Mackie, M.; Tiwary, S.; Jersie-Christensen, R. R.; Chiva, C.; Dickinson, M. R.; Kuhlwilm, M.; de Manuel, M. et al.; Gelabert, P.; Martinon-Torres, M.; Margvelashvili, A.; Arsuaga, J. L.; Carbonell, E.; Marques-Bonet, T.; Penkman, K.; Sabido, E.; Cox, J.; Olsen, J. V.; Lordkipanidze, D.; Racimo, F.; Lalueza-Fox, C.; de Castro, J. M. B.; Willerslev, E.; Cappellini, E.: Author Correction: The dental proteome of Homo antecessor. Nature 584 (7820), p. E19 - E19 (2020)

Yu, S.-H.; Ferretti, D.; Schessner, J. P.; Rudolph, J. D.; Borner, G. H. H.; Cox, J.: Expanding the Perseus Software for Omics Data Analysis With Custom Plugins. Current protocols in bioinformatics 71 (1), e105 (2020)

Yu, S.-H.; Kyriakidou, P.; Cox, J.: Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification. Journal of Proteome Research 19 (10), pp. 3945 - 3954 (2020)

Frottin, F.; Schueder, F.; Tiwary, S.; Gupta, R.; Körner, R.; Schlichthaerle, T.; Cox, J.; Jungmann, R.; Hartl, F. U.; Hipp, M. S.: The nucleolus functions as a phase-separated protein quality control compartment. Science 365 (6451), pp. 342 - 347 (2019)

Brüning, F.; Noya, S. B.; Bange, T.; Koutsouli, S.; Rudolph, J. D.; Tyagarajan, S.; Cox, J.; Mann, M.; Brown, S. A.; Robles, M. S.: Sleep-wake cycles drive daily dynamics of synaptic phosphorylation. SCIENCE 366 (6462), eaav3617, p. 201 (2019)

Iacobucci, C.; Piotrowski, C.; Aebersold, R.; Amaral, B. C.; Andrews, P.; Bernfur, K.; Borchers, C.; Brodie, N. I.; Bruce, J. E.; Cao, Y. et al.; Chaignepain, S.; Chavez, J. D.; Claverol, S.; Cox, J.; Davis, T.; Degliesposti, G.; Dong, M.-Q.; Edinger, N.; Emanuelsson, C.; Gay, M.; Goetze, M.; Gomes-Neto, F.; Gozzo, F. C.; Gutierrez, C.; Haupt, C.; Heck, A. J. R.; Herzog, F.; Huang, L.; Hoopmann, M. R.; Kalisman, N.; Klykov, O.; Kukacka, Z.; Liu, F.; MacCoss, M. J.; Mechtler, K.; Mesika, R.; Moritz, R. L.; Nagaraj, N.; Nesati, V.; Neves-Ferreira, A. G. C.; Ninnis, R.; Novak, P.; O'Reilly, F. J.; Pelzing, M.; Petrotchenko, E.; Piersimoni, L.; Plasencia, M.; Pukala, T.; Rand, K. D.; Rappsilber, J.; Reichmann, D.; Sailer, C.; Sarnowski, C. P.; Scheltema, R. A.; Schmidt, C.; Schriemer, D. C.; Shi, Y.; Skehel, J. M.; Slavin, M.; Sobott, F.; Solis-Mezarino, V.; Stephanowitz, H.; Stengel, F.; Stieger, C. E.; Trabjerg, E.; Trnka, M.; Vilaseca, M.; Viner, R.; Xiang, Y.; Yilmaz, S.; Zelter, A.; Ziemianowicz, D.; Leitner, A.; Sinz, A.: First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Analytical Chemistry 91 (11), pp. 6953 - 6961 (2019)

Mordret, E.; Dahan, O.; Asraf, O.; Rak, R.; Yehonadav, A.; Barnabas, G. D.; Cox, J.; Geiger, T.; Lindner, A. B.; Pilpel, Y.: Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity. MOLECULAR CELL 75 (3), pp. 427 - 441.e5 (2019)

Perez-Riverol, Y.; Csordas, A.; Bai, J.; Bernal-Llinares, M.; Hewapathirana, S.; Kundu, D. J.; Inuganti, A.; Griss, J.; Mayer, G.; Eisenacher, M. et al.; Perez, E.; Uszkoreit, J.; Pfeuffer, J.; Sachsenberg, T.; Yilmaz, S.; Tiwary, S.; Cox, J.; Audain, E.; Walzer, M.; Jarnuczak, A. F.; Ternent, T.; Brazma, A.; Vizcaino, J. A.: The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Research 47 (D1), pp. D442 - D450 (2019)

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