Publications of Jürgen Cox

Huffman, R. G.; Leduc, A.; Wichmann, C.; Di Gioia, M.; Borriello, F.; Specht, H.; Derks, J.; Khan, S.; Khoury, L.; Emmott, E. et al.; Petelski, A. A.; Perlman, D. H.; Cox, J.; Zanoni, I.; Slavov, N.: Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. Nature Methods 20, pp. 714 - 722 (2023)

Sinitcyn, P.; Richards, A. L.; Weatheritt, R. J.; Brademan, D. R.; Marx, H.; Shishkova, E.; Meyer, J. G.; Hebert, A. S.; Westphall, M. S.; Blencowe, B. J. et al.; Cox, J.; Coon, J. J.: Global detection of human variants and isoforms by deep proteome sequencing. Nature Biotechnology, s41587-023-01714-x (2023)

Gatto, L.; Aebersold, R.; Cox, J.; Demichev, V.; Derks, J.; Emmott, E.; Franks, A. M.; Ivanov, A. R.; Kelly, R. T.; Khoury, L. et al.; Leduc, A.; MacCoss, M. J.; Nemes, P.; Perlman, D. H.; Petelski, A. A.; Rose, C. M.; Schoof, E. M.; Van Eyk, J.; Vanderaa, C.; Yates III, J. R. R.; Slavov, N.: Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature Methods 20 (3), pp. 375 - 386 (2023)

Trulsson, F.; Akimov, V.; Robu, M.; van Overbeek, N.; Berrocal, D. A. P.; Shah, R. G.; Cox, J.; Shah, G. M.; Blagoev, B.; Vertegaal, A. C. O.: Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates. Nature Communications 13 (1), 2736 (2022)

Hamzeiy, H.; Ferretti, D.; Robles, M. S.; Cox, J.: Perseus plugin "Metis'' for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs. Cell Reports: Methods 2 (4), 100198 (2022)

Frohn, B. P.; Härtel, T.; Cox, J.; Schwille, P.: Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures. PLoS One 17 (3), e0266395 (2022)

Jayavelu, A. K.; Wolf, S.; Buettner, F.; Alexe, G.; Haeupl, B.; Comoglio, F.; Schneider, C.; Doebele, C.; Fuhrmann, D. C.; Wagner, S. et al.; Donato, E.; Andresen, C.; Wilke, A. C.; Zindel, A.; Jahn, D.; Splettstoesser, B.; Plessmann, U.; Muench, S.; Abou-El-Ardat, K.; Makowka, P.; Acker, F.; Enssle, J. C.; Cremer, A.; Schnutgen, F.; Kurrle, N.; Chapuy, B.; Loeber, J.; Hartmann, S.; Wild, P. J.; Wittig, I.; Huebschmann, D.; Kaderali, L.; Cox, J.; Bruene, B.; Roellig, C.; Thiede, C.; Steffen, B.; Bornhaeuser, M.; Trumpp, A.; Urlaub, H.; Stegmaier, K.; Serve, H.; Mann, M.; Oellerich, T.: The proteogenomic subtypes of acute myeloid leukemia. Cancer Cell 40 (3), pp. 301 - 317.e12 (2022)

Lin, M.-H.; Wu, P.-S.; Wong, T.-H.; Lin, I.-Y.; Lin, J.; Cox, J.; Yu, S.-H.: Benchmarking differential expression, imputation and quantification methods for proteomics data. Briefings in Bioinformatics 23 (3), bbac138 (2022)

Yilmaz, S.; Busch, F.; Nagaraj, N.; Cox, J.: Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx. Analytical Chemistry 94 (3), pp. 1608 - 1617 (2022)

Sinitcyn, P.; Hamzeiy, H.; Salinas Soto, F.; Itzhak, D.; McCarthy, F.; Wichmann, C.; Steger, M.; Ohmayer, U.; Distler, U.; Kaspar-Schoenefeld, S. et al.; Prianichnikov, N.; Yilmaz, S.; Rudolph, J. D.; Tenzer, S.; Perez-Riverol, Y.; Nagaraj, N.; Humphrey, S. J.; Cox, J.: MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nature Biotechnology 39, pp. 1563 - 1573 (2021)

Traube, F. R.; Ozdemir, D.; Sahin, H.; Scheel, C.; Glueck, A. F.; Geserich, A. S.; Oganesian, S.; Kostidis, S.; Iwan, K.; Rahimoff, R. et al.; Giorgio, G.; Mueller, M.; Spada, F.; Biel, M.; Cox, J.; Giera, M.; Michalakis, S.; Carell, T.: Redirected nuclear glutamate dehydrogenase supplies Tet3 with alpha-ketoglutarate in neurons. Nature Communications 12 (1), 4100 (2021)

Broch Trentini, D.; Pecoraro, M.; Tiwary, S.; Cox, J.; Mann, M.; Hipp, M. S.; Hartl, F. U.: Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 117 (8), pp. 4099 - 4108 (2020)

Kjell, J.; Fischer-Sternjak, J.; Thompson, A. J.; Friess, C.; Sticco, M. J.; Salinas, F.; Cox, J.; Martinelli, D. C.; Ninkovic, J.; Franze, K. et al.; Schiller, H. B.; Götz, M.: Defining the Adult Neural Stem Cell Niche Proteome Identifies Key Regulators of Adult Neurogenesis. CELL STEM CELL 26 (2), pp. 277 - 293.e8 (2020)

Leitner, A.; Bonvin, A. M. J. J.; Borchers, C. H.; Chalkley, R. J.; Chamot-Rooke, J.; Combe, C. W.; Cox, J.; Dong, M.-Q.; Fischer, L.; Gotze, M. et al.; Gozzo, F. C.; Heck, A. J. R.; Hoopmann, M. R.; Huang, L.; Ishihama, Y.; Jones, A. R.; Kalisman, N.; Kohlbacher, O.; Mechtler, K.; Moritz, R. L.; Netz, E.; Novak, P.; Petrotchenko, E.; Sali, A.; Scheltema, R. A.; Schmidt, C.; Schriemer, D.; Sinz, A.; Sobott, F.; Stengel, F.; Thalassinos, K.; Urlaub, H.; Viner, R.; Vizcaino, J. A.; Wilkins, M. R.; Rappsilber, J.: Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure 28 (11), pp. 1259 - 1268 (2020)

Prianichnikov, N.; Koch, H.; Koch, S.; Lubeck, M.; Heilig, R.; Brehmer, S.; Fischer, R.; Cox, J.: MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics. MOLECULAR & CELLULAR PROTEOMICS 19 (6), pp. 1058 - 1069 (2020)

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.: The dental proteome of Homo antecessor. Nature 580, pp. 235 - 238 (2020)

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)