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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.
Tyanova S, Temu T, Cox J. Tyanova S, et al. Among authors: cox j. Nat Protoc. 2016 Dec;11(12):2301-2319. doi: 10.1038/nprot.2016.136. Epub 2016 Oct 27. Nat Protoc. 2016. PMID: 27809316
Guidelines for Genome-Scale Analysis of Biological Rhythms.
Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB. Hughes ME, et al. Among authors: cox j. J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3. J Biol Rhythms. 2017. PMID: 29098954 Free PMC article.
Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research.
Tyanova S, Cox J. Tyanova S, et al. Among authors: cox j. Methods Mol Biol. 2018;1711:133-148. doi: 10.1007/978-1-4939-7493-1_7. Methods Mol Biol. 2018. PMID: 29344888
Deep proteome and transcriptome mapping of a human cancer cell line.
Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M. Nagaraj N, et al. Among authors: cox j. Mol Syst Biol. 2011 Nov 8;7:548. doi: 10.1038/msb.2011.81. Mol Syst Biol. 2011. PMID: 22068331 Free PMC article.
Proteomic maps of breast cancer subtypes.
Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T. Tyanova S, et al. Among authors: cox j. Nat Commun. 2016 Jan 4;7:10259. doi: 10.1038/ncomms10259. Nat Commun. 2016. PMID: 26725330 Free PMC article.
Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome.
Grassl N, Kulak NA, Pichler G, Geyer PE, Jung J, Schubert S, Sinitcyn P, Cox J, Mann M. Grassl N, et al. Among authors: cox j. Genome Med. 2016 Apr 21;8(1):44. doi: 10.1186/s13073-016-0293-0. Genome Med. 2016. PMID: 27102203 Free PMC article.
EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification.
Virreira Winter S, Meier F, Wichmann C, Cox J, Mann M, Meissner F. Virreira Winter S, et al. Among authors: cox j. Nat Methods. 2018 Jul;15(7):527-530. doi: 10.1038/s41592-018-0037-8. Epub 2018 Jun 18. Nat Methods. 2018. PMID: 29915187
BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes.
Meier F, Geyer PE, Virreira Winter S, Cox J, Mann M. Meier F, et al. Among authors: cox j. Nat Methods. 2018 Jun;15(6):440-448. doi: 10.1038/s41592-018-0003-5. Epub 2018 May 7. Nat Methods. 2018. PMID: 29735998
Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow.
Deshmukh AS, Cox J, Jensen LJ, Meissner F, Mann M. Deshmukh AS, et al. Among authors: cox j. J Proteome Res. 2015 Nov 6;14(11):4885-95. doi: 10.1021/acs.jproteome.5b00720. Epub 2015 Oct 28. J Proteome Res. 2015. PMID: 26457550
Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles.
Deeb SJ, Tyanova S, Hummel M, Schmidt-Supprian M, Cox J, Mann M. Deeb SJ, et al. Among authors: cox j. Mol Cell Proteomics. 2015 Nov;14(11):2947-60. doi: 10.1074/mcp.M115.050245. Epub 2015 Aug 26. Mol Cell Proteomics. 2015. PMID: 26311899 Free PMC article.
The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origin using both their global protein expression patterns and the 55-protein signature obtained previously from patient-derived cell lines (Deeb …
The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origi …
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