Joshua Elias

Publications

• A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Jirawatnotai S, Hu Y, Michowski W, Elias JE, Becks L, Bienvenu F, Zagozdzon A, Goswami T, Wang YE, Clark AB, Kunkel TA, van Harn T, Xia B, Correll M, Quackenbush J, Livingston DM, Gygi SP, Sicinski P. Nature. 2011; 474 (7350): 230-4
• The dynamic state of protein turnover: It's about time. Hinkson IV, Elias JE. Trends Cell Biol. 2011; 21 (5): 293-303
• The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries. Treeck M, Sanders JL, Elias JE, Boothroyd JC. Cell Host Microbe. 2011; 10 (4): 410-9
• A tissue-specific atlas of mouse protein phosphorylation and expression. Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP. Cell. 2010; 143 (7): 1174-89
• Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Elias JE, Gygi SP. Nat Methods. 2007; 4 (3): 207-14
• Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Elias JE, Haas W, Faherty BK, Gygi SP. Nat Methods. 2005; 2 (9): 667-75
• A role for the MRN complex in ATR activation via TOPBP1 recruitment. Duursma AM, Driscoll R, Elias JE, Cimprich KA. Mol Cell. 2013; 50 (1): 116-22
• Target-decoy search strategy for mass spectrometry-based proteomics. Elias JE, Gygi SP. Methods Mol Biol. 2010: 604 55-71
• Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P. Nature. 2010; 463 (7279): 374-8
• Identification of beta-secretase (BACE1) substrates using quantitative proteomics. Hemming ML, Elias JE, Gygi SP, Selkoe DJ. PLoS One. 2009; 4 (12): e8477
• Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements. Hemming ML, Elias JE, Gygi SP, Selkoe DJ. PLoS Biol. 2008; 6 (10): e257
• The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, Gygi SP. J Proteome Res. 2008; 7 (11): 4756-65
• Assessing enzyme activities using stable isotope labeling and mass spectrometry. Everley PA, Gartner CA, Haas W, Saghatelian A, Elias JE, Cravatt BF, Zetter BR, Gygi SP. Mol Cell Proteomics. 2007; 6 (10): 1771-7
• Catch-and-release reagents for broadscale quantitative proteomics analyses. Gartner CA, Elias JE, Bakalarski CE, Gygi SP. J Proteome Res. 2007; 6 (4): 1482-91
• Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. Li X, Gerber SA, Rudner AD, Beausoleil SA, Haas W, Villén J, Elias JE, Gygi SP. J Proteome Res. 2007; 6 (3): 1190-7
• Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP. J Proteome Res. 2006; 5 (5): 1224-31
• Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villén J, Gygi SP. Mol Cell Proteomics. 2006; 5 (7): 1326-37
• Characterization of mouse spleen cells by subtractive proteomics. Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP. Mol Cell Proteomics. 2005; 4 (10): 1459-70
• The Parkinson's disease-associated DJ-1 protein is a transcriptional co-activator that protects against neuronal apoptosis. Xu J, Zhong N, Wang H, Elias JE, Kim CY, Woldman I, Pifl C, Gygi SP, Geula C, Yankner BA. Hum Mol Genet. 2005; 14 (9): 1231-41
• BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number. Starita LM, Machida Y, Sankaran S, Elias JE, Griffin K, Schlegel BP, Gygi SP, Parvin JD. Mol Cell Biol. 2004; 24 (19): 8457-66
• Intensity-based protein identification by machine learning from a library of tandem mass spectra. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Nat Biotechnol. 2004; 22 (2): 214-9
• Large-scale characterization of HeLa cell nuclear phosphoproteins. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC, Gygi SP. Proc Natl Acad Sci U S A. 2004; 101 (33): 12130-5
• SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. Gibbons FD, Elias JE, Gygi SP, Roth FP. J Am Soc Mass Spectrom. 2004; 15 (6): 910-2
• Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. J Proteome Res. 2003 Jan-Feb; 2 (1): 43-50
• A proteomics approach to understanding protein ubiquitination. Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. Nat Biotechnol. 2003; 21 (8): 921-6