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Joshua E Elias - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
Proteomics, antigen presentation, host-microbe interactions, post-translational modifications
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Hao C, Elias JE, Lee PKH, Lam H. metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering. Microbiome. 11: 176. PMID 37550758 DOI: 10.1186/s40168-023-01602-1  0.358
2020 Zhang L, McAlpine PL, Heberling ML, Elias JE. Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass Spectrometry. Journal of Proteome Research. PMID 33331781 DOI: 10.1021/acs.jproteome.0c00464  0.305
2019 Zhang L, Winkler S, Schlottmann FP, Kohlbacher O, Elias JE, Skotheim JM, Ewald JC. Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast. Frontiers in Cell and Developmental Biology. 7: 338. PMID 31921850 DOI: 10.3389/Fcell.2019.00338  0.315
2019 Li TM, Coan JP, Krajewski K, Zhang L, Elias JE, Strahl BD, Gozani O, Chua KF. Binding to medium and long chain fatty acyls is a common property of HEAT and ARM repeat modules. Scientific Reports. 9: 14226. PMID 31578417 DOI: 10.1038/S41598-019-50817-6  0.35
2019 Casavant E, Park KT, Elias JE. Proteomic discovery of stool protein biomarkers for distinguishing pediatric inflammatory bowel disease flares. Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of the American Gastroenterological Association. PMID 31499250 DOI: 10.1016/J.Cgh.2019.08.052  0.36
2019 Devabhaktuni A, Lin S, Zhang L, Swaminathan K, Gonzalez CG, Olsson N, Pearlman SM, Rawson K, Elias JE. TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nature Biotechnology. PMID 30936560 DOI: 10.1038/S41587-019-0067-5  0.469
2019 Walczak CP, Leto DE, Zhang L, Riepe C, Muller RY, DaRosa PA, Ingolia NT, Elias JE, Kopito RR. Ribosomal protein RPL26 is the principal target of UFMylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 30626644 DOI: 10.1073/Pnas.1816202116  0.383
2019 Leto DE, Morgens DW, Zhang L, Walczak CP, Elias JE, Bassik MC, Kopito RR. Genome-wide CRISPR Analysis Identifies Substrate-Specific Conjugation Modules in ER-Associated Degradation. Molecular Cell. 73: 377-389.e11. PMID 30581143 DOI: 10.1016/J.Molcel.2018.11.015  0.392
2019 Kathuria KR, Chen B, Khodadoust MS, Olsson N, Davis MM, Elias JE, Levy R, Altman RB, Alizadeh AA. Maria-I: A Deep-Learning Approach for Accurate Prediction of MHC Class I Tumor Neoantigen Presentation Blood. 134: 84-84. DOI: 10.1182/Blood-2019-129334  0.335
2018 Boucher MJ, Ghosh S, Zhang L, Lal A, Jang SW, Ju A, Zhang S, Wang X, Ralph SA, Zou J, Elias JE, Yeh E. Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites. Plos Biology. 16: e2005895. PMID 30212465 DOI: 10.1371/Journal.Pbio.2005895  0.399
2018 Purzner T, Purzner J, Buckstaff T, Cozza G, Gholamin S, Rusert JM, Hartl TA, Sanders J, Conley N, Ge X, Langan M, Ramaswamy V, Ellis L, Litzenburger U, Bolin S, ... ... Elias JE, et al. Developmental phosphoproteomics identifies the kinase CK2 as a driver of Hedgehog signaling and a therapeutic target in medulloblastoma. Science Signaling. 11. PMID 30206138 DOI: 10.1126/Scisignal.Aau5147  0.3
2018 Pataki CI, Rodrigues J, Zhang L, Qian J, Efron B, Hastie T, Elias JE, Levitt M, Kopito RR. Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors. Proceedings of the National Academy of Sciences of the United States of America. PMID 30104359 DOI: 10.1073/Pnas.1807981115  0.303
2018 Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias J, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, et al. Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). Proteomics. e1800110. PMID 29791771 DOI: 10.1002/Pmic.201800110  0.314
2018 Yang AC, du Bois H, Olsson N, Gate D, Lehallier B, Berdnik D, Brewer KD, Bertozzi CR, Elias JE, Wyss-Coray T. Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics. Journal of the American Chemical Society. PMID 29775058 DOI: 10.1021/Jacs.8B03074  0.415
2018 Olsson N, Schultz LM, Zhang L, Khodadoust MS, Narayan R, Czerwinski DK, Levy R, Elias JE. T-cell immunopeptidomes reveal cell subtype surface markers derived from intracellular proteins. Proteomics. PMID 29493099 DOI: 10.1002/Pmic.201700410  0.325
2017 Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O. RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation. The Journal of Biological Chemistry. PMID 28655759 DOI: 10.1074/Jbc.M117.784371  0.34
2017 Hwang J, Walczak CP, Shaler TA, Olzmann JA, Zhang L, Elias JE, Kopito RR. Characterization of protein complexes of the endoplasmic reticulum associated degradation E3 ubiquitin ligase Hrd1. The Journal of Biological Chemistry. PMID 28411238 DOI: 10.1074/Jbc.M117.785055  0.404
2017 Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, ... ... Elias JE, et al. Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. Nature. PMID 28329770 DOI: 10.1038/Nature21433  0.308
2017 Zhang L, Elias JE. Relative Protein Quantification Using Tandem Mass Tag Mass Spectrometry. Methods in Molecular Biology (Clifton, N.J.). 1550: 185-198. PMID 28188531 DOI: 10.1007/978-1-4939-6747-6_14  0.461
2016 Gisselberg JE, Zhang L, Elias JE, Yeh E. The prenylated proteome of Plasmodium falciparum reveals pathogen-specific prenylation activity and drug mechanism-of-action. Molecular & Cellular Proteomics : McP. PMID 28040698 DOI: 10.1074/Mcp.M116.064550  0.369
2016 Schumacher FR, Delamarre L, Jhunjhunwala S, Modrusan Z, Phung QT, Elias JE, Lill JR. Building proteomic tool boxes to monitor MHC class I and class II peptides. Proteomics. PMID 27928884 DOI: 10.1002/Pmic.201600061  0.322
2016 Woo CM, Felix A, Zhang L, Elias JE, Bertozzi CR. Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars. Analytical and Bioanalytical Chemistry. PMID 27695962 DOI: 10.1007/S00216-016-9934-9  0.442
2016 Devabhaktuni A, Elias JE. Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets. Journal of Proteome Research. 15: 732-42. PMID 26743026 DOI: 10.1021/Acs.Jproteome.5B00861  0.351
2016 Khodadoust M, Olsson N, Wagar L, Chen B, Rawson K, Liu CL, Steiner D, Rao S, Zhang L, Stehr H, Newman AM, Czerwinski DK, Carlton V, Moorhead M, Faham M, ... ... Elias J, et al. Antigen Presentation Profiling Reveals T-Cell Recognition of Lymphoma Immunoglobulin Neoantigens Blood. 128: 915-915. DOI: 10.1182/Blood.V128.22.915.915  0.315
2015 Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE. The effect of microbial colonization on the host proteome varies by gastrointestinal location. The Isme Journal. PMID 26574685 DOI: 10.1038/Ismej.2015.187  0.381
2015 Lichtman JS, Sonnenburg JL, Elias JE. Monitoring host responses to the gut microbiota. The Isme Journal. 9: 1908-15. PMID 26057846 DOI: 10.1038/Ismej.2015.93  0.371
2015 Carlson SM, Moore KE, Sankaran SM, Reynoird N, Elias JE, Gozani O. A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme. The Journal of Biological Chemistry. 290: 12040-7. PMID 25795785 DOI: 10.1074/Jbc.M115.641530  0.304
2015 Schultz LM, Olsson N, Khodadoust M, Narayan R, Sagiv-Barfi I, Elias J, Levy R. T Regulatory Cells Exhibit Surface Expression of FoxP3 Derived Peptides Presented within Class I MHC Blood. 126: 2228-2228. DOI: 10.1182/Blood.V126.23.2228.2228  0.354
2014 Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P. The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Cell Cycle (Georgetown, Tex.). 13: 2889-900. PMID 25486477 DOI: 10.4161/15384101.2014.946850  0.489
2014 Treeck M, Sanders JL, Gaji RY, LaFavers KA, Child MA, Arrizabalaga G, Elias JE, Boothroyd JC. The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis. Plos Pathogens. 10: e1004197. PMID 24945436 DOI: 10.1371/Journal.Ppat.1004197  0.364
2013 Lichtman JS, Marcobal A, Sonnenburg JL, Elias JE. Host-centric proteomics of stool: a novel strategy focused on intestinal responses to the gut microbiota. Molecular & Cellular Proteomics : McP. 12: 3310-8. PMID 23982161 DOI: 10.1074/Mcp.M113.029967  0.326
2013 Hinkson IV, Bates JG, Elias J. Proteomics Meets Translation Analysis: An Attempt to Balance the Protein Turnover Equation Biophysical Journal. 104: 356a. DOI: 10.1016/J.Bpj.2012.11.1975  0.448
2011 Treeck M, Sanders JL, Elias JE, Boothroyd JC. The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries. Cell Host & Microbe. 10: 410-9. PMID 22018241 DOI: 10.1016/J.Chom.2011.09.004  0.358
2011 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, et al. A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Nature. 474: 230-4. PMID 21654808 DOI: 10.1038/Nature10155  0.457
2011 Hinkson IV, Elias JE. The dynamic state of protein turnover: It's about time. Trends in Cell Biology. 21: 293-303. PMID 21474317 DOI: 10.1016/J.Tcb.2011.02.002  0.448
2010 Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell. 143: 1174-89. PMID 21183079 DOI: 10.1016/J.Cell.2010.12.001  0.749
2010 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, et al. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 463: 374-8. PMID 20090754 DOI: 10.1038/Nature08684  0.486
2010 Elias JE, Gygi SP. Target-decoy search strategy for mass spectrometry-based proteomics. Methods in Molecular Biology (Clifton, N.J.). 604: 55-71. PMID 20013364 DOI: 10.1007/978-1-60761-444-9_5  0.523
2009 Hemming ML, Elias JE, Gygi SP, Selkoe DJ. Identification of beta-secretase (BACE1) substrates using quantitative proteomics. Plos One. 4: e8477. PMID 20041192 DOI: 10.1371/Journal.Pone.0008477  0.497
2008 Hemming ML, Elias JE, Gygi SP, Selkoe DJ. Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements. Plos Biology. 6: e257. PMID 18942891 DOI: 10.1371/Journal.Pbio.0060257  0.509
2008 Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, Gygi SP. The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. Journal of Proteome Research. 7: 4756-65. PMID 18798661 DOI: 10.1021/Pr800333E  0.663
2007 Everley PA, Gartner CA, Haas W, Saghatelian A, Elias JE, Cravatt BF, Zetter BR, Gygi SP. Assessing enzyme activities using stable isotope labeling and mass spectrometry. Molecular & Cellular Proteomics : McP. 6: 1771-7. PMID 17627935 DOI: 10.1074/Mcp.M700057-Mcp200  0.751
2007 Li X, Gerber SA, Rudner AD, Beausoleil SA, Haas W, Villén J, Elias JE, Gygi SP. Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. Journal of Proteome Research. 6: 1190-7. PMID 17330950 DOI: 10.1021/Pr060559J  0.76
2007 Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods. 4: 207-14. PMID 17327847 DOI: 10.1038/Nmeth1019  0.537
2007 Gartner CA, Elias JE, Bakalarski CE, Gygi SP. Catch-and-release reagents for broadscale quantitative proteomics analyses. Journal of Proteome Research. 6: 1482-91. PMID 17311443 DOI: 10.1021/Pr060605F  0.76
2006 Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP. Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. Journal of Proteome Research. 5: 1224-31. PMID 16674112 DOI: 10.1021/Pr0504891  0.774
2006 Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villén J, Gygi SP. Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Molecular & Cellular Proteomics : McP. 5: 1326-37. PMID 16635985 DOI: 10.1074/Mcp.M500339-Mcp200  0.754
2005 Elias JE, Haas W, Faherty BK, Gygi SP. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nature Methods. 2: 667-75. PMID 16118637 DOI: 10.1038/Nmeth785  0.562
2005 Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP. Characterization of mouse spleen cells by subtractive proteomics. Molecular & Cellular Proteomics : McP. 4: 1459-70. PMID 16037072 DOI: 10.1074/Mcp.M500137-Mcp200  0.759
2005 Xu J, Zhong N, Wang H, Elias JE, Kim CY, Woldman I, Pifl C, Gygi SP, Geula C, Yankner BA. The Parkinson's disease-associated DJ-1 protein is a transcriptional co-activator that protects against neuronal apoptosis. Human Molecular Genetics. 14: 1231-41. PMID 15790595 DOI: 10.1093/Hmg/Ddi134  0.437
2004 Starita LM, Machida Y, Sankaran S, Elias JE, Griffin K, Schlegel BP, Gygi SP, Parvin JD. BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number. Molecular and Cellular Biology. 24: 8457-66. PMID 15367667 DOI: 10.1128/Mcb.24.19.8457-8466.2004  0.478
2004 Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 12130-5. PMID 15302935 DOI: 10.1073/Pnas.0404720101  0.727
2004 Gibbons FD, Elias JE, Gygi SP, Roth FP. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. Journal of the American Society For Mass Spectrometry. 15: 910-2. PMID 15144981 DOI: 10.1016/J.Jasms.2004.02.011  0.518
2004 Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotechnology. 22: 214-9. PMID 14730315 DOI: 10.1038/Nbt930  0.537
2003 Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. A proteomics approach to understanding protein ubiquitination. Nature Biotechnology. 21: 921-6. PMID 12872131 DOI: 10.1038/Nbt849  0.594
2003 Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Journal of Proteome Research. 2: 43-50. PMID 12643542 DOI: 10.1021/Pr025556V  0.559
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