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Jimmie Ye, PhD

TitleAssistant Professor
SchoolUCSF School of Medicine
DepartmentEpidemiology & Biostatistics
Address513 Parnassus Avenue
San Francisco CA 94117
Phone415-476-6933
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    Collapse Biography 
    Collapse Education and Training
    University of California BerkeleyBS2002Electrical Engineering and Computer Sciences
    University of California BerkeleyBS2002Bioengineering
    University of California San DiegoPhD2009Bioinformatics and Systems Biology
    Broad InstitutePostdoc2014Cell Circuits Program

    Collapse Research 
    Collapse Research Activities and Funding
    Fine mapping rheumatic disease variants using functional genomic sequencing
    NIH R01AR071522May 1, 2017 - Feb 28, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
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    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye J, Lim WA, Marson A. CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. Sci Rep. 2017 Apr 07; 7(1):737. PMID: 28389661.
      View in: PubMed
    2. Van Dyken SJ, Nussbaum JC, Lee J, Molofsky AB, Liang HE, Pollack JL, Gate RE, Haliburton GE, Ye J, Marson A, Erle DJ, Locksley RM. A tissue checkpoint regulates type 2 immunity. Nat Immunol. 2016 Oct 17. PMID: 27749840.
      View in: PubMed
    3. Brown BC, Ye J, Price AL, Zaitlen N. Transethnic Genetic-Correlation Estimates from Summary Statistics. Am J Hum Genet. 2016 Jul 7; 99(1):76-88. PMID: 27321947.
      View in: PubMed
    4. Uricchio LH, Zaitlen NA, Ye J, Witte JS, Hernandez RD. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 Jul; 26(7):863-73. PMID: 27197206.
      View in: PubMed
    5. Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye J, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, Benoist C. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell. 2016 Jan 28; 164(3):564-78. PMID: 26824662; PMCID: PMC4743492 [Available on 01/28/17].
      View in: PubMed, PubMed Central
    6. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye J, Bluestone JA, Doudna JA, Marson A. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc Natl Acad Sci U S A. 2015 Aug 18; 112(33):10437-42. PMID: 26216948; PMCID: PMC4547290.
      View in: PubMed, PubMed Central
    7. Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye J, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Cell. 2015 Jul 30; 162(3):675-86. PMID: 26189680; PMCID: PMC4522370.
      View in: PubMed, PubMed Central
    8. Ye J, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, Stranger B, De Jager P, Mathis D, Regev A, Benoist C. Intersection of population variation and autoimmunity genetics in human T cell activation. Science. 2014 Sep 12; 345(6202):1254665. PMID: 25214635.
      View in: PubMed
    9. Raj T, Rothamel K, Mostafavi S, Ye J, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science. 2014 May 02; 344(6183):519-23. PMID: 24786080; PMCID: PMC4910825.
      View in: PubMed, PubMed Central
    10. Joo JW, Sul JH, Han B, Ye J, Eskin E. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. Genome Biol. 2014 Apr 07; 15(4):r61. PMID: 24708878; PMCID: PMC4053820.
      View in: PubMed, PubMed Central
    11. Lee MN, Ye J, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science. 2014 Mar 07; 343(6175):1246980. PMID: 24604203; PMCID: PMC4124741.
      View in: PubMed, PubMed Central
    12. Sul JH, Han B, Ye J, Choi T, Eskin E. Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches. PLoS Genet. 2013 Jun; 9(6):e1003491. PMID: 23785294; PMCID: PMC3681686.
      View in: PubMed, PubMed Central
    13. Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye J, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hůlková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ. Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet. 2013 Mar; 45(3):299-303. PMID: 23396133; PMCID: PMC3901305.
      View in: PubMed, PubMed Central
    14. Friese RS, Ye J, Nievergelt CM, Schork AJ, Mahapatra NR, Rao F, Napolitan PS, Waalen J, Ehret GB, Munroe PB, Schmid-Schönbein GW, Eskin E, O'Connor DT. Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome. Circ Cardiovasc Genet. 2012 Aug 01; 5(4):430-40. PMID: 22670052; PMCID: PMC3467001.
      View in: PubMed, PubMed Central
    15. Furlotte NA, Kang HM, Ye J, Eskin E. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. Bioinformatics. 2011 Jul 01; 27(13):i288-94. PMID: 21685083; PMCID: PMC3117390.
      View in: PubMed, PubMed Central
    16. Kang EY, Ye J, Shpitser I, Eskin E. Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples. J Comput Biol. 2010 Mar; 17(3):533-46. PMID: 20377462; PMCID: PMC3198891.
      View in: PubMed, PubMed Central
    17. Ye J, Galbraith SJ, Liao JC, Eskin E. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol. 2009 Mar; 5(3):e1000311. PMID: 19300475; PMCID: PMC2649002.
      View in: PubMed, PubMed Central
    18. Kang HM, Ye J, Eskin E. Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics. 2008 Dec; 180(4):1909-25. PMID: 18791227; PMCID: PMC2600931.
      View in: PubMed, PubMed Central
    19. Ye J, Eskin E. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. Bioinformatics. 2007 Jan 15; 23(2):e84-90. PMID: 17237110.
      View in: PubMed
    20. Bashir A, Ye J, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 2005 Jul; 15(7):998-1006. PMID: 15998912; PMCID: PMC1172044.
      View in: PubMed, PubMed Central
    21. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye J, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 Jan; 23(1):137-44. PMID: 15637633.
      View in: PubMed
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