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Jimmie Ye, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
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
    Genetic regulation and immunological function of ERAP2 haplotypes
    NIH R01AI136972Jun 15, 2018 - May 31, 2023
    Role: Principal Investigator
    Single-cell sequencing of peripheral blood cells in SLE patients
    NIH R21AI133337Jul 14, 2017 - Jun 30, 2019
    Role: Principal Investigator
    Fine mapping rheumatic disease variants using functional genomic sequencing
    NIH R01AR071522May 1, 2017 - Feb 28, 2022
    Role: Principal Investigator

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

    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. Binnewies M, Mujal AM, Pollack JL, Combes AJ, Hardison EA, Barry KC, Tsui J, Ruhland MK, Kersten K, Abushawish MA, Spasic M, Giurintano JP, Chan V, Daud AI, Ha P, Ye CJ, Roberts EW, Krummel MF. Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity. Cell. 2019 Apr 18; 177(3):556-571.e16. PMID: 30955881.
      View in: PubMed
    2. Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 2019 03 22; 20(1):63. PMID: 30902100.
      View in: PubMed
    3. Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Genome Res. 2018 12; 28(12):1812-1825. PMID: 30446528.
      View in: PubMed
    4. Byrnes LE, Wong DM, Subramaniam M, Meyer NP, Gilchrist CL, Knox SM, Tward AD, Ye CJ, Sneddon JB. Lineage dynamics of murine pancreatic development at single-cell resolution. Nat Commun. 2018 09 25; 9(1):3922. PMID: 30254276.
      View in: PubMed
    5. Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat Genet. 2018 Aug; 50(8):1140-1150. PMID: 29988122.
      View in: PubMed
    6. Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. 2018 Jul; 559(7715):E13. PMID: 29899441.
      View in: PubMed
    7. Rodda LB, Lu E, Bennett ML, Sokol CL, Wang X, Luther SA, Barres BA, Luster AD, Ye CJ, Cyster JG. Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity. Immunity. 2018 05 15; 48(5):1014-1028.e6. PMID: 29752062.
      View in: PubMed
    8. Principles of Systems Biology, No. 27. Cell Syst. 2018 03 28; 6(3):260-262. PMID: 29596778.
      View in: PubMed
    9. Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol. 2018 01; 36(1):89-94. PMID: 29227470.
      View in: PubMed
    10. Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, Ye CJ, Aschard H, Eskin E, Halperin E, Zaitlen N. An ancestry-based approach for detecting interactions. Genet Epidemiol. 2018 02; 42(1):49-63. PMID: 29114909.
      View in: PubMed
    11. Wilentzik R, Ye CJ, Gat-Viks I. Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks. Genetics. 2017 12; 207(4):1699-1709. PMID: 29046401.
      View in: PubMed
    12. Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N. Covariate selection for association screening in multiphenotype genetic studies. Nat Genet. 2017 Dec; 49(12):1789-1795. PMID: 29038595.
      View in: PubMed
    13. Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. 2017 09 07; 549(7670):111-115. PMID: 28854172.
      View in: PubMed
    14. Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A. CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. Sci Rep. 2017 04 07; 7(1):737. PMID: 28389661.
      View in: PubMed
    15. Van Dyken SJ, Nussbaum JC, Lee J, Molofsky AB, Liang HE, Pollack JL, Gate RE, Haliburton GE, Ye CJ, Marson A, Erle DJ, Locksley RM. A tissue checkpoint regulates type 2 immunity. Nat Immunol. 2016 Dec; 17(12):1381-1387. PMID: 27749840.
      View in: PubMed
    16. Brown BC, Ye CJ, Price AL, Zaitlen N. Transethnic Genetic-Correlation Estimates from Summary Statistics. Am J Hum Genet. 2016 07 07; 99(1):76-88. PMID: 27321947.
      View in: PubMed
    17. Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 07; 26(7):863-73. PMID: 27197206.
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    18. Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye CJ, 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.
      View in: PubMed
    19. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, 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
    20. Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, 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.
      View in: PubMed
    21. Ye CJ, 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
    22. Raj T, Rothamel K, Mostafavi S, Ye C, 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.
      View in: PubMed
    23. Joo JW, Sul JH, Han B, Ye C, 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
    24. Lee MN, Ye C, 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.
      View in: PubMed
    25. Sul JH, Han B, Ye C, 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
    26. Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hulková 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.
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    27. Friese RS, Ye C, 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
    28. Furlotte NA, Kang HM, Ye C, 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
    29. Kang EY, Ye C, 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.
      View in: PubMed
    30. Ye C, 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
    31. Kang HM, Ye C, 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
    32. Ye C, 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
    33. Bashir A, Ye C, 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
    34. 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 C, 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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