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Jimmie Ye, PhD

Title(s)Associate Professor, Medicine
SchoolSchool of Medicine
Address533 Parnassus Avenue
San Francisco CA 94117
Phone415-476-6933
ORCID ORCID Icon0000-0001-6560-3783 Additional info
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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 Overview 
    Collapse Overview
    The Ye lab is interested in how the interaction between genetics and environment affect human variation at the level of molecular phenotypes. To study these interactions, the lab couples high-throughput sequencing approaches that measure cellular response under environmental challenges with population genetics where such measurements are collected and analyzed across large patient cohorts. The lab develops novel experimental approaches that enable the large-scale collection of functional genomic data en masse and computational approaches that translate the data into novel biological insights. This approach is used to initially study primary human immune cells in both healthy and diseased patients to understand host pathogen interactions and its role in autoimmunity.

    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

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    Collapse In The News
    Collapse Featured Presentations
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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer. Cell. 2020 Jun 03. Oh DY, Kwek SS, Raju SS, Li T, McCarthy E, Chow E, Aran D, Ilano A, Pai CS, Rancan C, Allaire K, Burra A, Sun Y, Spitzer MH, Mangul S, Porten S, Meng MV, Friedlander TW, Ye CJ, Fong L. PMID: 32497499.
      View in: PubMed   Mentions:    Fields:    
    2. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv. 2020 May 17. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. PMID: 32511497.
      View in: PubMed   Mentions:
    3. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. Cell. 2020 Apr 30; 181(3):728-744.e21. Roth TL, Li PJ, Blaeschke F, Nies JF, Apathy R, Mowery C, Yu R, Nguyen MLT, Lee Y, Truong A, Hiatt J, Wu D, Nguyen DN, Goodman D, Bluestone JA, Ye CJ, Roybal K, Shifrut E, Marson A. PMID: 32302591.
      View in: PubMed   Mentions: 1     Fields:    
    4. Functional interpretation of single cell similarity maps. Nat Commun. 2019 09 26; 10(1):4376. DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N. PMID: 31558714.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    5. Ultrarare variants drive substantial cis heritability of human gene expression. Nat Genet. 2019 09; 51(9):1349-1355. Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N. PMID: 31477931.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    6. How mutations express themselves in blood-cell production. Nature. 2019 07; 571(7765):329-330. Raju S, Ye CJ. PMID: 31308526.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans. Nat Metab. 2019 Jun; 1(6):630-642. Garske KM, Pan DZ, Miao Z, Bhagat YV, Comenho C, Robles CR, Benhammou JN, Alvarez M, Ko A, Ye CJ, Pisegna JR, Mohlke KL, Sinsheimer JS, Laakso M, Pajukanta P. PMID: 31538139.
      View in: PubMed   Mentions:
    8. Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity. Cell. 2019 04 18; 177(3):556-571.e16. 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. PMID: 30955881.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    9. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 2019 03 22; 20(1):63. Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, Marioni JC. PMID: 30902100.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    10. 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. 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. PMID: 30446528.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    11. Lineage dynamics of murine pancreatic development at single-cell resolution. Nat Commun. 2018 09 25; 9(1):3922. Byrnes LE, Wong DM, Subramaniam M, Meyer NP, Gilchrist CL, Knox SM, Tward AD, Ye CJ, Sneddon JB. PMID: 30254276.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    12. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat Genet. 2018 08; 50(8):1140-1150. 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. PMID: 29988122.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    13. Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. 2018 07; 559(7715):E13. 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. PMID: 29899441.
      View in: PubMed   Mentions:    Fields:    
    14. Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity. Immunity. 2018 05 15; 48(5):1014-1028.e6. Rodda LB, Lu E, Bennett ML, Sokol CL, Wang X, Luther SA, Barres BA, Luster AD, Ye CJ, Cyster JG. PMID: 29752062.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    15. Principles of Systems Biology, No. 27. Cell Syst. 2018 03 28; 6(3):260-262. PMID: 29596778.
      View in: PubMed   Mentions:    Fields:    
    16. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol. 2018 01; 36(1):89-94. 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. PMID: 29227470.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    17. An ancestry-based approach for detecting interactions. Genet Epidemiol. 2018 02; 42(1):49-63. 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. PMID: 29114909.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    18. Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks. Genetics. 2017 12; 207(4):1699-1709. Wilentzik R, Ye CJ, Gat-Viks I. PMID: 29046401.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    19. Covariate selection for association screening in multiphenotype genetic studies. Nat Genet. 2017 Dec; 49(12):1789-1795. Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N. PMID: 29038595.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    20. Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. 2017 09 07; 549(7670):111-115. 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. PMID: 28854172.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    21. 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. Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A. PMID: 28389661.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansAnimalsCells
    22. A tissue checkpoint regulates type 2 immunity. Nat Immunol. 2016 Dec; 17(12):1381-1387. 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. PMID: 27749840.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    23. Transethnic Genetic-Correlation Estimates from Summary Statistics. Am J Hum Genet. 2016 07 07; 99(1):76-88. Brown BC, Ye CJ, Price AL, Zaitlen N. PMID: 27321947.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    24. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 07; 26(7):863-73. Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. PMID: 27197206.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    25. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell. 2016 Jan 28; 164(3):564-78. 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. PMID: 26824662.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    26. 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. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A. PMID: 26216948.
      View in: PubMed   Mentions: 136     Fields:    Translation:HumansCells
    27. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Cell. 2015 Jul 30; 162(3):675-86. 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. PMID: 26189680.
      View in: PubMed   Mentions: 98     Fields:    Translation:AnimalsCells
    28. Intersection of population variation and autoimmunity genetics in human T cell activation. Science. 2014 Sep 12; 345(6202):1254665. 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. PMID: 25214635.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    29. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science. 2014 May 02; 344(6183):519-23. 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. PMID: 24786080.
      View in: PubMed   Mentions: 148     Fields:    Translation:HumansCells
    30. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. Genome Biol. 2014 Apr 07; 15(4):r61. Joo JW, Sul JH, Han B, Ye C, Eskin E. PMID: 24708878.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    31. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science. 2014 Mar 07; 343(6175):1246980. 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. PMID: 24604203.
      View in: PubMed   Mentions: 126     Fields:    Translation:HumansCells
    32. Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches. PLoS Genet. 2013 Jun; 9(6):e1003491. Sul JH, Han B, Ye C, Choi T, Eskin E. PMID: 23785294.
      View in: PubMed   Mentions: 22     Fields:    Translation:Animals
    33. 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. 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. PMID: 23396133.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    34. 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. 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. PMID: 22670052.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    35. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. Bioinformatics. 2011 Jul 01; 27(13):i288-94. Furlotte NA, Kang HM, Ye C, Eskin E. PMID: 21685083.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    36. 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. Kang EY, Ye C, Shpitser I, Eskin E. PMID: 20377462.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    37. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol. 2009 Mar; 5(3):e1000311. Ye C, Galbraith SJ, Liao JC, Eskin E. PMID: 19300475.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    38. Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics. 2008 Dec; 180(4):1909-25. Kang HM, Ye C, Eskin E. PMID: 18791227.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimals
    39. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. Bioinformatics. 2007 Jan 15; 23(2):e84-90. Ye C, Eskin E. PMID: 17237110.
      View in: PubMed   Mentions: 8     Fields:    
    40. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 2005 Jul; 15(7):998-1006. Bashir A, Ye C, Price AL, Bafna V. PMID: 15998912.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    41. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 Jan; 23(1):137-44. 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. PMID: 15637633.
      View in: PubMed   Mentions: 402     Fields:    Translation:HumansAnimalsCells
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