Jimmie Ye, PhD

Title(s)Professor, Medicine
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSW, #001
San Francisco CA 94143
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
    Mapping gene-by-environment interactions using multiplexed single cell RNA-sequencing
    NIH R01HG011239Aug 7, 2020 - May 31, 2024
    Role: Principal Investigator
    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 Bibliographic 
    Collapse selected 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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. Identification and regulation of circulating tumor TCR-matched cytotoxic CD4+ lymphocytes by KLRG1 in bladder cancer. JCI Insight. 2025 Apr 29. Kwek SS, Yang H, Li T, Ilano A, Chow ED, Zhang L, Chang H, Luong D, Lea A, Clark M, Starzinski A, Shi Y, McCarthy E, Porten S, Meng MV, Ye CJ, Fong L, Oh DY. PMID: 40299576.
      View in: PubMed   Mentions:    Fields:    
    2. Defining the host dependencies and the transcriptional landscape of RSV infection and bystander activation. bioRxiv. 2025 Mar 26. Sunshine S, Puschnik A, Retallack H, Laurie MT, Liu J, Peng D, Knopp K, Zinter MS, Ye CJ, DeRisi JL. PMID: 40196489; PMCID: PMC11974880.
      View in: PubMed   Mentions:
    3. Phenotypic pleiotropy of missense variants in human B cell-confinement receptor P2RY8. bioRxiv. 2025 Mar 06. LaFlam TN, Billesbølle CB, Dinh T, Wolfreys FD, Lu E, Matteson T, An J, Xu Y, Singhal A, Brandes N, Ntranos V, Manglik A, Cyster JG, Ye CJ. PMID: 40093123; PMCID: PMC11908195.
      View in: PubMed   Mentions:
    4. SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci. Nat Biotechnol. 2025 Feb 05. Chang CR, Vykunta VS, Lee JHJ, Li K, Kochendoerfer C, Muldoon JJ, Wang CH, Mazumder T, Sun Y, Goodman DB, Nyberg WA, Liu C, Allain V, Rothrock A, Ye CJ, Marson A, Shy BR, Eyquem J. PMID: 39910194.
      View in: PubMed   Mentions:    Fields:    
    5. In vivo engineering of murine T cells using the evolved adeno-associated virus variant Ark313. Immunity. 2025 Feb 11; 58(2):499-512.e7. Nyberg WA, Wang CH, Ark J, Liu C, Clouden S, Qualls A, Caryotakis S, Wells E, Simon K, Garza C, Bernard PL, Lopez-Ichikawa M, Li Z, Seo J, Kimmerly GR, Muldoon JJ, Chen PA, Li M, Liang HE, Kersten K, Rosales A, Kuhn N, Ye CJ, Gardner JM, Molofsky A, Ricardo-Gonzalez RR, Asokan A, Eyquem J. PMID: 39909036.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    6. Endogenous antigens shape the transcriptome and TCR repertoire in an autoimmune arthritis model. J Clin Invest. 2024 Nov 26; 135(2). McCarthy EE, Yu S, Perlmutter N, Nakao Y, Naito R, Lin C, Riekher V, DeRisi J, Ye CJ, Weiss A, Ashouri JF. PMID: 39589811; PMCID: PMC11735108.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    7. Physical inactivity exacerbates pathologic inflammatory signalling at the single cell level in patients with systemic lupus. EBioMedicine. 2024 Dec; 110:105432. Patterson SL, Van Phan H, Ye CJ, Lanata C, González SC, Park J, Criswell LA, Barbour KE, Yazdany J, Dall'Era M, Sirota M, Katz P, Langelier CR. PMID: 39531917; PMCID: PMC11603005.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    8. Method of moments framework for differential expression analysis of single-cell RNA sequencing data. Cell. 2024 Oct 31; 187(22):6393-6410.e16. Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. PMID: 39454576; PMCID: PMC11556465.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    9. Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition. Nat Biotechnol. 2024 Sep 23. Mitchel J, Gordon MG, Perez RK, Biederstedt E, Bueno R, Ye CJ, Kharchenko PV. PMID: 39313646.
      View in: PubMed   Mentions: 4     Fields:    
    10. Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. Nat Genet. 2024 Oct; 56(10):2078-2092. Loeb GB, Kathail P, Shuai RW, Chung R, Grona RJ, Peddada S, Sevim V, Federman S, Mader K, Chu AY, Davitte J, Du J, Gupta AR, Ye CJ, Shafer S, Przybyla L, Rapiteanu R, Ioannidis NM, Reiter JF. PMID: 39256582.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    11. The evolution of computational research in a data-centric world. Cell. 2024 08 22; 187(17):4449-4457. Deshpande D, Chhugani K, Ramesh T, Pellegrini M, Shifman S, Abedalthagafi MS, Alqahtani S, Ye J, Liu XS, Leek JT, Brazma A, Ophoff RA, Rao G, Butte AJ, Moore JH, Katritch V, Mangul S. PMID: 39178828; PMCID: PMC11938813.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    12. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatol. 2024 Nov; 6(11):769-779. Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. PMID: 39143499; PMCID: PMC11557995.
      View in: PubMed   Mentions:
    13. Population Diversity at the Single-Cell Level. Annu Rev Genomics Hum Genet. 2024 Aug; 25(1):27-49. Gordon MG, Kathail P, Choy B, Kim MC, Mazumder T, Gearing M, Ye CJ. PMID: 38382493.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    14. CD4+ CAR T-cell exhaustion associated with early relapse of multiple myeloma after BCMA CAR T-cell therapy. Blood Adv. 2024 07 09; 8(13):3562-3575. Ledergor G, Fan Z, Wu K, McCarthy E, Hyrenius-Wittsten A, Starzinski A, Chang H, Bridge M, Kwek S, Cheung A, Bylsma S, Hansen E, Wolf J, Wong S, Shah N, Roybal KT, Martin T, Ye CJ, Fong L. PMID: 38574299; PMCID: PMC11319832.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    15. Single-cell RNA-Seq analysis reveals cell subsets and gene signatures associated with rheumatoid arthritis disease activity. JCI Insight. 2024 Jul 02; 9(16). Binvignat M, Miao BY, Wibrand C, Yang MM, Rychkov D, Flynn E, Nititham J, Tamaki W, Khan U, Carvidi A, Krueger M, Niemi E, Sun Y, Fragiadakis GK, Sellam J, Mariotti-Ferrandiz E, Klatzmann D, Gross AJ, Ye CJ, Butte AJ, Criswell LA, Nakamura MC, Sirota M. PMID: 38954480; PMCID: PMC11343607.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    16. Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. bioRxiv. 2024 Jun 22. Loeb GB, Kathail P, Shuai R, Chung R, Grona RJ, Peddada S, Sevim V, Federman S, Mader K, Chu A, Davitte J, Du J, Gupta AR, Ye CJ, Shafer S, Przybyla L, Rapiteanu R, Ioannidis N, Reiter JF. PMID: 38948875; PMCID: PMC11212968.
      View in: PubMed   Mentions:
    17. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet. 2024 Jun; 56(6):1156-1167. Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. PMID: 38811842; PMCID: PMC11176074.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    18. Functional genomics in inborn errors of immunity. Immunol Rev. 2024 03; 322(1):53-70. Hurabielle C, LaFlam TN, Gearing M, Ye CJ. PMID: 38329267; PMCID: PMC10950534.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    19. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol. 2024 01 22; 25(1):28. Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. PMID: 38254214; PMCID: PMC10801966.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    20. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs. Sci Immunol. 2023 12 22; 8(90):eabp8966. Bastard P, Vazquez SE, Liu J, Laurie MT, Wang CY, Gervais A, Le Voyer T, Bizien L, Zamecnik C, Philippot Q, Rosain J, Catherinot E, Willmore A, Mitchell AM, Bair R, Garçon P, Kenney H, Fekkar A, Salagianni M, Poulakou G, Siouti E, Sahanic S, Tancevski I, Weiss G, Nagl L, Manry J, Duvlis S, Arroyo-Sánchez D, Paz Artal E, Rubio L, Perani C, Bezzi M, Sottini A, Quaresima V, Roussel L, Vinh DC, Reyes LF, Garzaro M, Hatipoglu N, Boutboul D, Tandjaoui-Lambiotte Y, Borghesi A, Aliberti A, Cassaniti I, Venet F, Monneret G, Halwani R, Sharif-Askari NS, Danielson J, Burrel S, Morbieu C, Stepanovskyy Y, Bondarenko A, Volokha A, Boyarchuk O, Gagro A, Neuville M, Neven B, Keles S, Hernu R, Bal A, Novelli A, Novelli G, Saker K, Ailioaie O, Antolí A, Jeziorski E, Rocamora-Blanch G, Teixeira C, Delaunay C, Lhuillier M, Le Turnier P, Zhang Y, Mahevas M, Pan-Hammarström Q, Abolhassani H, Bompoil T, Dorgham K, COVID HGE Consortium, French COVID Study Group, COMET Consortium, Gorochov G, Laouenan C, Rodríguez-Gallego C, Ng LFP, Renia L, Pujol A, Belot A, Raffi F, Allende LM, Martinez-Picado J, Ozcelik T, Imberti L, Notarangelo LD, Troya J, Solanich X, Zhang SY, Puel A, Wilson MR, Trouillet-Assant S, Abel L, Jouanguy E, Ye CJ, Cobat A, Thompson LM, Andreakos E, Zhang Q, Anderson MS, Casanova JL, DeRisi JL. PMID: 35857576; PMCID: PMC9210448.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCellsPHPublic Health
    21. Protracted neuronal recruitment in the temporal lobes of young children. Nature. 2024 Feb; 626(8001):1056-1065. Nascimento MA, Biagiotti S, Herranz-Pérez V, Santiago S, Bueno R, Ye CJ, Abel TJ, Zhang Z, Rubio-Moll JS, Kriegstein AR, Yang Z, Garcia-Verdugo JM, Huang EJ, Alvarez-Buylla A, Sorrells SF. PMID: 38122823; PMCID: PMC10901738.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    22. Base-editing mutagenesis maps alleles to tune human T cell functions. Nature. 2024 Jan; 625(7996):805-812. Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, Marson A. PMID: 38093011; PMCID: PMC11065414.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    23. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. bioRxiv. 2023 Nov 10. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J. PMID: 37986917; PMCID: PMC10659396.
      View in: PubMed   Mentions:
    24. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun. 2023 10 06; 14(1):6245. Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. PMID: 37803001; PMCID: PMC10558542.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    25. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Cell. 2023 10 12; 186(21):4567-4582.e20. Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Hofman L, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. PMID: 37794590; PMCID: PMC10664023.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansCells
    26. Functional characterization of Alzheimer's disease genetic variants in microglia. Nat Genet. 2023 Oct; 55(10):1735-1744. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, Perera RM, Gan L, Li Y, Shen Y. PMID: 37735198; PMCID: PMC10939305.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    27. Modular pooled discovery of synthetic knockin sequences to program durable cell therapies. Cell. 2023 09 14; 186(19):4216-4234.e33. Blaeschke F, Chen YY, Apathy R, Daniel B, Chen AY, Chen PA, Sandor K, Zhang W, Li Z, Mowery CT, Yamamoto TN, Nyberg WA, To A, Yu R, Bueno R, Kim MC, Schmidt R, Goodman DB, Feuchtinger T, Eyquem J, Jimmie Ye C, Carnevale J, Satpathy AT, Shifrut E, Roth TL, Marson A. PMID: 37714135; PMCID: PMC10508323.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    28. Genome-wide prediction of disease variant effects with a deep protein language model. Nat Genet. 2023 09; 55(9):1512-1522. Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V. PMID: 37563329; PMCID: PMC10484790.
      View in: PubMed   Mentions: 101     Fields:    Translation:Humans
    29. Reply to Barton et al: signatures of natural selection during the Black Death. bioRxiv. 2023 Apr 07. Vilgalys TP, Klunk J, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. PMID: 37066254; PMCID: PMC10104142.
      View in: PubMed   Mentions:
    30. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. bioRxiv. 2023 Mar 22. Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. PMID: 36993359; PMCID: PMC10055432.
      View in: PubMed   Mentions:
    31. Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies. Sci Transl Med. 2022 11 09; 14(670):eabm1463. Goodman DB, Azimi CS, Kearns K, Talbot A, Garakani K, Garcia J, Patel N, Hwang B, Lee D, Park E, Vykunta VS, Shy BR, Ye CJ, Eyquem J, Marson A, Bluestone JA, Roybal KT. PMID: 36350984; PMCID: PMC9939256.
      View in: PubMed   Mentions: 26     Fields:    
    32. Evolution of immune genes is associated with the Black Death. Nature. 2022 Nov; 611(7935):312-319. Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. PMID: 36261521; PMCID: PMC9580435.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansCells
    33. Multi-context genetic modeling of transcriptional regulation resolves novel disease loci. Nat Commun. 2022 09 28; 13(1):5704. Thompson M, Gordon MG, Lu A, Tandon A, Halperin E, Gusev A, Ye CJ, Balliu B, Zaitlen N. PMID: 36171194; PMCID: PMC9519579.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    34. Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis. Cell Rep. 2022 09 20; 40(12):111384. Keenan BP, McCarthy EE, Ilano A, Yang H, Zhang L, Allaire K, Fan Z, Li T, Lee DS, Sun Y, Cheung A, Luong D, Chang H, Chen B, Marquez J, Sheldon B, Kelley RK, Ye CJ, Fong L. PMID: 36130508; PMCID: PMC10060099.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    35. Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity. Front Immunol. 2022; 13:902232. Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M. PMID: 35799782; PMCID: PMC9254730.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    36. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nat Commun. 2022 06 07; 13(1):3267. Oelen R, de Vries DH, Brugge H, Gordon MG, Vochteloo M, single-cell eQTLGen consortium, BIOS Consortium, Ye CJ, Westra HJ, Franke L, van der Wijst MGP. PMID: 35672358; PMCID: PMC9174272.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    37. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science. 2022 04 08; 376(6589):eabf1970. Perez RK, Gordon MG, Subramaniam M, Kim MC, Hartoularos GC, Targ S, Sun Y, Ogorodnikov A, Bueno R, Lu A, Thompson M, Rappoport N, Dahl A, Lanata CM, Matloubian M, Maliskova L, Kwek SS, Li T, Slyper M, Waldman J, Dionne D, Rozenblatt-Rosen O, Fong L, Dall'Era M, Balliu B, Regev A, Yazdany J, Criswell LA, Zaitlen N, Ye CJ. PMID: 35389781; PMCID: PMC9297655.
      View in: PubMed   Mentions: 157     Fields:    
    38. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science. 2022 04 08; 376(6589):eabf3041. Yazar S, Alquicira-Hernandez J, Wing K, Senabouth A, Gordon MG, Andersen S, Lu Q, Rowson A, Taylor TRP, Clarke L, Maccora K, Chen C, Cook AL, Ye CJ, Fairfax KA, Hewitt AW, Powell JE. PMID: 35389779.
      View in: PubMed   Mentions: 173     Fields:    
    39. Obesity alters pathology and treatment response in inflammatory disease. Nature. 2022 04; 604(7905):337-342. Bapat SP, Whitty C, Mowery CT, Liang Y, Yoo A, Jiang Z, Peters MC, Zhang LJ, Vogel I, Zhou C, Nguyen VQ, Li Z, Chang C, Zhu WS, Hastie AT, He H, Ren X, Qiu W, Gayer SG, Liu C, Choi EJ, Fassett M, Cohen JN, Sturgill JL, Crotty Alexander LE, Suh JM, Liddle C, Atkins AR, Yu RT, Downes M, Liu S, Nikolajczyk BS, Lee IK, Guttman-Yassky E, Ansel KM, Woodruff PG, Fahy JV, Sheppard D, Gallo RL, Ye CJ, Evans RM, Zheng Y, Marson A. PMID: 35355021; PMCID: PMC9165753.
      View in: PubMed   Mentions: 70     Fields:    Translation:AnimalsCells
    40. The development and evolution of inhibitory neurons in primate cerebrum. Nature. 2022 03; 603(7903):871-877. Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA. PMID: 35322231; PMCID: PMC8967711.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    41. Combined Single Cell Transcriptome and Surface Epitope Profiling Identifies Potential Biomarkers of Psoriatic Arthritis and Facilitates Diagnosis via Machine Learning. Front Immunol. 2022; 13:835760. Liu J, Kumar S, Hong J, Huang ZM, Paez D, Castillo M, Calvo M, Chang HW, Cummins DD, Chung M, Yeroushalmi S, Bartholomew E, Hakimi M, Ye CJ, Bhutani T, Matloubian M, Gensler LS, Liao W. PMID: 35309349; PMCID: PMC8924042.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    42. CRISPR activation and interference screens decode stimulation responses in primary human T cells. Science. 2022 02 04; 375(6580):eabj4008. Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A. PMID: 35113687; PMCID: PMC9307090.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    43. CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq. Pac Symp Biocomput. 2022; 27:337-348. He B, Thomson M, Subramaniam M, Perez R, Ye CJ, Zou J. PMID: 34890161.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    44. Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney. Am J Transplant. 2022 03; 22(3):876-885. Rashmi P, Sur S, Sigdel TK, Boada P, Schroeder AW, Damm I, Kretzler M, Hodgin J, Hartoularos G, Jimmie Ye C, Sarwal MM, Kidney Precision Medicine Project. PMID: 34687145; PMCID: PMC8897263.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    45. Monoclonal antibody-mediated neutralization of SARS-CoV-2 in an IRF9-deficient child. Proc Natl Acad Sci U S A. 2021 11 09; 118(45). Lévy R, Zhang P, Bastard P, Dorgham K, Melki I, Hadchouel A, Hartoularos GC, Neven B, Castelle M, Roy C, Toin T, Berteloot L, Bizien L, Abid H, Burgard M, Houhou-Fidouh N, Rozenberg F, Jouanguy E, Ye CJ, Gorochov G, Zhang Q, Casanova JL. PMID: 34702736; PMCID: PMC8609338.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    46. The effect of low-dose IL-2 and Treg adoptive cell therapy in patients with type 1 diabetes. JCI Insight. 2021 09 22; 6(18). Dong S, Hiam-Galvez KJ, Mowery CT, Herold KC, Gitelman SE, Esensten JH, Liu W, Lares AP, Leinbach AS, Lee M, Nguyen V, Tamaki SJ, Tamaki W, Tamaki CM, Mehdizadeh M, Putnam AL, Spitzer MH, Ye CJ, Tang Q, Bluestone JA. PMID: 34324441; PMCID: PMC8492314.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCellsCTClinical Trials
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    96. 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; PMCID: PMC4124741.
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    97. 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; PMCID: PMC3681686.
      View in: PubMed   Mentions: 52     Fields:    Translation:Animals
    98. 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; PMCID: PMC3901305.
      View in: PubMed   Mentions: 131     Fields:    Translation:HumansCells
    99. 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; PMCID: PMC3467001.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    100. 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; PMCID: PMC3117390.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
    101. 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; PMCID: PMC3198891.
      View in: PubMed   Mentions: 3     Fields:    
    102. 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; PMCID: PMC2649002.
      View in: PubMed   Mentions: 15     Fields:    
    103. 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; PMCID: PMC2600931.
      View in: PubMed   Mentions: 72     Fields:    
    104. 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: 3     Fields:    
    105. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 2005 Jul; 15(7):998-1006. Bashir A, Ye C, Price AL, Bafna V. PMID: 15998912; PMCID: PMC1172044.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    106. 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: 393     Fields:    
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