Jimmie Ye, PhD

Title(s)Associate Professor, Medicine
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSW, #1201E
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 Websites

    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

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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.
    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. Functional characterization of Alzheimer's disease genetic variants in microglia. Nat Genet. 2023 Sep 21. 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.
      View in: PubMed   Mentions:
    2. 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:
    3. 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:
    4. 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:
    5. 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: 7     Fields:    Translation:HumansCells
    6. 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: 22     Fields:    Translation:HumansCells
    7. 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: 4     Fields:    Translation:HumansCells
    8. 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: 3     Fields:    Translation:HumansCells
    9. 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: 2     Fields:    Translation:HumansCells
    10. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs. Sci Immunol. 2022 Jun 14; eabp8966. Bastard P, Vazquez S, 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, Keles S, 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: 21     Fields:    
    11. 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: 13     Fields:    Translation:HumansCells
    12. 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: 43     Fields:    Translation:HumansCells
    13. 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: 49     Fields:    Translation:HumansCells
    14. 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: 30     Fields:    Translation:AnimalsCells
    15. 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: 20     Fields:    Translation:AnimalsCells
    16. 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: 1     Fields:    Translation:HumansCells
    17. 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: 45     Fields:    Translation:HumansCells
    18. 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: 3     Fields:    Translation:Humans
    19. 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: 17     Fields:    Translation:HumansCells
    20. 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: 38     Fields:    Translation:HumansCellsCTClinical Trials
    21. CCR2 deficiency alters activation of microglia subsets in traumatic brain injury. Cell Rep. 2021 09 21; 36(12):109727. Somebang K, Rudolph J, Imhof I, Li L, Niemi EC, Shigenaga J, Tran H, Gill TM, Lo I, Zabel BA, Schmajuk G, Wipke BT, Gyoneva S, Jandreski L, Craft M, Benedetto G, Plowey ED, Charo I, Campbell J, Ye CJ, Panter SS, Nakamura MC, Eckalbar W, Hsieh CL. PMID: 34551293; PMCID: PMC8594931.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    22. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Sci Transl Med. 2021 Sep 22; 13(612):eabh2624. van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ, UCSF COMET consortium. PMID: 34429372; PMCID: PMC8601717.
      View in: PubMed   Mentions: 94     Fields:    Translation:Humans
    23. SCITO-seq: single-cell combinatorial indexed cytometry sequencing. Nat Methods. 2021 08; 18(8):903-911. Hwang B, Lee DS, Tamaki W, Sun Y, Ogorodnikov A, Hartoularos GC, Winters A, Yeung BZ, Nazor KL, Song YS, Chow ED, Spitzer MH, Ye CJ. PMID: 34354295; PMCID: PMC8643207.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    24. Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis. Blood Cancer Discov. 2021 09; 2(5):434-449. Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye CJ, Carbone DP, Munster PN, Fragiadakis GK, McCormick F, Andreadis C. PMID: 34514432; PMCID: PMC8425277.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    25. Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree. Elife. 2021 05 19; 10. Hendley AM, Rao AA, Leonhardt L, Ashe S, Smith JA, Giacometti S, Peng XL, Jiang H, Berrios DI, Pawlak M, Li LY, Lee J, Collisson EA, Anderson MS, Fragiadakis GK, Yeh JJ, Ye CJ, Kim GE, Weaver VM, Hebrok M. PMID: 34009124; PMCID: PMC8184217.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    26. XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment. Sci Adv. 2021 04; 7(17). Lee Y, Bogdanoff D, Wang Y, Hartoularos GC, Woo JM, Mowery CT, Nisonoff HM, Lee DS, Sun Y, Lee J, Mehdizadeh S, Cantlon J, Shifrut E, Ngyuen DN, Roth TL, Song YS, Marson A, Chow ED, Ye CJ. PMID: 33883145; PMCID: PMC8059935.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    27. Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures. Commun Biol. 2021 04 21; 4(1):488. Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Dall'Era M, Yazdany J, Criswell LA, Sirota M. PMID: 33883687; PMCID: PMC8060402.
      View in: PubMed   Mentions: 7  Translation:HumansCells
    28. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021 Mar 10. van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Voyer TL, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, UCSF COMET consortium, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. PMID: 33758859; PMCID: PMC7987018.
      View in: PubMed   Mentions:
    29. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nat Commun. 2021 02 17; 12(1):1096. Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV. PMID: 33597545; PMCID: PMC7889611.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    30. Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 03; 591(7848):124-130. Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33494096; PMCID: PMC8567458.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansCells
    31. No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. BMC Biol. 2021 01 20; 19(1):10. McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA. PMID: 33472616; PMCID: PMC7816397.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    32. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. Cell Rep. 2021 01 05; 34(1):108573. Bunis DG, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ, Sirota M, McCune JM, Burt TD. PMID: 33406429; PMCID: PMC10263444.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    33. Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis. Nat Commun. 2020 10 30; 11(1):5504. Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E. PMID: 33127880; PMCID: PMC7599215.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    34. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Res Sq. 2020 Oct 28. Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33140041; PMCID: PMC7605560.
      View in: PubMed   Mentions:
    35. Functional CRISPR dissection of gene networks controlling human regulatory T cell identity. Nat Immunol. 2020 11; 21(11):1456-1466. Schumann K, Raju SS, Lauber M, Kolb S, Shifrut E, Cortez JT, Skartsis N, Nguyen VQ, Woo JM, Roth TL, Yu R, Nguyen MLT, Simeonov DR, Nguyen DN, Targ S, Gate RE, Tang Q, Bluestone JA, Spitzer MH, Ye CJ, Marson A. PMID: 32989329; PMCID: PMC7577958.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    36. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 10; 38(10):1174-1183. 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 RP, 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: 32855547; PMCID: PMC7740072.
      View in: PubMed   Mentions: 149     Fields:    Translation:HumansCellsPHPublic Health
    37. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc. 2020 08; 15(8):2387-2412. Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. PMID: 32641802; PMCID: PMC7550205.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    38. Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM. Sci Rep. 2020 07 03; 10(1):11019. Alvarez M, Rahmani E, Jew B, Garske KM, Miao Z, Benhammou JN, Ye CJ, Pisegna JR, Pietiläinen KH, Halperin E, Pajukanta P. PMID: 32620816; PMCID: PMC7335186.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimals
    39. IL-27: An endogenous constitutive repressor of human monocytes. Clin Immunol. 2020 08; 217:108498. Frangieh M, McHenry A, Phillips R, Ye C, Bernier A, Laffel L, Elyaman W, Bradshaw EM. PMID: 32531345; PMCID: PMC8984538.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    40. Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer. Cell. 2020 06 25; 181(7):1612-1625.e13. 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; PMCID: PMC7321885.
      View in: PubMed   Mentions: 226     Fields:    Translation:HumansCells
    41. 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; PMCID: PMC7273265.
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    42. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. Cell. 2020 04 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; PMCID: PMC7219528.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansAnimalsCells
    43. 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; PMCID: PMC6763499.
      View in: PubMed   Mentions: 69     Fields:    Translation:Humans
    44. 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; PMCID: PMC6730564.
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    45. 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: 1     Fields:    Translation:Cells
    46. Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans. Nat Metab. 2019 06; 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; PMCID: PMC6752726.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    47. 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; PMCID: PMC6954108.
      View in: PubMed   Mentions: 231     Fields:    Translation:HumansAnimalsCells
    48. 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, participants in the 1st Human Cell Atlas Jamboree, Marioni JC. PMID: 30902100; PMCID: PMC6431044.
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    49. 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; PMCID: PMC6280757.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    50. 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; PMCID: PMC6156586.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    51. 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; PMCID: PMC6097927.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    52. 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; PMCID: PMC5971117.
      View in: PubMed   Mentions: 168     Fields:    Translation:AnimalsCells
    53. Principles of Systems Biology, No. 27. Cell Syst. 2018 03 28; 6(3):260-262. PMID: 29596778.
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    54. 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; PMCID: PMC5784859.
      View in: PubMed   Mentions: 322     Fields:    Translation:HumansCells
    55. 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; PMCID: PMC6065511.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    56. 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; PMCID: PMC5714474.
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    57. 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; PMCID: PMC5797835.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    58. 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; PMCID: PMC5675716.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansAnimalsCells
    59. 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; PMCID: PMC5428439.
      View in: PubMed   Mentions: 295     Fields:    Translation:HumansAnimalsCells
    60. 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; PMCID: PMC5275767.
      View in: PubMed   Mentions: 122     Fields:    Translation:AnimalsCells
    61. Transethnic Genetic-Correlation Estimates from Summary Statistics. Am J Hum Genet. 2016 07 07; 99(1):76-88. Brown BC, Asian Genetic Epidemiology Network Type 2 Diabetes Consortium, Ye CJ, Price AL, Zaitlen N. PMID: 27321947; PMCID: PMC5005434.
      View in: PubMed   Mentions: 113     Fields:    Translation:Humans
    62. 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; PMCID: PMC4937562.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    63. 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, Immunological Genome Project Consortium. PMID: 26824662; PMCID: PMC4743492.
      View in: PubMed   Mentions: 133     Fields:    Translation:HumansAnimalsCells
    64. 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; PMCID: PMC4547290.
      View in: PubMed   Mentions: 315     Fields:    Translation:HumansCells
    65. 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; PMCID: PMC4522370.
      View in: PubMed   Mentions: 226     Fields:    Translation:AnimalsCells
    66. 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; PMCID: PMC4751028.
      View in: PubMed   Mentions: 131     Fields:    Translation:HumansCells
    67. 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; PMCID: PMC4910825.
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    68. 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; PMCID: PMC4053820.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    69. 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.
      View in: PubMed   Mentions: 225     Fields:    Translation:HumansCells
    70. 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: 59     Fields:    Translation:Animals
    71. 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: 123     Fields:    Translation:HumansCells
    72. 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: 4     Fields:    Translation:HumansAnimalsCells
    73. 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: 12     Fields:    Translation:HumansAnimals
    74. 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: 4     Fields:    Translation:Animals
    75. 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: 21     Fields:    Translation:AnimalsCells
    76. 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: 80     Fields:    Translation:HumansAnimals
    77. 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:    
    78. 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: 15     Fields:    Translation:HumansAnimalsCells
    79. 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: 445     Fields:    Translation:HumansAnimalsCells
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