Jimmie Ye, PhD

Education
Postdoc, 2014 - Cell Circuits Program, Broad Institute
PhD, 2009 - Bioinformatics and Systems Biology, University of California San Diego
BS, 2002 - Bioengineering, University of California Berkeley
BS, 2002 - Electrical Engineering and Computer Sciences, University of California Berkeley
Websites
Publications

  1. 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. Identification and regulation of circulating tumor TCR-matched cytotoxic CD4+ lymphocytes by KLRG1 in bladder cancer. JCI insight 2025. PMID: 40299576


  2. Sunshine S, Puschnik A, Retallack H, Laurie MT, Liu J, Peng D, Knopp K, Zinter MS, Ye CJ, DeRisi JL. Defining the host dependencies and the transcriptional landscape of RSV infection and bystander activation. bioRxiv : the preprint server for biology 2025. PMID: 40196489


  3. 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. Phenotypic pleiotropy of missense variants in human B cell-confinement receptor P2RY8. bioRxiv : the preprint server for biology 2025. PMID: 40093123


  4. 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. SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci. Nature biotechnology 2025. PMID: 39910194


  5. 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. In vivo engineering of murine T cells using the evolved adeno-associated virus variant Ark313. Immunity 2025. PMID: 39909036


  6. McCarthy EE, Yu S, Perlmutter N, Nakao Y, Naito R, Lin C, Riekher V, DeRisi J, Ye CJ, Weiss A, Ashouri JF. Endogenous antigens shape the transcriptome and TCR repertoire in an autoimmune arthritis model. The Journal of clinical investigation 2024. PMID: 39589811


  7. 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. Physical inactivity exacerbates pathologic inflammatory signalling at the single cell level in patients with systemic lupus. EBioMedicine 2024. PMID: 39531917


  8. Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. Method of moments framework for differential expression analysis of single-cell RNA sequencing data. Cell 2024. PMID: 39454576


  9. Mitchel J, Gordon MG, Perez RK, Biederstedt E, Bueno R, Ye CJ, Kharchenko PV. Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition. Nature biotechnology 2024. PMID: 39313646


  10. 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. Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. Nature genetics 2024. PMID: 39256582


  11. Deshpande D, Chhugani K, Ramesh T, Pellegrini M, Shiffman 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. The evolution of computational research in a data-centric world. Cell 2024. PMID: 39178828


  12. 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. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatology 2024. PMID: 39143499


  13. Gordon MG, Kathail P, Choy B, Kim MC, Mazumder T, Gearing M, Ye CJ. Population Diversity at the Single-Cell Level. Annual review of genomics and human genetics 2024. PMID: 38382493


  14. Ledergor G, Fan Z, Wu K, McCarthy E, Hyrenius-Wittsten A, Starzinski A, Chang H, Bridge M, Kwek SS, Cheung A, Bylsma SA, Hansen E, Wolf JL, Wong SW, Shah N, Roybal KT, Martin TG, Ye CJ, Fong L. CD4+ CAR-T cell exhaustion associated with early relapse of multiple myeloma after BCMA CAR-T cell therapy. Blood advances 2024. PMID: 38574299


  15. Binvignat M, Miao BY, Wibrand C, Yang MM, Rychkov D, Flynn E, Nititham J, Tamaki W, Khan U, Carvidi A, Krueger M, Niemi EC, Sun Y, Fragiadakis GK, Sellam J, Mariotti-Ferrandiz E, Klatzmann D, Gross AJ, Ye CJ, Butte AJ, Criswell LA, Nakamura MC, Sirota M. Single-cell RNA-seq analysis reveals cell subsets and gene signatures associated with Rheumatoid Arthritis Disease Activity. JCI insight 2024. PMID: 38954480


  16. 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. Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. bioRxiv : the preprint server for biology 2024. PMID: 38948875


  17. 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. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics 2024. PMID: 38811842


  18. Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunological reviews 2024. PMID: 38329267


  19. Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome biology 2024. PMID: 38254214


  20. 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. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs. Science immunology 2022. PMID: 35857576


  21. 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. Protracted neuronal recruitment in the temporal lobe of young children. Nature 2023. PMID: 38122823


  22. 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. Base-editing mutagenesis maps alleles to tune human T cell functions. Nature 2023. PMID: 38093011


  23. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. bioRxiv : the preprint server for biology 2023. PMID: 37986917


  24. 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. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nature communications 2023. PMID: 37803001


  25. 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. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Cell 2023. PMID: 37794590


  26. 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. Functional characterization of Alzheimer's disease genetic variants in microglia. Nature genetics 2023. PMID: 37735198


  27. 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. Modular pooled discovery of synthetic knockin sequences to program durable cell therapies. Cell 2023. PMID: 37714135


  28. Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V. Genome-wide prediction of disease variant effects with a deep protein language model. Nature genetics 2023. PMID: 37563329


  29. 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. Reply to Barton et al: signatures of natural selection during the Black Death. bioRxiv : the preprint server for biology 2023. PMID: 37066254


  30. 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. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. bioRxiv : the preprint server for biology 2023. PMID: 36993359


  31. 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. Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies. Science translational medicine 2022. PMID: 36350984


  32. 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. Evolution of immune genes is associated with the Black Death. Nature 2022. PMID: 36261521


  33. Thompson M, Gordon MG, Lu A, Tandon A, Halperin E, Gusev A, Ye CJ, Balliu B, Zaitlen N. Multi-context genetic modeling of transcriptional regulation resolves novel disease loci. Nature communications 2022. PMID: 36171194


  34. 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. Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis. Cell reports 2022. PMID: 36130508


  35. Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M. Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity. Frontiers in immunology 2022. PMID: 35799782


  36. 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. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nature communications 2022. PMID: 35672358


  37. 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. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. A pilot telephone-based intervention for patients with poorly-controlled diabetes mellitus. 2022. PMID: 35389781


  38. 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. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. A pilot telephone-based intervention for patients with poorly-controlled diabetes mellitus. 2022. PMID: 35389779


  39. 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. Obesity alters pathology and treatment response in inflammatory disease. A pilot telephone-based intervention for patients with poorly-controlled diabetes mellitus. 2022. PMID: 35355021


  40. Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA. The development and evolution of inhibitory neurons in primate cerebrum. A pilot telephone-based intervention for patients with poorly-controlled diabetes mellitus. 2022. PMID: 35322231


  41. 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. Combined Single Cell Transcriptome and Surface Epitope Profiling Identifies Potential Biomarkers of Psoriatic Arthritis and Facilitates Diagnosis via Machine Learning. A pilot telephone-based intervention for patients with poorly-controlled diabetes mellitus. 2022. PMID: 35309349


  42. Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A. CRISPR activation and interference screens decode stimulation responses in primary human T cells. A pilot telephone-based intervention for patients with poorly-controlled diabetes mellitus. 2022. PMID: 35113687


  43. He B, Thomson M, Subramaniam M, Perez R, Ye CJ, Zou J. CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2022. PMID: 34890161


  44. 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. Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2021. PMID: 34687145


  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. Monoclonal antibody-mediated neutralization of SARS-CoV-2 in an IRF9-deficient child. Proceedings of the National Academy of Sciences of the United States of America 2021. PMID: 34702736


  46. 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. The effect of low-dose IL-2 and Treg adoptive cell therapy in patients with type 1 diabetes. JCI insight 2021. PMID: 34324441


  47. 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. CCR2 deficiency alters activation of microglia subsets in traumatic brain injury. Cell reports 2021. PMID: 34551293


  48. 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. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Science translational medicine 2021. PMID: 34429372


  49. 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. SCITO-seq: single-cell combinatorial indexed cytometry sequencing. Nature methods 2021. PMID: 34354295


  50. 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. Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis. Blood cancer discovery 2021. PMID: 34514432


  51. Hendley AM, Rao AA, Leonhardt L, Ashe S, Smith JA, Giacometti S, Peng XL, Jiang H, Berrios D, Pawlak M, Li LY, Lee J, Collisson EA, Anderson MS, Fragiadakis GK, Yeh JJ, Chun JY, Kim GE, Weaver VM, Hebrok M. Single cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree. eLife 2021. PMID: 34009124


  54. 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. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv : the preprint server for biology 2021. PMID: 33758859


  55. 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. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nature communications 2021. PMID: 33597545


  56. 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. Global absence and targeting of protective immune states in severe COVID-19. Nature 2021. PMID: 33494096


  57. McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA. No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. BMC biology 2021. PMID: 33472616


  58. 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. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. Cell reports 2021. PMID: 33406429


  59. Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E. Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis. Nature communications 2020. PMID: 33127880


  60. Krummel M, Combes A, Courau T, Kuhn N, Hu K, Ray A, Chen W, Cleary S, Chew N, Kushnoor D, Reeder G, Shen A, Tsui J, Hiam K, Sandoval PM, Zhu W, Lee D, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik C, Loudermilk R, Wilson M, Ye C, Fragiadakis G, Looney M, Chan V, Ward A, Carrillo S, Matthay M, Erle D, Woodruff P, Langelier C, Kangelaris K, Hendrickson C, Calfee C, Rao A. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Research square 2020. PMID: 33140041


  61. 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. Functional CRISPR dissection of gene networks controlling human regulatory T cell identity. Nature immunology 2020. PMID: 32989329


  62. 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. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nature biotechnology 2020. PMID: 32855547


  63. Keys KL, Mak ACY, White MJ, Eckalbar WL, Dahl AW, Mefford J, Mikhaylova AV, Contreras MG, Elhawary JR, Eng C, Hu D, Huntsman S, Oh SS, Salazar S, Lenoir MA, Ye JC, Thornton TA, Zaitlen N, Burchard EG, Gignoux CR. On the cross-population generalizability of gene expression prediction models. PLoS genetics 2020. PMID: 32797036


  64. Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulous-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature protocols 2020. PMID: 32641802


  65. Alvarez M, Rahmani E, Jew B, Garske KM, Miao Z, Benhammou JN, Ye CJ, Pisegna JR, Pietiläinen KH, Halperin E, Pajukanta P. Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM. Scientific Reports 2020. PMID: 32620816


  66. Frangieh M, McHenry A, Phillips R, Ye C, Bernier A, Laffel L, Elyaman W, Bradshaw EM. IL-27: An endogenous constitutive repressor of human monocytes. Clinical immunology (Orlando, Fla.) 2020. PMID: 32531345


  67. 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. Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer. Cell 2020. PMID: 32497499


  68. 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. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv : the preprint server for health sciences 2020. PMID: 32511497


  69. 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. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. Cell 2020. PMID: 32302591


  70. DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N. Functional interpretation of single cell similarity maps. Nature communications 2019. PMID: 31558714


  71. Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N. Ultrarare variants drive substantial cis heritability of human gene expression. Nature genetics 2019. PMID: 31477931


  72. Raju S, Ye CJ. How mutations express themselves in blood-cell production. Nature 2019. PMID: 31308526


  73. 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. Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans. Nature metabolism 2019. PMID: 31538139


  74. 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. PMID: 30955881


  75. 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 biology 2019. PMID: 30902100


  76. 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. Volume 28 of Issue 12. Genome research 2018. PMID: 30446528


  77. 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. Volume 9 of Issue 1. Nature communications 2018. PMID: 30254276


  78. 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. Volume 50 of Issue 8. Nature genetics 2018. PMID: 29988122


  79. 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. Volume 48 of Issue 5. Immunity 2018. PMID: 29752062


  80. . Principles of Systems Biology, No. 27. Cell systems 2018. PMID: 29596778


  81. 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. Volume 36 of Issue 1. Nature biotechnology 2017. PMID: 29227470


  82. 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. Volume 42 of Issue 1. Genetic epidemiology 2017. PMID: 29114909


  83. Wilentzik R, Ye CJ, Gat-Viks I. Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks. Volume 207 of Issue 4. Genetics 2017. PMID: 29046401


  84. 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. Volume 49 of Issue 12. Nature genetics 2017. PMID: 29038595


  85. 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. Volume 549 of Issue 7670. Nature 2017. PMID: 28854172


  86. 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. Volume 7 of Issue 1. Scientific Reports 2017. PMID: 28389661


  87. 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. Volume 17 of Issue 12. Nature immunology 2016. PMID: 27749840


  88. Brown BC, Ye CJ, Price AL, Zaitlen N. Transethnic Genetic-Correlation Estimates from Summary Statistics. Volume 99 of Issue 1. American journal of human genetics 2016. PMID: 27321947


  89. 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. Volume 26 of Issue 7. Genome research 2016. PMID: 27197206


  90. 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. Volume 164 of Issue 3. Cell 2016. PMID: 26824662


  91. 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. Volume 112 of Issue 33. Proceedings of the National Academy of Sciences of the United States of America 2015. PMID: 26216948


  92. 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. Volume 162 of Issue 3. Cell 2015. PMID: 26189680


  93. 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. Volume 345 of Issue 6202. Science (New York, N.Y.) 2014. PMID: 25214635


  94. 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. Volume 344 of Issue 6183. Science (New York, N.Y.) 2014. PMID: 24786080


  95. Joo JW, Sul JH, Han B, Ye C, Eskin E. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. Volume 15 of Issue 4. Genome biology 2014. PMID: 24708878


  96. 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. Volume 343 of Issue 6175. Science (New York, N.Y.) 2014. PMID: 24604203


  97. Sul JH, Han B, Ye C, Choi T, Eskin E. Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches. Volume 9 of Issue 6. PLoS genetics 2013. PMID: 23785294


  98. 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. Volume 45 of Issue 3. Nature genetics 2013. PMID: 23396133


  99. 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. Volume 5 of Issue 4. Circulation. Cardiovascular genetics 2012. PMID: 22670052


  100. Furlotte NA, Kang HM, Ye C, Eskin E. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. Volume 27 of Issue 13. Bioinformatics (Oxford, England) 2011. PMID: 21685083


  101. 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. Volume 17 of Issue 3. Journal of computational biology : a journal of computational molecular cell biology 2010. PMID: 20377462


  102. Ye C, Galbraith SJ, Liao JC, Eskin E. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. Volume 5 of Issue 3. PLoS computational biology 2009. PMID: 19300475


  104. Ye C, Eskin E. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. Volume 23 of Issue 2. Bioinformatics (Oxford, England) 2007. PMID: 17237110


  105. Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Volume 15 of Issue 7. Genome research 2005. PMID: 15998912


  106. 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. Volume 23 of Issue 1. Nature biotechnology 2005. PMID: 15637633