Jimmie Ye, PhD

Assistant Professor
Department of Epidemiology & Biostatistics
Institute for Human Genetics
+1 415 476-6933
Research 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.

Primary Thematic Area: 
Human Genetics
Secondary Thematic Area: 
Immunology
Research Summary: 
Genetics of human immune response

Websites

Publications: 

Identification and regulation of circulating tumor TCR-matched cytotoxic CD4+ lymphocytes by KLRG1 in bladder cancer.

JCI insight

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

Defining the host dependencies and the transcriptional landscape of RSV infection and bystander activation.

bioRxiv : the preprint server for biology

Sunshine S, Puschnik A, Retallack H, Laurie MT, Liu J, Peng D, Knopp K, Zinter MS, Ye CJ, DeRisi JL

Phenotypic pleiotropy of missense variants in human B cell-confinement receptor P2RY8.

bioRxiv : the preprint server for biology

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

SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci.

Nature biotechnology

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

In vivo engineering of murine T cells using the evolved adeno-associated virus variant Ark313.

Immunity

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