Jimmie Ye

Jimmie Ye, PhD, is a Professor in the School of Medicine at the University of California, San Francisco (UCSF). His research integrates high-throughput sequencing, population genetics, and computational biology to investigate how genetic and environmental interactions shape molecular phenotypes, with a focus on immune cells in health and disease. He leads the Ye Lab, which pioneers experimental and computational methods for large-scale functional genomics.

• Education: BS in Bioengineering and Electrical Engineering and Computer Sciences (UC Berkeley, 2002); PhD in Bioinformatics and Systems Biology (UC San Diego, 2009); Postdoctoral training in Cell Circuits (Broad Institute, 2014).

Dr. Ye’s research centers on functional genomics, single-cell RNA sequencing, and gene-environment interactions, particularly in the context of autoimmunity, host-pathogen responses, and immune cell regulation. His lab develops innovative tools to decode regulatory networks and cellular heterogeneity in human diseases.

His recent publications span high-impact journals such as Nature, Cell, and Science, with a strong emphasis on single-cell technologies, genetic regulation, and immune dysfunction. Research trends include mapping gene-by-environment interactions, dissecting autoimmune mechanisms in lupus and arthritis, and engineering immune cells for therapy.

Scientific Funding and Grants:

• NIH R01HG011239: Mapping gene-by-environment interactions using multiplexed single-cell RNA-seq.
• NIH R01AI136972: Genetic regulation and immunological function of ERAP2 haplotypes.
• NIH R21AI133337: Single-cell sequencing of peripheral blood cells in SLE patients.
• NIH R01AR071522: Fine mapping rheumatic disease variants using functional genomic sequencing.

Dr. Ye serves as Principal Investigator on all these projects, demonstrating sustained leadership in genomic medicine. He collaborates widely across immunology, computational biology, and clinical research. Although specific advisees are not listed, his lab environment fosters interdisciplinary training in genomics and data science. He maintains an active research presence through the Yelab Website and professional posts on X (@yimmieg).