Functionalization of Immune Disease-Associated Variants

Understanding causal variants in autoimmune disease.
YeResearchTopic3 v03

While current technologies have led to discovery of many genetic variants, their functions are not well studied. Our lab is interested in characterizing the causal variants associated with autoimmune disease and the role they play. In our efforts to immunophenotype 1.2 millions PBMCs in 165 lupus patients, we have mapped thousands of genetic variants that are shared and specific in multiple circulating immune cell types. By integrating GWAS data, they were further identified to be associated with several autoimmune diseases and Alzheimer’s disease in addition to SLE. In another study to analyze the co-accessible chromatin regions in activated T cells from 105 individuals, we have identified thousands of genetic variants that are associated with multiple autoimmune disease including Celiac’s and Crohn’s disease and Rheumatoid Arthritis. Further analysis have shown these variants modulates cis-regulatory elements to influence gene expressions in various T cell populations.


Alumni Research Team

Rachel Gate, Co-founder of Dropprint Genomics

Andrew Lu, MSTP student at UCLA/CalTech

Lenka Maliskova, Lab Manager at UCSF Genomics Colab

Meena Subramaniam, Co-founder of Dropprint Genomics

Sasha Targ, MD student at UCSF medical school

Erden Tumurbaatar, Staff member at the Schumer lab at Stanford University


Selected Publications

Genetic Determinants of Co-Accessible Chromatin Regions in Activated T Cells across Humans
Nature Genetics. 2018
scRNA-seq Reveals the Cellular and Genetic Correlates of Systemic Lupus Erythematosus

Research Team

Matin Bikaran

Staff Research Associate

Gracie Gordon

Graduate Student, BMI, NIH F31 Award Recipient

George Hartoularos

Graduate Student, BMI, NSF Graduate Research Fellowship Recipient

MinCheol Kim

Graduate Student, MSTP, Bioengineering

David Lee

Staff Research Associate

Yang Sun, Ph.D.

Lab Manager


Media highlights of Ye Lab's research.
We Need Volunteers To Improve Our Understanding of the Human Immune System
‘AutoImmunoprofiler’ Builds on Success in Cancer Research to Advance Treatments for Autoimmune Diseases