Immune Cell Census of Health and Disease

Understanding genetic and environmental effects on human immunity in health and disease.

We believe creating a reference dataset of immunophenotypes in disease and health status is an essential step to understand the role of immune circuits in disease and treatment. So far, we have actively sequenced over 2.6 million single cells in more than 550 individuals with- and without disease. The efforts include multimodal immunoprofiling of 1). Over 1.2 million single cells in 165 patients with lupus and 99 healthy controls, revealing the cellular and molecular changes in immune circuits associated with the disease; 2). Over 600,000 cells in 130 longitudinal samples collected in a prostate cancer immunotherapy clinical trial to understand the immunophenotypes of responders and non-responders; 3). Over 30,000 T cells from bladder cancer patients to understand mechanisms of anti-PD-1 immunotherapy response; 4). We have also profiled over 600,000 immune cells from over 50 patients with COVID-19 in a longitudinal study at the early stage of the global pandemic. This study has led to our understanding of the causal role certain immune circuits play and suggests they could be predictive in clinical phenotypes like disease severity.

To construct the human Immune Cell Census (ICC) for healthy individual, we aim to profile 5-10 million single-cell across different ethnicity backgrounds and time scales (diurnal cycle, menstrual cycle, seasonal cycle, natural aging), and from different compartments (peripheral blood and cerebrospinal fluid). We are also developing computational methods for the analysis of population-scale single-cell genomic data and integrate our pipelines with the Human Cell Atlas Data Coordination Platform. The goal is to establish a foundational resource for future population-scale single-cell studies of immune diseases.


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

scRNA-seq Reveals the Cellular and Genetic Correlates of Systemic Lupus Erythematosus
Intratumoral CD4+ T Cells Mediate Anti-Tumor Cytotoxicity in Human Bladder Cancer
Cell. 2020

Research Team

Matin Bikaran

Staff Research Associate

Raymund Bueno, Ph.D.

Bioinformatics Scientist

Gracie Gordon

Graduate Student, BMI, NIH F31 Award Recipient

MinCheol Kim

Graduate Student, MSTP, Bioengineering

David Lee

Staff Research Associate

Elizabeth McCarthy

Graduate Student, MSTP, Bioinformatics, NIH F30 Award Recipient

Anton Ogorodnikov, Ph.D.

Bioinformatics Scientist

Yang Sun, Ph.D.

Lab Manager

Alyssa Ward, Ph.D.

Project 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