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Ziyuan He headshot

Ziyuan He, Ph.D

Bioinformatics Scientist II


Ziyuan is a bioinformatics scientist in the Informatics & Computational Biology group at the Allen Institute for Immunology. His work at the institute focuses on generating mechanistic insights into the immune system by analyzing single-cell multi-omics immunological data in various healthy and disease conditions, including Rheumatoid Arthritis.

Ziyuan earned his PhD in Biomedical Sciences (Immunology and Microbiology track) at Tulane University. His dissertation work in Dr. Marcelo Kuroda’s lab at Tulane National Primate Center and California National Primate Center focused on myeloid cell immunology in rhesus macaques and aging. He developed mathematical models and estimated the in vivo half-lives of neutrophils, basophils, and classical monocytes in rhesus macaques, investigating the effects of aging on neutrophil development and kinetics in elderly rhesus macaques. He received postdoctoral training in Dr. Kari Nadeau’s lab at Stanford University, where he worked on multiomic data analysis to understand the immunephenotype, microbiome, and allergen changes in food allergy during oral immunotherapy clinical trials. During the COVID-19 pandemic, he analyzed electronic health record data to understand the risk factors for COVID-19 and its relationship with asthma and was involved in multiple clinical trial efforts to combat the virus.

Research Focus:

Ziyuan's long-term research interests lie at the intersection of immunology and data science. He applies computational analytical approaches to comprehensively understand the human immune system in health and disease.

Science Programs at Allen Institute