Staff Profiles

Ziyuan He, Ph.D.

Bioinformatics Scientist I

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

Ziyuan got his PhD in Biomedical Sciences (Immunology and Microbiology track) from 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 cells immunology in rhesus macaque and aging. He developed the mathematical models and estimated the in vivo half-lives of neutrophils, basophils, and classical monocytes in rhesus macaques and investigated the effects of aging on neutrophil development and kinetic in elderly rhesus macaques. He received his postdoctoral training in Dr. Kari Nadeau’s lab at Stanford University where he worked on microbiome changes and cross-reactive allergens in oral immunotherapy clinical trials for food allergy. Upon COVID-19 pandemic, he worked on the electronic heath record data analysis to understand the risk factors towards COVID-19 and also involved in multiple clinical trial efforts at Stanford to combat COVID-19.


Research Interests

Ziyuan’s long-term research interests lay at the intersection of immunology and data science and apply the computational analytical approaches to comprehensive understand the human immune system in healthy and diseases.


  • Bioinformatics
  • Immunology
  • High dimensional flow cytometry

Research Programs

  • Computational immunology

Selected Publications View Publications

Asthma phenotypes, associated comorbidities, and long-term symptoms in COVID-19

March 24, 2021

Eggert L, He Z, Collins W, Lee A S, Dhondalay G, Jiang S Y, Fitzpatrick J, Snow T T, Pinsky B A, Artandi M, Barman L, Puri R, Wittman R, Ahuja, N, Blomkalns A, O'Hara R, Cao S, Desai M, Sindher S B, Nadeau K, Chinthrajah S,

Comparison of predictors for terminal disease progression in SIV/SHIV-infected rhesus macaques

March 11, 2021

Takahashi N, Ardeshir A, Holder GE, Cai Y, Sugimoto C, Mori K, Arainga M, He Z, Fukuyo Y, Kim WK, Didier ES, Kuroda MJ

Increased diversity of gut microbiota during active oral immunotherapy in peanut-allergic adults

March 2021

He Z, Vadali VG, Szabady RL, Zhang W, Norman JM, Roberts B, Tibshirani R, Desai M, Chinthrajah RS, Galli SJ, Andorf S, Nadeau KC

Clinical trials in a COVID-19 pandemic: Shared infrastructure for continuous learning in a rapidly changing landscape

Clinical Trials
February 3, 2021

Hedlin H, Garcia A, Weng Y, He Z, Sundaram V, Bunning B, Balasubramanian V, Cunanan K, Kapphahn K, Gummidipundi S, Purington N, Boulos M, Desai M

Asthma as a predictor of more severe outcomes in COVID-19 infection

Journal of Allergy and Clinical Immunology
February 1, 2021

Eggert L, Cao S, He Z, Gopal Dhondalay K, Jiang S, Collins W, Sindher S, Nadeau K, Chinthrajah R S

Mass Cytometry Reveals Immune Signatures Associated With Desensitization Through Multi-Food Oral Immunotherapy

Journal of Allergy and Clinical Immunology
February 1, 2021

He Z, Dunham D, Zhou X, Lyu S, Manohar M, Chinthrajah S, Andorf S, Nadeau K