Yongqun (Oliver) He, PhD, MS

 Oliver He
Professor of Laboratory Animal Medicine
Veterinarian
Laboratory Animal Medicine
Professor of Learning Health Sciences
Medical School
[email protected]
Available to mentor
Yongqun (Oliver) He, PhD, MS
Oliver He
Professor
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    • About

    He laboratory has focused on computational medicine and bioinformatics research, with primary research interests in the areas of vaccinology, host-pathogen interactions, nephrology, ontology, literature mining, and machine learning. Our primary scientific research domains are microbiology, vaccinology, nephrology, and comparative medicine. Our primary technical research is artificial intelligence (AI), with a focus on ontology, semantic web, literature mining, and machine learning. We are also interested in applying our technologies to other interesting areas as well.
    See more: https://hegroup.org

    Links
    • He group

    Center Memberships
    • Center Member
      Center for Global Health Equity
    • Center Member
      MM-PKUHSC Joint Institute
    • Center Member
      Center for Computational Medicine and Bioinformatics
    • Center Member
      Global REACH

    Recent Publications

     See All Publications
    • Journal Article
      SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis
      Huffman A, Yeh FY, Hur J, Zheng J, Masci AM, Wu G, Tao C, Athey B, He Y. Scientific Data, 2026 Dec 1; 13 (1): DOI:10.1038/s41597-026-06558-z
    • Journal Article
      Systematic annotation and analysis of susceptibility genes associated with vaccine adverse events
      Song Q, Su J, Pan C, Zhang X, Yang B, He Y, Xie J. BMC Medical Genomics, 2026 Dec 1; 19 (1): DOI:10.1186/s12920-025-02292-4
      PMID: 41361427
    • Preprint
      COVID-19 mRNA Vaccination Reduces Guillain-Barré Syndrome Risk: Evidence from a Large Longitudinal Cohort Study
      Li J, Pan Y, Han Y, Zhou C, Zhao L, He Y. 2026 Jul 8; openRxiv, DOI:10.64898/2026.07.02.26357163
    • Journal Article
      Evaluating Safety of XBB.1.5-Containing COVID-19 mRNA Vaccines Using a Self-Controlled Case Series Study
      Pan Y, Han Y, Zhou C, Zheng J, Zhao L, Ye X, He Y. Nature Communications, 2025 May 14;
    • Preprint
      VaxjoGNN: A Graph Neural Network for Ontology-Grounded Vaccine Adjuvant Recommendation.
      Zheng Y, He Y. 2025 Dec 1; DOI:10.1101/2025.11.27.690985
      PMID: 41383772
    • Preprint
      Immune Biomarkers, Profiles, and Responses: A Vaccine Ontology Perspective.
      He Y, Huffman A, Zheng J, Masci AM, Lin AY, Smith B. 2025 Jul 22; DOI:10.1101/2025.07.18.665557
      PMID: 40777277
    • Preprint
      Mapping and Harmonization of CVX vaccine terms to the Vaccine Ontology.
      Pan Y, Manuel W, Abeysinghe R, Zheng J, Davydov A, Yang Q, Lin AY, Cui L, He YO. 2025 Jul 18; DOI:10.1101/2025.07.15.664501
      PMID: 40791563
    • Preprint
      VaxKG: Integrating The Vaccine Ontology And VIOLIN For Advanced Vaccine Queries And LLM-Powered Chat Systems.
      Yeh F-YL, Asato M, Zheng J, He YO. 2025 Jul 18; DOI:10.1101/2025.07.15.664450
      PMID: 40791355

    Featured News & Stories

         Anthony Huffman
    Department News

    Building Better Ontologies

    Huffman’s dissertation work is in ontology; in information science, this is how real-world entities and their relationships are represented. Modern bioinformatics is interested in representing this in a way that computers can understand.