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Curriculum vitae for Joshua Chiou. Experience in statistical genetics, translational proteomics, and computational biology at Lilly and Pfizer.

2025 - now
Senior Advisor, Genomics
Lilly
2021 - 2025
Senior Principal Computational Geneticist 2 roles
Senior Computational Geneticist · 2021 - 2023
Pfizer
2016 - 2021
PhD, Biomedical Sciences
University of California, San Diego · Gaulton Lab
2015 - 2016
Development Scientist 2 roles
Research Associate · 2015
IncellDx
2015
Microbiology Intern
National Aeronautics and Space Administration
2011 - 2015
B.S., Microbiology, Immunology, and Molecular Genetics
University of California, Los Angeles

Experience

  • 2025 - now

    Boston, MA

    LLY
    Senior Advisor, Genomics
    Lilly
    I collaborate with clinicians, biologists, and statisticians to generate mechanistic and biomarker insights from large-scale proteomics across phase 2/3 obesity trials, while building the analytical infrastructure supporting clinical omics research.
  • 2021 - 2025

    Cambridge, MA

    PFE
    Senior Principal Computational Geneticist
    Pfizer
    Senior Principal Computational Geneticist
    2023 - 2025
    I collaborated with cross-functional teams for cardiovascular and renal target discovery integrating human genetics, functional genomics, and large language models, while driving delivery of scalable cloud infrastructure for large-scale genomics analysis across the organization.
    Senior Computational Geneticist
    2021 - 2023
    I partnered with biologists to identify novel targets for cardiovascular and renal disease through integrative multi-omics, with several advancing into the portfolio, and served as the genetics expert for indication expansion teams.
  • 2016 - 2021

    La Jolla, CA

    UCSD
    Graduate Student Researcher
    UC San Diego
    I led the largest GWAS for type 1 diabetes, implicating novel disease-relevant cell types through integration of human genetics and single-cell epigenomics, and published broadly across top journals throughout my PhD.
  • 2015 - 2016

    Menlo Park, CA

    IDx
    Development Scientist
    IncellDx
    Development Scientist
    2016
    Research Associate
    2015 - 2016
    I optimized a cell-based companion diagnostic assay for HIV that was subsequently acquired by a major pharmaceutical company.
  • 2015

    Houston, TX

    NASA
    Microbiology Intern
    National Aeronautics and Space Administration
    Johnson Space Center
    I developed a rapid assay for improved detection of infectious herpesviruses in astronauts.

Education

  • 2016 - 2021

    La Jolla, CA

    UCSD
    PhD, Biomedical Sciences
    University of California, San Diego
    Dissertation: Understanding pancreatic mechanisms of diabetes risk with genetic association and single cell epigenome data
    Advisor: Dr. Kyle Gaulton
  • 2011 - 2015

    Los Angeles, CA

    UCLA
    B.S., Microbiology, Immunology, and Molecular Genetics
    University of California, Los Angeles

Selected Publications

38 publications · Google Scholar · ORCID
  1. Plasma proteomic associations with genetics and health in the UK Biobank
    Sun BB, Chiou J, Traylor M, and 62 more authors
    Nature, 2023
    DOI Scholar View project
  2. Interpreting type 1 diabetes risk with genetics and single-cell epigenomics
    Chiou J, Geusz RJ, Okino M, and 13 more authors
    Nature, 2021
    DOI Scholar View project
  3. Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes
    Wang G*, Chiou J*, Zeng C, and 18 more authors
    *Equal contribution
    Nature Genetics, 2023
    DOI Scholar
  4. Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk
    Chiou J*, Zeng C*, Zhang C, and 17 more authors
    *Equal contribution
    Nature Genetics, 2021
    DOI Scholar View project
  5. Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk
    Greenwald WW*, Chiou J*, Yan J, and 19 more authors
    *Equal contribution
    Nature Communications, 2019
    DOI Scholar

Honors & Awards

  • 2023
    • Solving the Science ChallengePfizer Integrative Biology
  • 2020
    • Charles J. Epstein Trainee Award for Excellence in Human Genetics Research, FinalistASHGsource
    • Annual Investigator Meeting ScholarshipHIRNsource
  • 2018-2020
    • Genetics Training Program FellowshipUC San Diegosource
  • 2018
    • Charles J. Epstein Trainee Award for Excellence in Human Genetics Research, SemifinalistASHGsource
    • Graduate Research Fellowship, Honorable MentionNSF
  • 2014
    • J.W. and Nellie MacDowell ScholarshipUCLA

Professional Activities

  • 2023
    • McKinsey Leadership Essentials
  • 2022-now
    • Ad hoc reviewer: Nature Communications, Diabetes, BMJ Open Diabetes Research & Care, Communications Biology, Scientific Reports, BBA Molecular Basis of Disease
  • 2016-now
    • Member, American Society for Human Genetics (ASHG)

Invited Talks & Presentations

  • 2025

    Boston, MA

    Advancing Early Target Discovery through Large-Scale Proteomics and Expansion Plans for the UKB-PPP
    Festival of Genomics Boston
    • Invited talk

Technical Skills

Statistical Genetics
GWAS ExWAS Fine-mapping Colocalization Mendelian randomization pQTL eQTL Polygenic risk scores Meta-analysis Causal variant-to-gene mapping PLINK REGENIE
Genomics
scRNA-seq scATAC-seq Bulk ATAC-seq Multi-omic integration
Proteomics & Translational Research
Olink SomaScan Clinical trial proteomics Biomarker discovery EHR integration Survival analysis Target identification In silico validation Phenotyping
Machine Learning & AI
Machine learning Predictive modeling Deep learning LLM integration Agentic AI workflows Prompt engineering
Programming
Python R SQL pandas polars dask scanpy PyTorch scikit-learn Plotly Dash Streamlit
Cloud & Infrastructure
AWS (S3, EC2, Batch) HPC clusters Unix Nextflow Docker Singularity Conda Pixi uv Git FAIR data principles