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Curriculum vitae for Joshua Chiou. Experience in statistical genetics, translational proteomics, and computational biology at Lilly and Pfizer.
Joshua Chiou, PhD
Director, Genomics · Lilly
chioujosh@gmail.com · joshchiou.github.io · Boston, MA
LLY
2025–now
Director, Genomics 2 roles
Lilly
PFE
2021–2025
Senior Principal Computational Geneticist 2 roles
Pfizer
UCSD
2016–2021
PhD, Biomedical Sciences
University of California, San Diego · Gaulton Lab
IDx
2015–2016
Development Scientist 2 roles
IncellDx
NASA
2015
Microbiology Intern
National Aeronautics and Space Administration
UCLA
2011–2015
BS, Microbiology, Immunology, and Molecular Genetics
University of California, Los Angeles
Experience
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2025–now Boston, MA
Director, Genomics
Lilly Director, Genomics2026–nowI lead translational proteomics across late-stage obesity and cardiometabolic trials, including head-to-head comparisons such as SURMOUNT-5, using large-scale proteomics to explain how drugs work and to find biomarkers that inform clinical development.Senior Advisor, Genomics2025–2026I worked with clinicians, biologists, and statisticians on large-scale proteomics from phase 2/3 obesity trials to study drug mechanisms and biomarkers, and built the analysis infrastructure for clinical omics. -
2021–2025 Cambridge, MA
Senior Principal Computational Geneticist
Pfizer Senior Principal Computational Geneticist2023–2025I worked with cross-functional teams on cardiovascular and renal target discovery, combining human genetics, functional genomics, and large language models. I also led the team that built the cloud infrastructure for genomics analysis across the organization.Senior Computational Geneticist2021–2023I worked with biologists to find new targets for cardiovascular and renal disease using multi-omics data, and I was the genetics expert for indication expansion teams. -
2016–2021 La Jolla, CA
Graduate Student Researcher
UC San Diego I led the largest genome-wide association study (GWAS) of type 1 diabetes at the time and combined it with single-cell epigenomics to identify new disease-relevant cell types in the pancreas. -
2015–2016 Menlo Park, CA
Development Scientist
IncellDx Development Scientist2016Research Associate2015–2016I optimized a cell-based companion diagnostic assay for HIV; the assay was later acquired by a major pharmaceutical company. -
2015 Houston, TX
Microbiology Intern
National Aeronautics and Space Administration Johnson Space Center I developed a rapid assay to detect infectious herpesviruses in astronauts.
Education
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2016–2021 La Jolla, CA
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
BS, Microbiology, Immunology, and Molecular Genetics
University of California, Los Angeles
Selected Publications
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Plasma proteomic associations with genetics and health in the UK BiobankMeasured about 3,000 blood proteins in 54,000 UK Biobank participants and mapped more than 14,000 genetic variants that influence their levels, most of them previously unknown.Nature, 2023 -
Interpreting type 1 diabetes risk with genetics and single-cell epigenomicsCombined a genetic study of type 1 diabetes in more than 500,000 samples with single-cell maps of the pancreas and implicated exocrine pancreas cells, not just immune cells, in disease risk.Nature, 2021 -
Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetesIdentified two beta cell subtypes whose abundance shifts in type 2 diabetes and whose accessible chromatin is enriched for type 2 diabetes risk variants.Nature Genetics, 2023 -
Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes riskMapped chromatin accessibility in thousands of individual islet cells to show which cell types and cell states carry type 2 diabetes genetic risk.Nature Genetics, 2021
Honors & Awards
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2023 - Solving the Science ChallengePfizer Integrative Biology
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2018–2020 - Genetics Training Program FellowshipUC San Diegosource
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2018 - Charles J. Epstein Trainee Award for Excellence in Human Genetics Research, SemifinalistASHGsource
- Graduate Research Fellowship, Honorable MentionNSF
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2014 - J.W. and Nellie MacDowell ScholarshipUCLA
Professional Activities
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2023 - McKinsey Leadership Essentials
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2022–now - Ad hoc reviewer: Nature Communications, Diabetes, BMJ Open Diabetes Research & Care, Communications Biology, Scientific Reports, BBA: Molecular Basis of Disease
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2016–now - Member, American Society of Human Genetics (ASHG)
Talks & Presentations
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2026 Milan, Italy
Tirzepatide was associated with differential proteomic responses compared to semaglutide: exploratory findings from the SURMOUNT-5 trial
EASD 62nd Annual Meeting - Oral presentation
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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