publications

Full publication list in reverse chronological order.

39 publications · Google Scholar · ORCID

Selected

  1. Plasma proteomic associations with genetics and health in the UK Biobank
    Measured 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.
    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
    Combined 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.
    Chiou J, Geusz RJ, Okino M, and 13 more authors
    Nature, 2021
    DOI Scholar Code View project
  3. Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes
    Identified two beta cell subtypes whose abundance shifts in type 2 diabetes and whose accessible chromatin is enriched for type 2 diabetes risk variants.
    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
    Mapped chromatin accessibility in thousands of individual islet cells to show which cell types and cell states carry type 2 diabetes genetic risk.
    Chiou J*, Zeng C*, Cheng Z, 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
    Mapped 3D chromatin contacts in pancreatic islets to connect distal type 2 diabetes risk variants to the genes they likely regulate.
    Greenwald WW*, Chiou J*, Yan J*, and 19 more authors
    *Equal contribution
    Nature Communications, 2019
    DOI Scholar

All publications

2026

  1. Genetic dose-response modelling predicts drug mechanisms, dosing, and adverse events
    Stefanucci L, Considine D, Ke Z, and 21 more authors, including Chiou J
    medRxiv, 2026
    Preprint DOI

2025

  1. Single-cell multiome and spatial profiling reveals pancreas cell type-specific gene regulatory programs of type 1 diabetes progression
    Melton R, Jimenez S, Elison W, and 20 more authors, including Chiou J
    Science Advances, 2025
    DOI Scholar
  2. Restoration of branched chain amino acid catabolism improves kidney function in preclinical cardiovascular-kidney-metabolic syndrome models
    Bollinger E, Williams G, Piper ME, and 28 more authors, including Chiou J
    Kidney International, 2025
    DOI Scholar
  3. Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits
    Okamoto J, Yin X, Ryan B, and 10 more authors, including Chiou J
    Genome Biology, 2025
    DOI Scholar
  4. Genetic discovery and risk prediction for type 1 diabetes in individuals without high-risk HLA-DR3/DR4 haplotypes
    McGrail C, Chiou J, Elgamal R, and 4 more authors
    Diabetes Care, 2025
    DOI Scholar
  5. Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus
    Freimann K, Brümmer A, Warmerdam R, and 18 more authors, including Chiou J
    Nature Communications, 2025
    DOI

2024

  1. A fast machine learning dataloader for epigenetic tracks from BigWig files
    Retel JS, Poehlmann A, Chiou J, and 2 more authors
    Bioinformatics, 2024
    DOI Scholar
  2. Probabilistic Fine-mapping of Putative Causal Genes
    Okamoto J, Yin X, Ryan B, and 10 more authors, including Chiou J
    bioRxiv, 2024
    Preprint DOI Scholar
  3. Circulating pancreatic enzyme levels are a causal biomarker of type 1 diabetes
    Elgamal RM, Melton RL, Chiou J, and 2 more authors
    medRxiv, 2024
    Preprint DOI Scholar
  4. The influence of HLA genetic variation on plasma protein expression
    Krishna C, Chiou J, Sakaue S, and 9 more authors
    Nature Communications, 2024
    DOI Scholar

2023

  1. Plasma proteomic associations with genetics and health in the UK Biobank
    Measured 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.
    Sun BB, Chiou J, Traylor M, and 62 more authors
    Nature, 2023
    DOI Scholar View project
  2. Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes
    Identified two beta cell subtypes whose abundance shifts in type 2 diabetes and whose accessible chromatin is enriched for type 2 diabetes risk variants.
    Wang G*, Chiou J*, Zeng C*, and 18 more authors
    *Equal contribution
    Nature Genetics, 2023
    DOI Scholar
  3. The GPCR-Gαs-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure
    Wu VH, Yung BS, Faraji F, and 18 more authors, including Chiou J
    Nature Immunology, 2023
    DOI Scholar
  4. Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex immune trait variants using single nucleus ATAC-seq in peripheral blood
    Benaglio P, Newsome J, Han JY, and 9 more authors, including Chiou J
    PLOS Genetics, 2023
    DOI Scholar
  5. Nutrient regulation of the islet epigenome controls adaptive insulin secretion
    Wortham M, Liu F, Harrington AR, and 19 more authors, including Chiou J
    Journal of Clinical Investigation, 2023
    DOI Scholar
  6. High-throughput genetic clustering of type 2 diabetes loci reveals heterogeneous mechanistic pathways of metabolic disease
    Kim H, Westerman KE, Smith K, and 11 more authors, including Chiou J
    Diabetologia, 2023
    DOI Scholar
  7. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
    Benaglio P, Zhu H, Okino M, and 20 more authors, including Chiou J
    Cell Genomics, 2023
    DOI Scholar

2022

  1. Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
    Mahajan A, Spracklen CN, Zhang W, and 22 more authors, including Chiou J
    Nature Genetics, 2022
    DOI Scholar

2021

  1. Interpreting type 1 diabetes risk with genetics and single-cell epigenomics
    Combined 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.
    Chiou J, Geusz RJ, Okino M, and 13 more authors
    Nature, 2021
    DOI Scholar Code View project
  2. Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk
    Mapped chromatin accessibility in thousands of individual islet cells to show which cell types and cell states carry type 2 diabetes genetic risk.
    Chiou J*, Zeng C*, Cheng Z, and 17 more authors
    *Equal contribution
    Nature Genetics, 2021
    DOI Scholar View project
  3. Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development
    Geusz RJ*, Wang A*, Chiou J*, and 11 more authors
    *Equal contribution
    eLife, 2021
    DOI Scholar
  4. A single-cell atlas of chromatin accessibility in the human genome
    Zhang K, Hocker JD, Miller M, and 9 more authors, including Chiou J
    Cell, 2021
    DOI Scholar
  5. Systematic analysis of binding of transcription factors to noncoding variants
    Yan J, Qiu Y, Santos AM, and 15 more authors, including Chiou J
    Nature, 2021
    DOI Scholar
  6. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors
    Geusz RJ, Wang A, Lam DK, and 12 more authors, including Chiou J
    Nature Communications, 2021
    DOI Scholar
  7. Mutations and variants of ONECUT1 in diabetes
    Philippi A, Heller S, Costa IG, and 25 more authors, including Chiou J
    Nature Medicine, 2021
    DOI Scholar
  8. An atlas of gene regulatory elements in adult mouse cerebrum
    Li YE, Preissl S, Hou X, and 25 more authors, including Chiou J
    Nature, 2021
    DOI Scholar
  9. Cardiac cell type-specific gene regulatory programs and disease risk association
    Hocker JD, Poirion OB, Zhu F, and 15 more authors, including Chiou J
    Science Advances, 2021
    DOI Scholar
  10. Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes
    Aylward A, Okino M, Benaglio P, and 5 more authors, including Chiou J
    PLOS Genetics, 2021
    DOI Scholar
  11. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
    Muus C, Luecken MD, Eraslan G, and 232 more authors, including Chiou J
    Nature Medicine, 2021
    DOI Scholar
  12. Understanding pancreatic mechanisms of diabetes risk with genetic association and single cell epigenome data
    Chiou J
    PhD Thesis, UC San Diego, 2021
    Scholar

2020

  1. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes
    Wang A*, Chiou J*, Poirion O*, and 23 more authors
    *Equal contribution
    eLife, 2020
    DOI Scholar
  2. An atlas of dynamic chromatin landscapes in mouse fetal development
    Gorkin DU, Barozzi I, Zhao Y, and 24 more authors, including Chiou J
    Nature, 2020
    DOI Scholar
  3. Common DNA sequence variation influences 3-dimensional conformation of the human genome
    Gorkin DU, Qiu Y, Hu M, and 10 more authors, including Chiou J
    Genome Biology, 2020
    DOI Scholar

2019

  1. Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk
    Mapped 3D chromatin contacts in pancreatic islets to connect distal type 2 diabetes risk variants to the genes they likely regulate.
    Greenwald WW*, Chiou J*, Yan J*, and 19 more authors
    *Equal contribution
    Nature Communications, 2019
    DOI Scholar
  2. A network of microRNAs acts to promote cell cycle exit and differentiation of human pancreatic endocrine cells
    Jin W, Mulas F, Gaertner B, and 13 more authors, including Chiou J
    iScience, 2019
    DOI Scholar
  3. Illuminating the Onco-GPCRome: Novel G protein-coupled receptor-driven oncocrine networks and targets for cancer immunotherapy
    Wu V, Yeerna H, Nohata N, and 7 more authors, including Chiou J
    Journal of Biological Chemistry, 2019
    DOI Scholar
  4. The long noncoding RNA ROCKI regulates inflammatory gene expression
    Zhang Q, Chao T, Patil VS, and 13 more authors, including Chiou J
    EMBO Journal, 2019
    DOI Scholar
  5. Shared genetic risk contributes to type 1 and type 2 diabetes etiology
    Aylward A, Chiou J, Okino M, and 2 more authors
    Human Molecular Genetics, 2019
    DOI Scholar

2018

  1. Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: a soft clustering analysis
    Udler MS, Kim J, Grotthuss MV, and 13 more authors, including Chiou J
    PLOS Medicine, 2018
    DOI Scholar

2015

  1. Protein chainmail variants in dsDNA viruses
    Zhou ZH, and Chiou J
    AIMS Biophysics, 2015
    DOI Scholar

Talks and presentations

  • 2026
    Tirzepatide was associated with differential proteomic responses compared to semaglutide: exploratory findings from the SURMOUNT-5 trial
    EASD 62nd Annual Meeting · Milan, Italy · Oral presentation
    abstract
  • 2025
    Advancing Early Target Discovery through Large-Scale Proteomics and Expansion Plans for the UKB-PPP
    Festival of Genomics Boston · Boston, MA · Invited talk

Press