Joshua Chiou

VIDRA models genetic dose-response relationships to predict drug mechanisms, therapeutic potential, and adverse events using phenotypically associated variants.

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

This study uses single-cell multiomics and spatial transcriptomics to identify gene regulatory programs in pancreatic cell types that drive type 1 diabetes progression.

This study identifies genetic risk factors for type 1 diabetes in individuals without high-risk HLA-DR3/DR4 haplotypes and develops a new risk score for better classification.

This paper introduces INTERFACE, a probabilistic fine-mapping method that improves the identification of causal genes by integrating colocalization and transcriptome-wide association evidence.

The paper identifies causal biomarkers for type 1 diabetes using protein QTLs and GWAS, revealing roles of pancreatic enzymes and immune processes in disease risk.

This study identifies 504 plasma proteins influenced by HLA genetic variation in 45,330 Europeans, revealing their roles in immune function and disease.

The paper introduces Multi-INTACT, a method that integrates transcriptome-wide association studies with protein QTL data to identify causal genes for metabolites, finding that both gene products are relevant for most gene nominations.

The paper maps genetic associations with plasma proteins in 54,306 UK Biobank participants, identifying 10,248 new protein quantitative trait loci (pQTLs) and expanding the genetic architecture of the plasma proteome.

The paper integrates single-cell multiomic data with genetics to identify gene regulatory changes in beta cells associated with type 2 diabetes.

This paper clusters T2D genetic loci into ten groups using bNMF, identifying distinct biological mechanisms and clinical associations.

The paper identifies T1D risk genes and regulatory elements that influence beta cell survival under proinflammatory cytokine exposure using functional genomics and genetics.

This study identifies 277 T2D loci using diverse populations and improves fine-mapping to assess causal genes and mechanisms, enhancing clinical translation.

The paper creates a chromatin accessibility atlas across 25 adult human tissues, identifying over 750,000 cis-regulatory elements and linking them to gene regulatory programs and disease-associated variants.

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

This study combines large-scale GWAS and single-cell epigenomics to identify cell type-specific mechanisms of type 1 diabetes risk.

The paper defines cardiac cell type-specific cis-regulatory elements and links disease risk variants to these elements in human hearts.

This study identifies glucocorticoid-responsive gene regulatory programs in pancreatic islets and links them to type 2 diabetes risk through chromatin and gene expression analysis.

The paper uses single-cell chromatin accessibility to identify cell type- and state-specific regulatory programs associated with type 2 diabetes risk.

The paper identifies T2D risk variants in pancreatic progenitor-specific enhancers and shows their role in regulating developmental genes involved in pancreas morphogenesis.

The paper uses snATAC-seq to map chromatin accessibility QTLs in immune cell types and fine-maps complex trait loci, identifying cell type-specific causal variants.

The paper shows FOXA pioneer factors prime some enhancers but require lineage-specific TFs to activate others, influencing endodermal organ fate decisions.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

The paper uses single nucleus ATAC-seq and RNA-seq to show age-related changes in chromatin accessibility and gene expression linked to SARS-CoV-2 entry genes in human lung cells.

This study identifies DNA sequence variants that influence 3D chromatin conformation and links them to gene expression and disease risk.

The paper identifies miRNAs that promote cell cycle exit and differentiation of human pancreatic endocrine cells through regulatory networks.

The paper identifies distal enhancer networks in pancreatic islets associated with type 2 diabetes risk by integrating chromatin accessibility, conformation, and genetic data.

This paper clusters T2D genetic loci using multi-trait associations to identify disease mechanisms and subtypes, finding distinct clinical outcomes linked to each cluster.

This study identifies shared genetic risk factors between type 1 and type 2 diabetes, showing overlapping regulatory elements and causal variants affecting islet function and growth.