Kelly A. Frazer

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

Genetics of growth rate in induced pluripotent stem cells

The paper identifies genetic factors influencing iPSC growth rates, finding rare variants in WDR54 and a polygenic background explaining most variance.

Admixture mapping identifies complex trait associations with local ancestry in the All of Us Research Program

This study uses admixture mapping in the All of Us Research Program to identify local ancestry associations with complex traits, finding distinct patterns between African and Native American ancestry.

Characterization of shared and ancestry-specific signals driving complex traits using multi-ancestry fine-mapping

The paper introduces PIPSORT, a method to detect shared and ancestry-specific genetic signals in complex traits, and applies it to GWAS data from diverse populations.

Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci

The paper identifies multi-omic QTLs in early developmental tissues and shows that GWAS loci often involve complex regulatory variants not captured by eQTLs alone.

IFNγ activates an immune-like regulatory network in the cardiac vascular endothelium

This study investigates how IFNγ affects cardiac vascular endothelium by analyzing RNA-seq and ATAC-seq data from iPSC-derived cells, revealing immune-like regulatory changes and GWAS variant overlaps.

Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription

The paper shows that phosphorylated CTCF binds the SIRT1 promoter under oxidative stress, activating a cardioprotective transcriptional program in cardiomyocytes.

Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations

The paper identifies regulatory network modules in human stem cells, showing epigenetic and genetic factors influence pluripotency state differences.

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

The paper maps eQTLs in fetal-like pancreatic progenitor cells, identifying regulatory variants that influence diabetes risk by affecting gene expression and splicing in early development.

Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

This study identifies causal genetic variants for cardiac traits by integrating spatiotemporal eQTL analysis with GWAS data, showing stage- and tissue-specific effects.

Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines

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

Affinity-optimizing variants within cardiac enhancers disrupt heart development and contribute to cardiac traits

The paper identifies ETS affinity-optimizing SNVs in heart enhancers that disrupt development and contribute to cardiac traits in Ciona and human iPSC-CMs.

In heart failure reactivation of RNA-binding proteins drives the transcriptome into a fetal state

The paper identifies reactivation of fetal-specific RNA-binding protein isoforms in heart failure, leading to a fetal transcriptome state.

Insights into genetic factors contributing to variability in SARS-CoV-2 susceptibility and COVID-19 disease severity

This study identifies genetic loci associated with SARS-CoV-2 susceptibility and disease severity using GWAS and colocalization, and links them to eQTLs in various tissues.

Regulatory variants active in iPSC-derived pancreatic progenitor cells are associated with Type 2 Diabetes in adults

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

The paper maps regulatory effects of human disease variants in pluripotent cells, identifying cis- and trans-QTL across 18,556 genes and linking them to GWAS traits.

Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

The paper examines how structural variants and short tandem repeats affect gene expression and complex traits, identifying high-impact variants associated with multiple genes and GWAS traits.

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

The paper discovers and genotypes a comprehensive set of structural variants and short tandem repeats using multiple algorithms and replicates, creating a well-characterized map of these variants.

Cellular deconvolution of GTEx tissues powers eQTL studies to discover thousands of novel disease and cell-type associated regulatory variants

The paper deconvolutes GTEx tissues to estimate cell-type proportions and identifies cell-type-associated eQTLs, revealing novel regulatory variants linked to disease.

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease

This study systematically analyzes the MHC region to uncover genetic associations between HLA types, gene expression, and disease, revealing novel insights into disease mechanisms.

A network of microRNAs acts to promote cell cycle exit and differentiation of human pancreatic endocrine cells

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

Human iPSC gene signatures and X chromosome dosage impact response to WNT inhibition and cardiac differentiation fate

The paper investigates how non-genetic variability in iPSC lines affects their response to WNT inhibition and cardiac differentiation, identifying 91 signature genes and X chromosome dosage differences as key factors.

Allele-specific NKX2-5 binding underlies multiple genetic associations with human EKG traits

The paper identifies allele-specific NKX2-5 binding variants associated with EKG traits by integrating iPSC-CM data and GWAS, showing their role in heart rate loci and cardiac enhancer activity.

Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci

The paper uses iPSC-derived retinal pigment epithelium to identify and functionally characterize causal variants at AMD risk loci, finding rs943080 as the probable causal variant at VEGFA.

Pancreatic islet chromatin accessibility and conformation defines distal enhancer networks of type 2 diabetes risk

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

Chromatin co-accessibility is highly structured, spans entire chromosomes, and mediates long range regulatory genetic effects

The paper analyzes co-accessibility across chromosomes using ATAC-seq and identifies its regulatory effects on gene expression and disease-relevant genes.

Integration of phased Hi-C and molecular phenotype data to study genetic and epigenetic effects on chromatin looping

The paper investigates how genetic and epigenetic factors influence chromatin looping strength across cell types and haplotypes, finding that loop strength changes correlate with significant gene expression differences.

Insights into the mutational burden of human induced pluripotent stem cells using an integrative omics approach

This study analyzes the mutational burden in human iPSCs using whole genome sequencing and integrates transcriptome and epigenome data to identify mutation patterns and their impact on gene expression.