Hiroko Matsui

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.

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.

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

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.

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.

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.

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.