Masayuki P. Yamamoto

ibSLS: A Biobank for Democratizing Access to Multi-Omics Data and Biospecimens from Spaceflight Research

ibSLS provides a platform for accessing multi-omics data and biospecimens from spaceflight research to support biomedical and disease studies.

An evolutionary landscape of sesame: chromosomal variation, allopolyploid speciation and metabolic specialization.

This study reconstructs the genome and karyotype evolution of Sesamum and related species, revealing hybridization events and genetic changes linked to metabolic specialization.

The electrophilic metabolite of kynurenine, kynurenine-CKA, targets C151 in Keap1 to derepress Nrf2.

This study shows that kynurenine-CKA targets C151 in Keap1 to increase Nrf2 activity and anti-inflammatory effects in macrophages.

Genomic analyses reveal new insights into Alzheimer's disease

This study identifies 118 new genetic loci associated with Alzheimer's disease across diverse ancestries and discovers 48 novel risk loci, including those enriched in neuronal cell types.

JG2: an updated version of the Japanese population-specific reference genome

This paper updates the Japanese population-specific reference genome JG1 to JG2 using Hi-C and meta-assembly methods, improving coverage and accuracy for genetic research.

Additive associations of variants at the expression quantitative trait loci of TFR2 and EPO in a linkage disequilibrium block with hypochromic erythropoiesis

The paper identifies genetic variants associated with erythrocyte traits and iron metabolism in a Japanese population, revealing a linkage disequilibrium block linked to hypochromic erythropoiesis.

A fine-scale genetic map of the Japanese population

This paper constructs a fine-scale genetic map of the Japanese population using whole-genome sequencing data, identifies recombination hotspots, and shows improved haplotype phasing and imputation accuracy.

Next-generation sequencing analysis with a population-specific reference genome

The paper develops resources for NGS analysis using the Japanese reference genome JG, including variant calling, annotation, and coordinate conversion tools.

Erythropoietin production in embryonic neural cells is controlled by hypoxia-inducible factors and histone deacetylases in an undifferentiated state

This study identifies hypoxia-inducible factors and histone deacetylases as regulators of EPO production in embryonic neural cells under hypoxic conditions.

A global atlas of genetic associations of 220 deep phenotypes

Cross-population GWAS of 220 phenotypes in BioBank Japan, UK Biobank, and FinnGen (n=628,000) identifies 5,343 previously unreported loci and decomposes summary statistics into latent genetic components for disease subtyping.

Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs

The paper introduces Japonica Array NEO, a SNP array for the Japanese population with enhanced coverage and disease risk SNPs, showing high imputation quality and utility in genotyping cohorts.

The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision

This study shows that LSD1 promotes erythropoiesis by repressing myeloid fate, and inhibiting myeloid factors reverses lineage conversion caused by LSD1 inactivation in mice and human HSPC.

Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes in a 3,552 Japanese whole-genome sequence dataset (3.5KJPNv2)

The paper identifies seven new potentially pathogenic BRCA1/BRCA2 variants in a Japanese population using computational scores and cohort analysis.

Construction and Integration of Three De Novo Japanese Human Genome Assemblies toward a Population-Specific Reference

This paper constructs and integrates three de novo Japanese human genome assemblies to create a population-specific reference, improving variant calling accuracy for Japanese individuals.

Large scale genome-wide association study in a Japanese population identified 45 novel susceptibility loci for 22 diseases

A large-scale GWAS in 212,453 Japanese individuals identified 45 novel susceptibility loci for 22 diseases, highlighting the importance of non-European population studies.

Transethnic meta-analysis of genome-wide association studies identifies three new loci and characterizes population-specific differences for coronary artery disease

This study identifies three new CAD loci through transethnic GWAS and highlights population-specific genetic differences between Japanese and European populations.

A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer's disease

A Recurrent Neural Network Based Method for Genotype Imputation on Phased Genotype Data

This paper introduces a recurrent neural network method for genotype imputation using phased genotype data, showing comparable accuracy to existing methods for common variants and better performance when haplotype data is limited.

3.5KJPNv2, An allele frequency panel of 3,552 Japanese Individuals

The paper constructs a population-level allele frequency panel of 3,552 Japanese individuals using a standardized pipeline and makes it publicly available.