Gen Tamiya

Genomic properties representing plant sex chromosome evolution interpreted with genome language models

The paper uses a genome language model to analyze plant Y chromosomes from Silene and Humulus, identifying shared genomic features and evolutionary patterns despite structural divergence.

Genome-wide Association Study of Social Isolation in 63 497 Japanese Individuals from the General Population

This study identifies genetic loci associated with social isolation in a Japanese population using GWAS, finding associations with ACADSB, HMX3, LINC02315, and LRFN5.

Palette polygenic risk score framework improves risk prediction by capturing clinical heterogeneity of type 2 diabetes

The paper introduces a polygenic risk score framework that improves type 2 diabetes risk prediction by accounting for clinical subtypes and pathway-specific contributions.

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.

Deep embedded clustering by relevant scales and genome-wide association study in autism

The paper clusters ASD patients using a deep embedded algorithm and performs cluster-based GWAS, identifying 90 significant loci associated with ASD subgroups.

Interparental Gene Conversion in General Population: A Novel Mechanism For Loss of Heterozygosity

The paper identifies interparental gene conversion events in the general population, finding one event per 21.8 births and linking it to loss of heterozygosity and potential genetic disease mechanisms.

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.

The evolution of fitness during range expansions in different dimensions

This paper introduces a simulation tool for range expansions in different dimensions and analyzes fitness dynamics in 3D expansions for the first time.

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.

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.

Clustering by phenotype and genome-wide association study in autism

The paper uses clustering and genome-wide association studies to identify subgroups in autism spectrum disorder and finds significant loci associated with these subgroups.

Endogenization and excision of human herpesvirus 6 in human genomes

The paper analyzes HHV-6 integration in human genomes, identifies co-evolution with chr22q, and reports evidence of in vivo excision and reactivation.

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.

Automated acquisition of knowledge beyond pathologists

This study develops a deep learning method to automatically extract explainable features from histopathological images, achieving higher accuracy than human pathologists in predicting prostate cancer recurrence.

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.