Chunyu Liu

MetaboXcan: A multiomic framework linking genetically predicted metabolites, gene expression, and complex traits

MetaboXcan predicts plasma metabolites from genetic data and associates them with complex traits, identifying disease risk genes and metabolites in chronic kidney disease.

A Mammalian Genomic Signature Shaped by Single Nucleotide Variants Regulates Transcriptome Integrity and Diversity

The paper identifies a genomic signature, G-tract-AG motifs, that regulates transcriptome integrity and diversity through repression of AG usage and SNV-induced splicing activation.

Specificity of Aberrant Exons in a Saturated Background of Differentially Expressed Exons

The paper identifies cancer-specific exonic fragments by analyzing differentially expressed exons and somatic SNVs, revealing their association with tumor suppressor genes and potential for antigen discovery.

CLUSTERING OF RARE VARIANTS FOR CAUSAL VARIANTS IDENTIFICATION AND EFFECT DIRECTION CLASSIFICATION

This paper introduces a clustering method to identify causal rare variants and classify their effect directions using summary statistics from gene-based tests.

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study

The paper identifies 83 rare lncRNA variant sets associated with blood lipid levels using WGS data from the TOPMed program and validates some in UK Biobank data.

Heteroplasmic Mitochondrial Genetic Variation in the Human Heart

The paper examines heteroplasmic mitochondrial genetic variants in human cardiac tissues and finds they differ from those in blood and skeletal muscle, with higher variant counts in cardiac tissue linked to age.

An integrative analysis of clinical and epigenetic biomarkers of mortality

The paper integrates DNA methylation with clinical risk factors to improve mortality prediction, identifying CpG biomarkers associated with all-cause, cardiovascular, and cancer mortality.

A Bioinformatics Pipeline for Estimating Mitochondria DNA Copy Number and Heteroplasmy Levels from Whole Genome Sequencing Data

This paper presents a bioinformatics pipeline to estimate mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data, showing improved accuracy in capturing mitochondrial genetic features.

Presence and Transmission of Mitochondrial Heteroplasmic Mutations in Human Populations of European and African Ancestry

The paper examines the concordance and characteristics of mitochondrial heteroplasmic mutations in maternal pairs of European and African ancestry, finding higher concordance in close relatives and associations with age and nuclear genome regions.

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

Novel genetic determinants of telomere length from a trans-ethnic analysis of 109,122 whole genome sequences in TOPMed

This study identifies 59 sentinel variants and two novel genes associated with telomere length using whole genome sequences from 109,122 trans-ethnic individuals.

Cardiovascular Disease Related Proteomic Biomarkers of Alcohol Consumption

This study identifies 20 alcohol-associated proteins and shows complex relationships between alcohol consumption, circulating proteins, and cardiovascular disease risk factors.

Mitochondrial DNA Copy Number (mtDNA-CN) Can Influence Mortality and Cardiovascular Disease via Methylation of Nuclear DNA CpGs

This study identifies CpGs associated with mtDNA-CN and shows they influence disease-related phenotypes through nDNA methylation and gene expression changes.

Genome-wide association and functional studies identify 46 novel loci for alcohol consumption and suggest common genetic mechanisms with neuropsychiatric disorders

This study identifies 46 novel genetic loci associated with alcohol consumption and suggests shared genetic mechanisms with neuropsychiatric disorders using GWAS and functional analyses.