Denghui Chen

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

This paper expands the RatGTEx resource with transcriptome-wide associations across 3,160 RNA-seq samples, identifying 7,473 gene-trait links and 144,876 QTLs for 22,599 genes.

Genomic SEM reveals shared genetic architecture and expands locus discovery for locomotor activity in heterogeneous stock rats

The paper uses Genomic SEM to identify loci underlying locomotor activity in rats, finding 31 loci compared to fewer from other methods.

Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats

The paper identifies non-SNP variants as significant regulators of gene expression and addiction-related traits in HS rats using joint cis-eQTL analysis.

Genome-wide association study in Heterogeneous Stock rats identifies genetic loci associated with aversion-based learning and cocaine aversion

Genome-wide association study of cocaine self-administration behavior in Heterogeneous Stock rats

This study performs a GWAS on cocaine self-administration in rats, identifying six genome-wide significant loci, including one linked to carboxylesterase genes involved in cocaine metabolism.

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats

The paper identifies host genetic effects on microbiome composition in rats and finds evidence of indirect genetic effects contributing to missing heritability.

RatXcan: A framework for cross-species integration of genome-wide association and gene expression data

RatXcan extends transcriptome-wide association studies to rats, enabling cross-species integration of GWAS and gene expression data to identify shared genetic mechanisms of complex traits.

Genome-wide association study reveals multiple loci for nociception and opioid consumption behaviors associated with heroin vulnerability in outbred rats

This study identifies genetic loci associated with opioid use disorder-related behaviors in rats using a genome-wide association approach and network-based clustering.

A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations

The paper describes a cost-effective, high-throughput genotyping method for heterogeneous stock rats using low-coverage sequencing data, achieving high accuracy comparable to high-coverage sequencing.

Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population

The paper genotypes Y and mitochondrial chromosomes in heterogeneous stock rats and finds no significant associations with complex traits, except for gene expression on these chromosomes.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

Genome-wide association study of delay discounting in Heterogenous Stock rats

This study identifies genetic loci associated with delay discounting in Heterogenous Stock rats using GWAS, implicating Slc35f1 and Adgrl3 as potential genes involved in this behavior.

Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and AHR, ATF3, GATA3, HNF1B, POU2F2, and TFCP2 transcription factors as potential candidates to explain incomplete penetrance

This paper identifies genetic variants and transcription factors associated with unilateral renal agenesis in rats, suggesting a threshold mechanism involving KIT and interacting transcription factors.