Hao Chen

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.

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

Trex-QTL identifies trans-eQTLs with global effects on molecular phenotypes, showing improved power and replicating known loci in rat brain data.

This study identifies time-dependent epistatic interactions between Oprm1 and Fgf12 that modulate opioid-induced locomotion in mice and links Fgf12 to opioid behavior in humans.

This study shows that testing juvenile zebrafish in groups rather than isolation reduces stress, improves behavioral stability, and enhances detection of nicotine reward.

This study shows that female rats with paternal WMI lineage exhibit increased oxycodone consumption and accelerated escalation compared to reciprocal offspring, indicating a parent-of-origin effect in addiction vulnerability.

This study evaluates three deep learning models for optic nerve axon quantification on a novel rat dataset, finding reduced performance compared to published benchmarks.

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

This study shows chronic compression transforms macrophages into a pro-tumor state, resembling glioma-associated macrophages, independent of tumor cell factors.

The paper identifies genome-wide promoter-enhancer interactions in rat brain using Hi-C data and CTCF binding sites, revealing regulatory elements linked to developmental processes.

GNQA, a retrieval-augmented GPT question-answering system over 3000 GeneNetwork, aging and diabetes papers, cites source paragraphs; RAGAS rated answer relevance above human thumbs-up ratings (89% vs 76%).

The paper integrates genomic and transcriptomic data from a soybean diversity panel to identify regulatory elements and genes involved in symbiotic nitrogen fixation, revealing key circadian clock genes and eQTLs.

This study examines how genetic factors and sex influence oxycodone self-administration in rats, finding sex differences in intake and heritability in specific strains.

This study identifies genomic loci associated with cue-reactivity in rats, linking them to incentive salience and drug abuse-related traits.

This study quantifies protein expression in rat brains, identifies pQTLs, and links them to behavioral traits and human disorders.

The paper presents a Hi-C dataset from rat frontal cortex to study strain-specific chromatin architecture and its impact on gene expression and neurological traits.

This study constructs a rat pangenome from linked-read data to enhance variant discovery and genotype-phenotype mapping in recombinant inbred strains.

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

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.

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.

This study shows that young porcine plasma treatment reduces epigenetic age in multiple rat organs and improves physiological function.

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.

The paper develops universal epigenetic clocks that accurately estimate age across mammalian tissues using DNA methylation data from 185 species.

The paper compares risky decision-making and impulsivity between two Lewis rat substrains, finding significant phenotypic differences linked to genetic variants.

This study inactivates PDE4B in rat nucleus accumbens shell using CRISPR/Cas9 and shows it increases nicotine self-administration motivation despite higher effort requirements.

The paper simulates GWAS in rats to show that larger sample sizes lead to an exponential increase in the number of significant loci detected.

The paper identifies cis-QTLs and eQTLs in HS rats across five brain regions, finds colocalization with human GWAS results, and shows higher eQTL density compared to human data.

This study identifies GLH proteins' role in controlling Argonaute pathway specificity and promoting transgenerational silencing in C. elegans by binding to target mRNAs and amplifying small RNAs.

The paper identifies the conserved role of α2δ subunits of calcium channels in nicotine-motivated behavior across species using C. elegans and human GWAS data.

The paper uses linked-read whole-genome sequencing to identify DNA variants in BXD mice and maps them to phenotypes, enabling systems genetics and precision medicine.