Houcheng Li

Reference-free isoform discovery links unannotated RNA processing to disease risk

Torino, a reference-free framework for isoform discovery, identifies RNA processing patterns linked to disease risk by analyzing read coverage variation across species and disease states.

Genetic regulation of circulating metabolome in cattle

The paper presents a cattle metabolome atlas linking genetic variants to metabolites and traits, revealing colocalization with eQTL and causal gene-metabolite-trait networks.

Genetic control of the transcriptional response to active tuberculosis disease and treatment

The paper identifies cis-eQTL and reQTL in TB patients during treatment using RNA-seq data and variant imputation, showing changes in cell type proportions and gene expression.

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

The paper uses long-read RNA-seq to uncover isoform-level and context-specific regulatory effects in cattle, improving the resolution of molecular atlases and GWAS loci.

The enhanced multi-tissue atlas of regulatory effects in cattle

The paper presents CattleGTEx, a resource characterizing regulatory effects in cattle, resolving GWAS signals and providing insights into adaptive evolution and selection.

Sex-specific Genetic Regulatory Effects in Chickens

The paper identifies sex-specific genetic regulatory effects in chickens using whole-genome sequencing and transcriptomes, revealing sex-dependent gene regulation and structural variants.

Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs

This study constructs a multi-tissue cell atlas of pigs, identifies cell-type-specific gene regulation, and links these to complex traits and human phenotypes.

A multi-tissue atlas of genetic regulatory effects in sheep

The paper presents a multi-tissue sheep atlas identifying regulatory variants and their effects on molecular phenotypes, revealing allelic heterogeneity and evolutionary patterns.

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

The paper constructs a bovine epigenomic atlas to annotate regulatory elements and decode the regulatory syntax of the cattle genome, aiding in fine-mapping GWAS loci for complex traits.

An atlas of cell type specific regulatory effects in cattle

The paper constructs a cattle cell-type-specific regulatory variant atlas by integrating bulk and single-cell RNA-seq data, identifying eQTL and linking them to GWAS loci for breeding insights.

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

The ChickenGTEx project provides a multi-tissue reference of regulatory variants in chicken, analyzing their functional impacts and utility in genetics, genomics, and evolutionary studies.

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets

This study shows that high-fiber maternal diets alter gene expression and chromatin accessibility in fetuses and piglets, improving metabolic health and immune tolerance.

A compendium of genetic regulatory effects across pig tissues

The paper presents PigGTEx, a resource linking genetic variants to transcriptomic phenotypes in pigs, showing pigs' similarity to humans in gene regulation and complex traits.