Lingzhao Fang

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.

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

The paper identifies context-dependent genetic regulation of gene expression in pigs using quantile regression, revealing eQTLs that are conserved with humans and influence disease-relevant genes.

SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.

The paper maps a multi-layered molecular QTL atlas in chicken to understand complex trait regulation across tissues and developmental stages.

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.

This study profiles allele-specific expression across 42 tissues and 34 pig breeds using an open-source pipeline, revealing widespread and tissue-specific allelic imbalance.

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.

LATTE quantifies TE expression across species and identifies TE-eQTLs, revealing distinct regulatory mechanisms and additional associations with complex traits.

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

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

OmiGA improves molQTL mapping in complex populations by using an efficient linear mixed model, enhancing power and reducing false positives.

This study integrates genomic and transcriptomic analyses across lactation stages in dairy cattle to identify temporal genetic variants and molecular mechanisms associated with feed intake.

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.

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

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.

GSOR and MTAO detect widespread cis-regulatory effects on bovine complex traits by linking gene expression with genetic scores and multi-trait associations.

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

The paper analyzes the genomic data of 385 horses from 49 breeds to explore the demographic history and genetic factors influencing body size in ponies, identifying cis-regulatory elements and genetic affinities.

The paper performs a multi-breed meta-GWAS in pigs to identify genomic regions associated with complex traits and integrates with PigGTEx to prioritize variant-gene-tissue-trait circuits.

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

The paper constructs a sheep developmental gene expression atlas and identifies key genes associated with economically important traits by analyzing gene expression across developmental stages.

The paper creates an enriched gene atlas for the GRCg7b chicken assembly, increasing the number of annotated lncRNAs and PCGs and providing functional annotations across 47 tissues.

The paper introduces a large chicken reference panel with 13,187 genomes, showing improved imputation accuracy and statistical power for genome-wide association studies.

This study identifies selection signatures and loci associated with complex traits in pigs by analyzing multi-omics data from Eastern and Western breeds.

This paper develops DeepGCF, a deep learning method to predict functional conservation between human and pig using epigenome and transcriptome data, showing improved performance and insights into regulatory and heritability patterns.

The paper quantifies how gene expression and splicing QTL explain heritability in cattle traits using Bayesian methods across 16 tissues.

This study presents a chromosome-scale genome assembly of Nicotiana tabacum, identifies genetic structure correlates, and builds a genotype-to-phenotype map for multiple traits using GenBank-scale data.

The paper introduces a web server for multi-species transcriptome-wide association study (TWAS) analysis, enabling gene expression prediction and trait association in humans and farm animals.