Huaijun Zhou

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

This study examines the evolution of alternative splicing and enhancer divergence in rainbow trout ohnologues after a whole-genome duplication, showing that independent splicing and enhancer rewiring are key factors in their long-term evolutionary fate.

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

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.

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

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 improves bovine genome annotation by integrating multi-omics data to identify novel transcripts and gene functions, and constructs a trait similarity network.

The paper uses Oxford Nanopore long-read sequencing to annotate transcript isoforms in 19 chicken tissues, identifying novel transcripts and highlighting tissue-specific expression patterns.

The paper builds a TE atlas in pigs, showing young SINEs' roles in gene regulation, genetic diversity, and complex traits through multi-omics analysis.

This study maps transcription initiation sites in 31 bovine tissues, revealing promoter activity, pervasive transcription, and tissue-specific promoter usage comparable to human and mouse.

The paper identifies a conserved cell type set in cerebellar nuclei across species and shows how it was duplicated to form new regions, with a shift in dominance in humans.

The paper identifies and compares chromatin accessibility in cattle, pig, and mouse tissues using ATAC-seq, finding species-specific regulatory elements and conservation patterns.