David Evan MacHugh

The paper analyzes genomic data from Eurasian curlews to assess genetic diversity, population structure, and selection signals in declining populations.

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 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 identifies candidate genes for trypanotolerance in African cattle by integrating genomic and transcriptomic data from hybrid populations.

This study uses multi-omics approaches to analyze how M. bovis infection reprograms the epigenome of bovine alveolar macrophages, identifying key genes and pathways involved in the host response.

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

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 develops mRNA-based classifiers using RNA-seq and machine learning to accurately distinguish bTB-positive from bTB-negative cattle and other pathogens.

This study compares gene expression in trypanotolerant and trypanosusceptible cattle during trypanosome infection across multiple tissues and time points, identifying immune-related and coagulation genes associated with trypanotolerance.

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.

This study integrates transcriptomic, genomic, and GWAS data to identify genes and eQTLs associated with the PB transcriptome response to M. bovis infection in cattle.

The paper uses local ancestry inference tools to analyze admixture in African and European cattle populations, identifying functional consequences of ancestry on disease resistance and physiological traits.

This study uses whole-genome sequencing and SNP arrays to analyze Criollo cattle from Colombia and Venezuela, revealing African and Asian admixture and selection signatures linked to adaptive traits.

This study integrates multi-omics data from bovine and human macrophages infected with M. bovis and M. tuberculosis to identify genes and pathways associated with resistance to mycobacterial infection.

The paper identifies a 170-gene transcriptional signature in bovine peripheral blood post-M. bovis infection following PPD-b stimulation, suggesting potential biomarkers for bTB diagnostics.

The paper integrates multi-omics data with genome-wide association results to identify infection response pathways and genomic variants associated with resistance to bovine tuberculosis.

The paper identifies transcriptional and chromatin changes in bovine alveolar macrophages during Mycobacterium bovis infection and links them to genetic variants associated with tuberculosis resistance.

This study uses population genomics to analyze the Galway sheep breed, finding gene flow from British Leicester and Suffolk sheep, intermediate genetic diversity, and genomic signatures of selection related to meat and wool production.

This study analyzes inbreeding trends in Thoroughbred horses, showing a significant decline in genetic diversity linked to popular sire lines and selection for athletic traits.

This study identifies eQTL in Thoroughbred skeletal muscle, revealing heritable variation in genes related to cofactor metabolism and potential impacts on athletic performance.

This study examines the DNA methylome of bovine alveolar macrophages infected with Mycobacterium bovis and finds no significant changes in DNA methylation, but identifies genes with intermediate promoter methylation enriched for immune-related functions.

The paper assesses globin mRNA impact on RNA-seq in horses and cattle, finding low levels that eliminate the need for globin depletion.

This study compares the transcriptomic and proteomic profiles of Mycobacterium tuberculosis and Mycobacterium bovis, revealing distinct host responses in bovine macrophages.

This study uses genome-wide SNP data to assess genetic diversity and conservation status of Kerry cattle, revealing reduced effective population size and increased inbreeding.