Ernest Bailey
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View article: Equus in Online Mendelian Inheritance in Animals (OMIA)
Equus in Online Mendelian Inheritance in Animals (OMIA) Open
Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes information for Equus inherited traits/diseases (collectively called phenes). The database focuses on Mendelian traits and their likel…
View article: The localization of centromere protein A is conserved among tissues
The localization of centromere protein A is conserved among tissues Open
Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is complet…
View article: Development of a TaqMan® Allelic Discrimination qPCR Assay for Rapid Detection of Equine CXCL16 Allelic Variants Associated With the Establishment of Long-Term Equine Arteritis Virus Carrier State in Stallions
Development of a TaqMan® Allelic Discrimination qPCR Assay for Rapid Detection of Equine CXCL16 Allelic Variants Associated With the Establishment of Long-Term Equine Arteritis Virus Carrier State in Stallions Open
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of equids. Following natural infection, up to 70% of the infected stallions can remain persistently infe…
View article: Parental bias in expression and interaction of genes in the equine placenta
Parental bias in expression and interaction of genes in the equine placenta Open
Significance The placenta is the fetomaternal interface, which is essential for fetal growth and survival, playing a central role in the health of both the fetus and its mother. The dynamic gene expression during pregnancy dramatically con…
View article: Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations
Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations Open
The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred h…
View article: Genome‐wide association study for host genetic factors associated with equine herpesvirus type‐1 induced myeloencephalopathy
Genome‐wide association study for host genetic factors associated with equine herpesvirus type‐1 induced myeloencephalopathy Open
Background Equid herpesvirus (EHV‐1) infections in horses can lead to equine herpesvirus myeloencephalopathy (EHM), characterised by neurological clinical signs. The sporadic occurrence of the disease in horse herds suggests a host genetic…
View article: Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition
Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Landscape of Overlapping Gene Expression in The Equine Placenta
Landscape of Overlapping Gene Expression in The Equine Placenta Open
Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. These different-strand overlapping genes are potential sense–antisense (SAS) pairs, which might have regulatory effects…
View article: EquCab3, an Updated Reference Genome for the Domestic Horse
EquCab3, an Updated Reference Genome for the Domestic Horse Open
EquCab2, a high-quality reference genome for the domestic horse, was released in 2007. Since then, it has served as the foundation for nearly all genomic work done in equids. Recent advances in genomic sequencing technology and computation…
View article: Equine Arteritis Virus Has Specific Tropism for Stromal Cells and CD8<sup>+</sup>T and CD21<sup>+</sup>B Lymphocytes but Not for Glandular Epithelium at the Primary Site of Persistent Infection in the Stallion Reproductive Tract
Equine Arteritis Virus Has Specific Tropism for Stromal Cells and CD8<sup>+</sup>T and CD21<sup>+</sup>B Lymphocytes but Not for Glandular Epithelium at the Primary Site of Persistent Infection in the Stallion Reproductive Tract Open
Equine arteritis virus (EAV) has a global impact on the equine industry as the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of equids. A distinctive feature of EAV infection is that it …
View article: Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds
Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds Open
Background To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole…
View article: Additional file 1: Table S1. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 1: Table S1. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
Whole genome sequencing (WGS) samples. Whole genome sequencing samples with horse identification and read depth. 153 Individuals representing 24 breeds (Twilight is included as 4 entries). Table includes horse identifier, breed, contributi…
View article: Additional file 6: of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 6: of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
Position of variants discovered from WGS data. File contains chromosome, bp position, distance from previous discovered SNP and alternate allele frequency for the 23 million SNP set. (TSV 828110 kb)
View article: Additional file 7: of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 7: of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
MNEc2M SNP information. Contains information for SNPs included on the MNEc2M array. Columns include MNEc identifiers, EquCab 2.0 coordinates, and fields indicating if the SNP was discovered in Draft and Pony groups (which were under-repres…
View article: Additional file 3: Table S3. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 3: Table S3. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
SNP validation by discovery by variant calling group. SNPs discovered from whole genome sequence (See calling groups in Additional file 1: Table S1) were validated by assessing the minor allele frequency in individuals genotyped on the MNE…
View article: Additional file 5: Table S5. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 5: Table S5. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
Sample breed and tagging breed groups. Samples (n = 485) from either whole genome sequence (WGS) or from the 2M test array (SNP) were assigned to one of 15 tagging breed groups based on their reported breed. (XLSX 21 kb)
View article: Additional file 8: of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 8: of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
Breed specific tagging SNPs. File containing informative tagging SNPs broken down by breed. (CSV 172641 kb)
View article: Additional file 2: Table S2. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 2: Table S2. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
SNP50 breed informativeness. Impact of breed on SNP50 informativeness. Table shows informativeness (MAF ≥ 0.05) of the legacy, SNP50 SNP set for light, draft, and pony breeds described by McCue et al. [1, 2]. Mean number of informative SNP…
View article: Additional file 4: Table S4. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Additional file 4: Table S4. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds Open
MNEc670k SNP information. Contains information on MNEc670k SNPs. Includes Affymetrix probe ID, genetic coordinates, MNEc Identifier, tissue origin indicating high quality genotyping in either hair root or blood, Affymetrix assigned genotyp…
View article: Allelic Variation in CXCL16 Determines CD3+ T Lymphocyte Susceptibility to Equine Arteritis Virus Infection and Establishment of Long-Term Carrier State in the Stallion
Allelic Variation in CXCL16 Determines CD3+ T Lymphocyte Susceptibility to Equine Arteritis Virus Infection and Establishment of Long-Term Carrier State in the Stallion Open
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of horses and other equid species. Following natural infection, 10-70% of the infected stallions can bec…
View article: Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies Open
Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and…
View article: Equine Arteritis Virus Uses Equine CXCL16 as an Entry Receptor
Equine Arteritis Virus Uses Equine CXCL16 as an Entry Receptor Open
Previous studies in our laboratory have identified equine CXCL16 (EqCXCL16) to be a candidate molecule and possible cell entry receptor for equine arteritis virus (EAV). In horses, the CXCL16 gene is located on equine chromosome 11 (ECA11)…