Shannon Clarke

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

The paper introduces the RUMIGEN EpiChip, a DNA methylation array for cattle, demonstrating its utility in studying phenotypic variation and age prediction through methylation analysis.

Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

Universal DNA methylation age across mammalian tissues

The paper develops universal epigenetic clocks that accurately estimate age across mammalian tissues using DNA methylation data from 185 species.

Development of epigenetic clocks for New Zealand livestock

This paper develops epigenetic clocks for New Zealand livestock using DNA methylation data to predict chronological age accurately across multiple species.

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)

The paper performs a global analysis of transcription start sites (TSS) in the ovine reference genome using CAGE sequencing, identifying novel TSS and validating them with bisulfite sequencing.

Exclusion and genomic relatedness methods for assignment of parentage using genotyping-by-sequencing data

The paper develops methods to assign parentage using low-depth sequencing data by combining relatedness estimates and excess mismatch rate metrics, showing consistency with microsatellite results.

Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data

This paper develops a method to accurately estimate linkage disequilibrium from low coverage sequencing data by accounting for under-called heterozygous genotypes.