Shannon Clarke

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.

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

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

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

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.

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.

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