James Breen

The paper surveys genetic professionals on functional evidence use in variant classification and identifies the need for expert recommendations and guidelines.

This paper identifies a 20-miRNA signature to detect haemolysis in microRNA-seq data from clinical plasma samples.

DraculR detects haemolysis contamination in small RNA sequencing data by calculating a haemolysis metric from microRNA expression data.

The paper identifies core and flanking DNA interactions in bHLH-PAS transcription factors that determine binding specificity and link to obesity.

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

The paper identifies a PGR-A isoform-RUNX interaction that drives chromatin remodelling at promoters during ovulation, revealing a mechanism for ovulation-specific gene regulation.

This paper introduces 3DFAACTS-SNP, a workflow that identifies T1D risk variants with regulatory mechanisms using Treg-specific epigenomic data, finding 36 candidate SNPs and 51 target genes.

geaR is an R package for evolutionary analysis of genome-wide genotype data, enabling efficient querying and analysis of genetic diversity and admixture using GDS format.