Bernard J. Pope

The Landscape of Prostate Tumour Methylation

This study maps epigenomic heterogeneity in prostate cancer by analyzing 3,001 methylomes and identifies four subtypes with distinct clinical and molecular features.

A mosaic of genomic architectures underpins parasitism loss in a jawless vertebrate

The paper identifies genomic architectures associated with parasitism loss in lampreys, showing distinct genomic features across different ecotypes and highlighting independent evolutionary paths.

Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western Europe

This study examines reproductive modes in Ludwigia grandiflora subsp. hexapetala populations, finding clonal reproduction dominates but with sexual reproduction rates varying and genetic diversity differences between floral morphs.

Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications

The paper shows adenomas from individuals with biallelic MUTYH or NTHL1 variants have mutational signatures similar to CRCs, suggesting adenomas can be used for variant classification and cancer prevention.

A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome

This study resolves the etiology of suspected Lynch syndrome tumors by analyzing somatic and germline mutations, methylation, and immunohistochemistry in 137 tumors, identifying key causes of DNA mismatch repair deficiency.

Evaluating multiple next-generation sequencing derived tumor features to accurately predict DNA mismatch repair status

The paper evaluates multiple next-generation sequencing features to predict DNA mismatch repair status in tumors, finding that combining features improves accuracy across different cancer types.

VIVID: a web application for variant interpretation and visualisation in multidimensional analyses

VIVID is a web tool that visualizes and interprets DNA variants in 3D on protein models to study genetic variation and its association with phenotypes.

Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights

The paper presents a new high-quality genome assembly and annotation for Cryptosporidium parvum IOWA, revealing structural and functional insights into its genome and evolutionary relationships with related species.

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

SNPPar detects homoplasic SNPs in microbial genomes to identify convergent evolution and adaptive traits with high accuracy and efficiency.

Germline and Tumor Whole Genome Sequencing as a Diagnostic Tool to Resolve Suspected Lynch Syndrome

This study uses germline and tumor whole genome sequencing to identify the cause of mismatch repair deficiency in suspected Lynch syndrome cases, finding that most cases are due to somatic mutations rather than inherited variants.

Best Practice Data Life Cycle Approaches for the Life Sciences

The paper provides best practice data life cycle approaches for life sciences researchers focusing on omics datasets and computational data analysis.