Peter J. Bailey

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

Pan-cancer evolution signatures link clonal expansion to dynamic changes in the tumour immune microenvironment

The paper identifies pan-cancer evolutionary signatures linked to clonal expansion and immune microenvironment changes using TCGA data.

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.