Joshua Armenia

Cancer-driving mutations are enriched in genic regions intolerant to germline variation

The paper introduces OncMTR, a metric identifying genic regions intolerant to germline variation but enriched for cancer-driving mutations, and shows it improves genetic signal detection for hematologic malignancies.

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.

Enabling cross-study analysis of RNA-Sequencing data

This paper presents a pipeline to unify RNA-seq data from different studies by removing batch effects, enabling cross-study analysis.