Phineas T. Hamilton

A-LAVA identifies germline variants affecting metabolic pathways in cancer genomes through SNP, gene, and pathway-level analysis, improving accuracy by correcting for overlapping gene sets and reducing false positives.

The paper identifies self-reactive intra-epithelial plasma cells in ovarian cancer that correlate with improved prognosis and suggest a mechanism for immune response against tumor heterogeneity.

The paper shows that alternative splicing of ARS2 generates cytoplasmic isoforms that switch ARS2's function from inhibiting to promoting nonsense-mediated mRNA decay and enhance arsenic stress response.

The paper analyzes the interaction between tumor and immune clones in ovarian cancer, finding that immune contexture patterns mirror malignant spread and that foldback inversions correlate with poor outcomes.