Thomas B.K. Watkins

The paper introduces contextualized network inference to estimate sample-specific transcriptional networks for 7000 tumors, improving accuracy and enabling novel prognostic subtyping.

Refphase uses multi-sample reference phasing to infer haplotype-specific copy numbers and reveal intra-tumour heterogeneity in cancer samples.

MEDICC2 infers cancer phylogenies from copy-number data, accounting for whole-genome doubling and parallel evolution, and performs well on simulated and real datasets.

This paper introduces CAMDAC, a method to deconvolve tumor-normal DNA methylation profiles while accounting for copy number changes, revealing epigenetic instability and distinct patterns in lung cancer.

The paper investigates how whole genome doubling (WGD) in cancer may mitigate Muller’s Ratchet by reducing negative selection on mutations in essential genes after duplication.

The paper investigates genetic epistasis in EGFR-mutant lung cancers using over 2,000 cases, showing that genetic combinations, not single drivers, dominate tumor progression and clinical outcomes.