Gordon Saksena

TangentXY improves copy-number estimation for sex chromosomes, revealing associations between chrX and chrY copy-number alterations and cancer features.

The paper introduces a framework for assessing the quality of whole genome cancer sequences using a star rating system based on five QC measures, providing a tool for researchers to evaluate and exclude low-quality data.

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

The paper introduces Tangent and Pseudo-Tangent pipelines for copy-number inference from cancer genome data, improving noise reduction and accuracy in SNP array and WES analyses.

The paper identifies and characterizes coding and non-coding driver mutations across 2,500 cancer genomes, revealing new candidates and questioning previous findings.

Four levers for cheaper cloud genomics on FireCloud: size virtual disks dynamically, tune VM provisioning from monitoring data, buy preemptible machines, and parallelise tasks at the right width.

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.