Joshua M Stuart

Latest

• Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods
• Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
• A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery
• Exploring Integrative Analysis Using the BioMedical Evidence Graph
• A community effort to create standards for evaluating tumor subclonal reconstruction
• Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
• Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
• Valection: design optimization for validation and verification studies
• Germline contamination and leakage in whole genome somatic single nucleotide variant detection
• A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
• TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
• Prophetic Granger Causality to infer gene regulatory networks
• Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
• Global optimization of somatic variant identification in cancer genomes with a global community challenge
• The Cancer Genome Atlas Pan-Cancer analysis project