Lucas Lochovsky

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

CNAEL is a web application and protocol that streamlines clinical analysis and reporting of NGS-derived tumor copy number profiles, reducing curation time significantly.

NIMBus identifies mutational hotspots by integrating mutation data with genomic features to account for heterogeneity, revealing known drivers and regulatory disruptions in cancer.

RADAR identifies variants affecting RNA-binding protein function by integrating conservation, RNA structure, and tissue-specific data to prioritize noncoding variants.

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

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

The paper analyzes 2500 cancer genomes to assess the molecular functional impact of mutations, finding that some putative passenger variants may influence gene activity and contribute to cancer phenotypes.

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