Jack M. Fu

The paper compares structural variant detection using short-read and long-read sequencing in three trios, showing lrWGS finds more SVs but srWGS has high concordance in non-repetitive regions.

Short-read genome sequencing of 14,891 diverse genomes yields 433,371 structural variants (SVs) for gnomAD; loss-constrained genes also resist duplication, and clinical SV carrier rates are benchmarked.

The paper develops MDTS, a method for detecting de novo copy number deletions in parent-offspring trios from targeted sequencing, achieving higher precision and scalability than existing tools.

The paper develops a linear model to estimate transcript-level abundances from reduced-representation RNA-seq data in recount2, evaluating it on simulated and real data.