Lei Yang

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper uses long-read assemblies to analyze human LINE-1 retrotransposons, revealing their recent activity, population diversity, and evolutionary dynamics.

The paper presents a scalable CNV analysis workflow applied to rare disease cohorts, identifying 39 candidate pathogenic SVs within 2 days using collaborative tools and databases.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

The paper profiles LINE-1 activity at allelic resolution in a single human genome, finding that some LINE-1s are active in vitro but not in vivo, and some old LINE-1s retain activity and may be adaptive.

The paper studies the molecular evolution of a recently endogenized retrovirus in mule deer, showing increased diversity through horizontal acquisition and recombination.

The paper shows that retrocopying generates new APOBEC3 antiviral proteins in primates, expanding their functional repertoire to counteract viral evolution.

The paper analyzes LGL leukemia patient genomes to detect retrovirus integration sites but finds no new retroviruses, instead identifying polymorphic HERV-K provirus sites more prevalent in LGL patients.

The paper estimates the number and sequence of intact LINE-1 transposons in a diploid human genome using long-read assemblies, finding at least 290 intact LINE-1s.

The paper develops a computational framework to assess the genome-wide distribution of polymorphic HERV-K in human populations using whole genome short read data and identifies population-specific variations.