William T. Harvey

Synergy between HA cleavage site sequence and NA-mediated plasminogen recruitment as a virulence mechanism for low pathogenic avian influenza

This study identifies a virulence mechanism in low pathogenic avian influenza viruses where neuraminidase recruits plasminogen to cleave hemagglutinin, enhancing pathogenicity.

Genetic reassortment and diversification of host specificity have driven evolutionary trajectories of lineages of panzootic H5N1 influenza

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The Winners Take It All? Global Evolutionary Success ofH5Nx Reassortants in the 2020-2024 Panzootic

This study identifies 209 H5Nx reassortant strains of avian influenza viruses from 2020-2024, showing that reassortants from Europe had greater host range and persistence than those from Asia.

Co-occurrence networks from wetland bird surveys predict H5N1 genetic similarity between wild birds with strong effects of time, space and viral clustering.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

The SARS-CoV-2 Spike Protein Mutation Explorer: Using an Interactive Application to Improve the Public Understanding of SARS-CoV-2 Variants of Concern

The paper develops an interactive 3D tool to explain SARS-CoV-2 spike protein mutations and variants, showing it improves public understanding compared to existing resources.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

This study analyzes the population genomics of Bacillus anthracis in Tanzania, revealing unexpected within-host diversity and transmission patterns influenced by livestock movements.

Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

Mako: a graph-based pattern growth approach to detect complex structural variants

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.