James Hadfield

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

The paper identifies a reassortant A(H3N2) virus, A2/re, which became dominant in the 2017-2018 influenza season despite lacking HA mutations and showing no antigenic difference from previous strains.

The paper analyzes Ct genomic diversity and identifies SNPs associated with ocular localization and disease severity in a West African trachoma-endemic population.

Phandango provides an interactive web tool for exploring large-scale bacterial population genomics datasets by integrating multiple analysis outputs.