Matthew D. Hall

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

The paper identifies and masks artefactual variants in SARS-CoV-2 sequencing data to improve the accuracy of within-host diversity and transmission analysis.

The paper identifies a bias in phylogenetic branch lengths when using the discrete Gamma model and recommends replacing it with the FreeRate model.

This study analyzes HCV within-host dynamics post-DAA treatment failure, finding persistent viral subpopulations and lineage-specific evolutionary rates.

The paper evaluates two tools for HIV transmission direction prediction using short and long-read sequencing data from serodiscordant couples, showing long reads improve phylogenetic resolution and transmission prediction accuracy.

This study adjusts for sampling bias in SARS-CoV-2 Ct values and finds that viral variant and age affect within-host viral burdens, with variant effects varying by vaccination status.

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

This paper introduces veSEQ-HIV, a cost-effective, high-throughput sequencing method for HIV that recovers complete genomes and quantifies viral load, enabling drug resistance monitoring and transmission analysis.

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.