Simon D. W. Frost

This paper demonstrates the immunogenicity and efficacy of a computationally designed DNA vaccine against H1N1 influenza in swine and mice, showing broad neutralizing antibody responses and reduced viral shedding.

This paper develops a vaccine candidate using DIOSvax-H5inter nanocages that elicits cross-clade neutralising antibodies and T cell responses against diverse H5 influenza strains.

This paper develops a frequentist non-parametric method for phylodynamic inference and applies it to study cholera and COVID-19 epidemics.

The paper generates bat induced pluripotent stem cells and finds they contain endogenous viral sequences, suggesting a deep entanglement between bats and viruses.

This study uses deep sequencing to analyze pneumococcal genetic diversity in infants and mothers, revealing transmission patterns and treatment impacts on resistant strains.

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.

This study analyzes the pan-genome of Mycobacterium africanum and related lineages to explore their evolutionary dynamics and geographic distribution.

The paper analyzes gene expression in wild Ugandan red colobus to show SIV infection does not cause chronic immune activation and identifies upregulation of CD101 as a potential tolerance mechanism.

fastbaps provides a fast Bayesian clustering method for genetic data, outperforming existing methods in speed while maintaining comparable accuracy on real and simulated datasets.

The paper shows that false viral sequence clusters can lead to incorrect phylodynamic parameter estimates, such as underestimating population size and overestimating growth rates.