Simon D. W. Frost

Simultaneous broad protection against Ebola Sudan, Marburg and Lassa viruses conferred by a DNA primed MVA-vectored multivalent vaccine

Immunogenicity and Efficacy of Digitally Immune Optimised H1N1 Vaccine Candidates in Swine and Murine Animal Models

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.

Digitally immune optimised haemagglutinin with nanocage plug-and-display elicits broadly neutralising pan-H5 influenza subtype vaccine responses

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.

Model design for non-parametric phylodynamic inference and applications to pathogen surveillance

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

Bat pluripotent stem cells reveal unique entanglement between host and viruses

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

Pneumococcal within-host diversity during colonisation, transmission and treatment

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

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

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.

Pan-genome analysis of Mycobacterium africanum: insights to dynamics and evolution

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

Genome-wide patterns of gene expression in a wild primate indicate species-specific mechanisms associated with tolerance to natural simian immunodeficiency virus infection

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.

Fast Hierarchical Bayesian Analysis of Population Structure

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

Biased phylodynamic inferences from analysing clusters of viral sequences

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