T. Vaughan

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering

EpiFusion improves estimation of outbreak dynamics by integrating phylodynamic and epidemiological data using particle filtering, enhancing accuracy and efficiency in large, poorly sampled epidemics.

Robust phylodynamic analysis of genetic sequencing data from structured populations

The paper improves the bdmm algorithm in BEAST 2 to handle larger genetic datasets, enabling more precise phylodynamic analysis of structured populations.

Infectious disease phylodynamics with occurrence data

The paper shows that incorporating occurrence data with birth-death models improves estimates of the basic reproductive number in phylodynamic analyses, while coalescent models are less affected by sampling biases but cannot use occurrence data.

The ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data

The paper derives the conditional probability distribution of ancestral population size given a reconstructed phylogenetic tree and occurrence data, with applications in epidemiology and macroevolution.

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

This study uses Bayesian inference to analyze reassortment networks in human influenza viruses, finding that reassortment events occur more frequently on fitter parts of the network.

The probability distribution of the reconstructed phylogenetic tree with occurrence data

The paper derives a probability distribution for phylogenetic trees with occurrence data, enabling parameter estimation in epidemiology and macroevolution.

A single dose of antibody-drug conjugate cures a stage 1 model of African trypanosomiasis.

This paper demonstrates that a single dose of an antibody-drug conjugate targeting the trypanosome receptor HpHbR completely cures a stage 1 mouse model of African trypanosomiasis.