T. G. Vaughan

This paper introduces a formal method to quantify the impact of genome sequences and sampling times on phylodynamic inference, using simulations and real outbreak data to identify trade-offs and guidelines for analysis.

This study uses phylodynamic analysis of H5N8 virus sequences to quantify transmission dynamics between poultry farms and wild birds in Europe during the 2016-17 epidemic and identifies key drivers of cross-border spread.

This paper introduces a new evolutionary model, FBD-MSC, that integrates genealogical and fossilization processes to improve divergence time estimates in Caninae.

This paper extends the structured coalescent to account for reassortment in segmented viruses, showing it leads to different estimates of population sizes, migration, and clock rates compared to models without reassortment.

The paper improves the multi-type birth-death model in BEAST 2 to handle larger datasets and reports results on Influenza A virus migration and seasonal dynamics.

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.

The paper introduces a multi-state birth-death model to estimate lineage-specific speciation and extinction rates without requiring prior trait hypotheses, showing its effectiveness on simulated and empirical datasets.