T. G. Vaughan

Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach

This paper introduces the Transmission Tree (TnT) model to improve understanding of epidemic dynamics by integrating pathogen gene sequences and clinical data through a Bayesian approach.

The Fossilised Birth-Death Model is Identifiable

The paper proves that time-dependent fossilised birth-death models are identifiable, but shows that adding a removal after sampling parameter makes them unidentifiable.

Decoding the fundamental drivers of phylodynamic inference

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.

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe

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.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

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

Joint inference of migration and reassortment patterns for viruses with segment genomes

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.

Improved multi-type birth-death phylodynamic inference in BEAST 2

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.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

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.

A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

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.