Timothy G. Vaughan

This study evaluates spike clock models in phylogenetics, finding they are supported in most datasets and improve estimates of speciation and extinction rates.

This study shows that phylodynamic migration rate estimates for HIV-1 within hosts are overestimated under selection using common models like BEAST2.

This paper introduces a Bayesian method to infer multi-type population trajectories from genomic data, demonstrating its application to MERS-CoV genomes to estimate human and camel case numbers and spillover events.

This paper introduces the SRFBD model to improve phylogenetic inference by incorporating stratigraphic range data, showing it produces older divergence times and higher sampling proportions compared to the FBD model.

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

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.

ReMASTER improves phylodynamic simulation in BEAST 2.7 by offering a more efficient and flexible approach to modeling and simulating phylogenetic trees and population dynamics.

The paper compares sequencing and assembly methods' impact on plasmid and chromosomal phylogenies and horizontal gene transfer inference in E. coli.

TreeKnit infers ancestral reassortment graphs from segment trees of influenza viruses, showing high accuracy and speed compared to Bayesian methods.

This study compares structured coalescent and multitype birth-death models for inferring migration rates between subpopulations using simulated phylogenies, finding MBD outperforms SC in epidemic outbreaks.

The paper introduces a multi-state birth-death model to detect HIV transmission clusters from phylogenetic trees, showing it reliably infers cluster structure and transmission parameters.

IcyTree provides a browser-based tool for visualizing phylogenetic trees and networks with interactive features and efficient rendering.