117 citations · 132 across the 10 of their papers we have counts for
10 papers · 1 filter
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Marius Brusselmans, Luiz Max Carvalho, Samuel L. Hong +7
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distrib…
Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction
Mandev S. Gill, Philippe Lemey, Marc A. Suchard +2
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive…
Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in South America
Luiz Max Carvalho, Nuno Rodrigues Faria, Andres M. Perez +5
Although foot-and-mouth disease virus (FMDV) incidence has decreased in South America over the last years, the pathogen still circulates in the region and the risk of re-emergence…
Epidemic reconstruction in a phylogenetics framework: transmission trees as partitions
Matthew Hall, Andrew Rambaut
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure…
piBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
Filip Bielejec, Philippe Lemey, Luiz Max Carvalho +3
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framewo…
Inferring Heterogeneous Evolutionary Processes Through Time: from sequence substitution to phylogeography
Filip Bielejec, Philippe Lemey, Guy Baele +2
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifi…