40 citations · 70 across the 24 of their papers we have counts for
15 papers · 1 filter
Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors
Xiang Ji, Benjamin Redelings, Shuo Su +6
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires pri…
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…
Random-effects substitution models for phylogenetics via scalable gradient approximations
Andrew F. Magee, Andrew J. Holbrook, Jonathan E. Pekar +7
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present…
Scalable Bayesian divergence time estimation with ratio transformations
Xiang Ji, Alexander A. Fisher, Shuo Su +5
Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With t…
Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis
Gabriel W. Hassler, Brigida Gallone, Leandro Aristide +6
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor…
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…
Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation
Guy Baele, Mandev S. Gill, Philippe Lemey +1
Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution…
Relaxed random walks at scale
Alexander A. Fisher, Xiang Ji, Philippe Lemey +1
Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny a…
A Relaxed Drift Diffusion Model for Phylogenetic Trait Evolution
Mandev S. Gill, Lam Si Tung Ho, Guy Baele +2
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of…
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…
Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
Gabriela B. Cybis, Janet S. Sinsheimer, Trevor Bedford +3
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate…
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…
Integrating influenza antigenic dynamics with molecular evolution
Trevor Bedford, Marc A. Suchard, Philippe Lemey +7
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed thr…
The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing
Philippe Lemey, Andrew Rambaut, Trevor Bedford +8
Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely…