40 citations · 70 across the 24 of their papers we have counts for
8 papers · 1 filter
Inhomogeneous continuous-time Markov chains to infer flexible time-varying evolutionary rates
Pratyusa Datta, Philippe Lemey, Marc A. Suchard
Reconstructing evolutionary histories and estimating the rate of evolution from molecular sequence data is of central importance in evolutionary biology and infectious disease rese…
Accelerating Bayesian inference of dependency between complex biological traits
Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão +5
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible wh…
Shrinkage-based random local clocks with scalable inference
Alexander A. Fisher, Xiang Ji, Akihiko Nishimura +2
Local clock models propose that the rate of molecular evolution is constant within phylogenetic sub-trees. Current local clock inference procedures scale poorly to large taxa probl…
Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
Zhenyu Zhang, Akihiko Nishimura, Paul Bastide +5
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced f…
Inferring phenotypic trait evolution on large trees with many incomplete measurements
Gabriel Hassler, Max R. Tolkoff, William L. Allen +3
Comparative biologists are often interested in inferring covariation between multiple biological traits sampled across numerous related taxa. To properly study these relationships,…
Phylogenetic Factor Analysis
Max R. Tolkoff, Michael L. Alfaro, Guy Baele +2
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian di…
Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates
Mandev S. Gill, Philippe Lemey, Shannon N. Bennett +2
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics. Kingman's coalescent process enab…
Synonymous and Nonsynonymous Distances Help Untangle Convergent Evolution and Recombination
Peter B. Chi, Sujay Chattopadhyay, Philippe Lemey +2
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation an…