66 citations · 73 across the 7 of their papers we have counts for
7 papers
On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2
Gustavo Didier, Nathan E. Glatt-Holtz, Andrew J. Holbrook +2
The continuous-time Markov chain (CTMC) is the mathematical workhorse of evolutionary biology. Learning CTMC model parameters using modern, gradient-based methods requires the deri…
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…
How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
Andrew F. Magee, Michael D. Karcher, Frederick A. Matsen +1
Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judg…
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
Mathieu Fourment, Andrew F. Magee, Chris Whidden +3
The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for…
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Chris Whidden, Brian C. Claywell, Thayer Fisher +3
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree spac…
Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories
James R. Faulkner, Andrew F. Magee, Beth Shapiro +1
Phylodynamics is an area of population genetics that uses genetic sequence data to estimate past population dynamics. Modern state-of-the-art Bayesian nonparametric methods for rec…
The Dawn of Open Access to Phylogenetic Data
Andrew F. Magee, Michael R. May, Brian R. Moore
The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary re…