| The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 JE Pekar, A Magee, E Parker, N Moshiri, K Izhikevich, JL Havens, ... Science 377 (6609), 960-966, 2022 | 251 | 2022 |
| The dawn of open access to phylogenetic data AF Magee, MR May, BR Moore PLoS One 9 (10), e110268, 2014 | 52 | 2014 |
| 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology M Fourment, AF Magee, C Whidden, A Bilge, FA Matsen IV, VN Minin Systematic biology 69 (2), 209-220, 2020 | 48 | 2020 |
| Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts AF Magee, S Höhna, TI Vasylyeva, AD Leaché, VN Minin PLOS Computational Biology 16 (10), e1007999, 2020 | 38 | 2020 |
| Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories JR Faulkner, AF Magee, B Shapiro, VN Minin Biometrics 76 (3), 677-690, 2020 | 26 | 2020 |
| Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability BT Kopperud, AF Magee, S Höhna Proceedings of the National Academy of Sciences 120 (7), e2208851120, 2023 | 24 | 2023 |
| CRABS: Congruent rate analyses in birth–death scenarios S Höhna, BT Kopperud, AF Magee Methods in Ecology and Evolution 13 (12), 2709-2718, 2022 | 11 | 2022 |
| Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies C Whidden, BC Claywell, T Fisher, AF Magee, M Fourment, FA Matsen IV Systematic biology 69 (2), 280-293, 2020 | 11 | 2020 |
| Data Integration in Bayesian Phylogenetics GW Hassler, AF Magee, Z Zhang, G Baele, P Lemey, X Ji, M Fourment, ... Annual Review of Statistics and Its Application 10, 353-377, 2023 | 10 | 2023 |
| Impact of K-Pg Mass Extinction Event on Crocodylomorpha Inferred from Phylogeny of Extinct and Extant Taxa AF Magee, S Höhna bioRxiv, 2021.01. 14.426715, 0 | 10 | |
| How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error A Magee, M Karcher, FA Matsen IV, VM Minin Bayesian Analysis 19 (2), 565-593, 2024 | 8 | 2024 |
| Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis AF Magee, SK Hilton, WS DeWitt Molecular Biology and Evolution 38 (10), 4603-4615, 2021 | 6 | 2021 |
| Random-effects substitution models for phylogenetics via scalable gradient approximations AF Magee, AJ Holbrook, JE Pekar, IW Caviedes-Solis, FA Matsen IV, ... Systematic Biology, syae019, 2024 | 5 | 2024 |
| On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2 G Didier, NE Glatt-Holtz, AJ Holbrook, AF Magee, MA Suchard Proceedings of the National Academy of Sciences 121 (3), e2318989121, 2024 | 4 | 2024 |
| The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 JE Pekar, S Lytras, M Ghafari, AF Magee, E Parker, JL Havens, ... bioRxiv, 2023.07. 12.548617, 2023 | 4 | 2023 |
| ACDC: Analysis of Congruent Diversification Classes S Höhna, BT Kopperud, AF Magee bioRxiv, 2022 | 3 | 2022 |
| Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models Y Shao, AF Magee, TI Vasylyeva, MA Suchard PLOS Computational Biology 20 (3), e1011640, 2024 | 1 | 2024 |
| Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer (preprint) D McBride, S Garushyants, J Franks, A Magee, S Overend, D Huey, ... | | 2023 |
| The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 (preprint) JE Pekar, S Lytras, M Ghafari, AF Magee, E Parker, JL Havens, ... | | 2023 |
| Reliable and interpretable inference of evolutionary history using Bayesian phylogenetic approaches AF Magee University of Washington, 2021 | | 2021 |