publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2025

  1. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2
    Jonathan E Pekar, Spyros Lytras, Mahan Ghafari, and 8 more authors
    Cell, 2025
  2. Genomics reveals zoonotic and sustained human mpox spread in West Africa
    Edyth Parker, Ifeanyi F Omah, Delia Doreen Djuicy, and 8 more authors
    Nature, 2025

2024

  1. How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
    Andrew Magee, Michael Karcher, Frederick A Matsen IV, and 1 more author
    Bayesian analysis, 2024
  2. Random-effects substitution models for phylogenetics via scalable gradient approximations
    Andrew F Magee, Andrew J Holbrook, Jonathan E Pekar, and 7 more authors
    Systematic Biology, 2024
  3. 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, and 2 more authors
    Proceedings of the National Academy of Sciences, 2024
  4. Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models
    Yucai Shao, Andrew F Magee, Tetyana I Vasylyeva, and 1 more author
    PLOS Computational Biology, 2024

2023

  1. Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
    Bjørn T Kopperud, Andrew F Magee, and Sebastian Höhna
    Proceedings of the National Academy of Sciences, 2023
  2. Data integration in Bayesian phylogenetics
    Gabriel W Hassler, Andrew F Magee, Zhenyu Zhang, and 5 more authors
    Annual Review of Statistics and its Application, 2023
  3. Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
    Dillon S McBride, Sofya K Garushyants, John Franks, and 8 more authors
    Nature Communications, 2023

2022

  1. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
    Jonathan E Pekar, Andrew Magee, Edyth Parker, and 8 more authors
    Science, 2022
  2. CRABS: congruent rate analyses in birth–death scenarios
    Sebastian Höhna, Bjørn T Kopperud, and Andrew F Magee
    Methods in Ecology and Evolution, 2022

2021

  1. Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis
    Andrew F Magee, Sarah K Hilton, and William S DeWitt
    Molecular Biology and Evolution, 2021

2020

  1. 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
    Mathieu Fourment, Andrew F Magee, Chris Whidden, and 3 more authors
    Systematic Biology, 2020
  2. Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts
    Andrew F Magee, Sebastian Höhna, Tetyana I Vasylyeva, and 2 more authors
    PLoS Computational Biology, 2020
  3. Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories
    James R Faulkner, Andrew F Magee, Beth Shapiro, and 1 more author
    Biometrics, 2020
  4. Systematic exploration of the high likelihood set of phylogenetic tree topologies
    Chris Whidden, Brian C Claywell, Thayer Fisher, and 3 more authors
    Systematic Biology, 2020

2019

  1. Learning, using, and extending variational distributions of phylogenetic trees
    Frederick A Matsen IV, Michael Karcher, Mathieu Fourment, and 3 more authors
    In Proceedings of the 14th Machine Learning in Computational Biology (MLCB) Meeting, Dec 2019

2014

  1. The dawn of open access to phylogenetic data
    Andrew F Magee, Michael R May, and Brian R Moore
    PLoS One, 2014