Magee AF - Search Results

1

Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.

McBride DS, Garushyants SK, Franks J, Magee AF, Overend SH, Huey D, Williams AM, Faith SA, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting JM, Tonkovich MJ, Genders JT, Montoney AJ, Kasnyik K, Linder TJ, Bevins SN, Lenoch JB, Chandler JC, DeLiberto TJ, Koonin EV, Suchard MA, Lemey P, Webby RJ, Nelson MI, Bowman AS. McBride DS, et al. Among authors: magee af. Nat Commun. 2023 Aug 28;14(1):5105. doi: 10.1038/s41467-023-40706-y. Nat Commun. 2023. PMID: 37640694 Free PMC article.

2

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.

Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching Zi Yan K, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. Pekar JE, et al. Science. 2022 Aug 26;377(6609):960-966. doi: 10.1126/science.abp8337. Epub 2022 Jul 26. Science. 2022. PMID: 35881005 Free PMC article.

3

On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2.

Didier G, Glatt-Holtz NE, Holbrook AJ, Magee AF, Suchard MA. Didier G, et al. Among authors: magee af. Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2318989121. doi: 10.1073/pnas.2318989121. Epub 2024 Jan 12. Proc Natl Acad Sci U S A. 2024. PMID: 38215186 Free PMC article.

4

Random-effects substitution models for phylogenetics via scalable gradient approximations.

Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Matsen Iv FA, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. Magee AF, et al. Syst Biol. 2024 May 7:syae019. doi: 10.1093/sysbio/syae019. Online ahead of print. Syst Biol. 2024. PMID: 38712512

5

Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies.

Whidden C, Claywell BC, Fisher T, Magee AF, Fourment M, Matsen FA. Whidden C, et al. Among authors: magee af. Syst Biol. 2020 Mar 1;69(2):280-293. doi: 10.1093/sysbio/syz047. Syst Biol. 2020. PMID: 31504997 Free PMC article.

6

Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability.

Kopperud BT, Magee AF, Höhna S. Kopperud BT, et al. Among authors: magee af. Proc Natl Acad Sci U S A. 2023 Feb 14;120(7):e2208851120. doi: 10.1073/pnas.2208851120. Epub 2023 Feb 9. Proc Natl Acad Sci U S A. 2023. PMID: 36757894 Free PMC article.

7

Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories.

Faulkner JR, Magee AF, Shapiro B, Minin VN. Faulkner JR, et al. Among authors: magee af. Biometrics. 2020 Sep;76(3):677-690. doi: 10.1111/biom.13276. Epub 2020 May 7. Biometrics. 2020. PMID: 32277713

8

Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis.

Magee AF, Hilton SK, DeWitt WS. Magee AF, et al. Mol Biol Evol. 2021 Sep 27;38(10):4603-4615. doi: 10.1093/molbev/msab163. Mol Biol Evol. 2021. PMID: 34043795 Free PMC article.

9

Rejoinder for discussion on "Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories".

Faulkner JR, Magee AF, Shapiro B, Minin VN. Faulkner JR, et al. Among authors: magee af. Biometrics. 2020 Sep;76(3):695-699. doi: 10.1111/biom.13273. Epub 2020 May 7. Biometrics. 2020. PMID: 32378741 No abstract available.

10

The dawn of open access to phylogenetic data.

Magee AF, May MR, Moore BR. Magee AF, et al. PLoS One. 2014 Oct 24;9(10):e110268. doi: 10.1371/journal.pone.0110268. eCollection 2014. PLoS One. 2014. PMID: 25343725 Free PMC article.

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