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Results: 1 to 20 of 73

1.

Inferring epidemiological dynamics with bayesian coalescent inference: the merits of deterministic and stochastic models.

Popinga A, Vaughan T, Stadler T, Drummond AJ.

Genetics. 2015 Feb;199(2):595-607. doi: 10.1534/genetics.114.172791. Epub 2014 Dec 19.

PMID:
25527289
[PubMed - in process]
2.

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration.

Gavryushkina A, Welch D, Stadler T, Drummond AJ.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003919. doi: 10.1371/journal.pcbi.1003919. eCollection 2014 Dec.

PMID:
25474353
[PubMed - in process]
Free PMC Article
3.

Calibrated Birth-Death Phylogenetic Time-Tree Priors for Bayesian Inference.

Heled J, Drummond AJ.

Syst Biol. 2014 Nov 14. pii: syu089. [Epub ahead of print]

PMID:
25398445
[PubMed - as supplied by publisher]
4.

Efficient Bayesian inference under the structured coalescent.

Vaughan TG, Kühnert D, Popinga A, Welch D, Drummond AJ.

Bioinformatics. 2014 Aug 15;30(16):2272-9. doi: 10.1093/bioinformatics/btu201. Epub 2014 Apr 20.

PMID:
24753484
[PubMed - in process]
Free PMC Article
5.

BEAST 2: a software platform for Bayesian evolutionary analysis.

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ.

PLoS Comput Biol. 2014 Apr 10;10(4):e1003537. doi: 10.1371/journal.pcbi.1003537. eCollection 2014 Apr.

PMID:
24722319
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model.

Kühnert D, Stadler T, Vaughan TG, Drummond AJ.

J R Soc Interface. 2014 Feb 26;11(94):20131106. doi: 10.1098/rsif.2013.1106. Print 2014 May 6.

PMID:
24573331
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Recursive algorithms for phylogenetic tree counting.

Gavryushkina A, Welch D, Drummond AJ.

Algorithms Mol Biol. 2013 Oct 28;8(1):26. doi: 10.1186/1748-7188-8-26.

PMID:
24164709
[PubMed]
Free PMC Article
8.

Influenza a virus migration and persistence in North American wild birds.

Bahl J, Krauss S, Kühnert D, Fourment M, Raven G, Pryor SP, Niles LJ, Danner A, Walker D, Mendenhall IH, Su YC, Dugan VG, Halpin RA, Stockwell TB, Webby RJ, Wentworth DE, Drummond AJ, Smith GJ, Webster RG.

PLoS Pathog. 2013;9(8):e1003570. doi: 10.1371/journal.ppat.1003570. Epub 2013 Aug 29.

PMID:
24009503
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A stochastic simulator of birth-death master equations with application to phylodynamics.

Vaughan TG, Drummond AJ.

Mol Biol Evol. 2013 Jun;30(6):1480-93. doi: 10.1093/molbev/mst057. Epub 2013 Mar 16.

PMID:
23505043
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Simulating gene trees under the multispecies coalescent and time-dependent migration.

Heled J, Bryant D, Drummond AJ.

BMC Evol Biol. 2013 Feb 18;13:44. doi: 10.1186/1471-2148-13-44.

PMID:
23418788
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).

Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):228-33. doi: 10.1073/pnas.1207965110. Epub 2012 Dec 17.

PMID:
23248286
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Bayesian selection of nucleotide substitution models and their site assignments.

Wu CH, Suchard MA, Drummond AJ.

Mol Biol Evol. 2013 Mar;30(3):669-88. doi: 10.1093/molbev/mss258. Epub 2012 Dec 11.

PMID:
23233462
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.

Baele G, Li WL, Drummond AJ, Suchard MA, Lemey P.

Mol Biol Evol. 2013 Feb;30(2):239-43. doi: 10.1093/molbev/mss243. Epub 2012 Oct 22.

PMID:
23090976
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Mapping the origins and expansion of the Indo-European language family.

Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD.

Science. 2012 Aug 24;337(6097):957-60. doi: 10.1126/science.1219669. Erratum in: Science. 2013 Dec 20;342(6165):1446.

PMID:
22923579
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Bayesian phylogenetics with BEAUti and the BEAST 1.7.

Drummond AJ, Suchard MA, Xie D, Rambaut A.

Mol Biol Evol. 2012 Aug;29(8):1969-73. doi: 10.1093/molbev/mss075. Epub 2012 Feb 25.

PMID:
22367748
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Within-host demographic fluctuations and correlations in early retroviral infection.

Vaughan TG, Drummond PD, Drummond AJ.

J Theor Biol. 2012 Feb 21;295:86-99. doi: 10.1016/j.jtbi.2011.11.016. Epub 2011 Nov 25.

PMID:
22133472
[PubMed - indexed for MEDLINE]
17.

Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics.

Li WL, Drummond AJ.

Mol Biol Evol. 2012 Feb;29(2):751-61. doi: 10.1093/molbev/msr232. Epub 2011 Sep 22.

PMID:
21940644
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases.

Kühnert D, Wu CH, Drummond AJ.

Infect Genet Evol. 2011 Dec;11(8):1825-41. doi: 10.1016/j.meegid.2011.08.005. Epub 2011 Aug 31. Review.

PMID:
21906695
[PubMed - indexed for MEDLINE]
Free Article
19.

Estimating the basic reproductive number from viral sequence data.

Stadler T, Kouyos R, von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard HF, Drummond AJ, Bonhoeffer S; Swiss HIV Cohort Study.

Mol Biol Evol. 2012 Jan;29(1):347-57. doi: 10.1093/molbev/msr217. Epub 2011 Sep 2.

PMID:
21890480
[PubMed - indexed for MEDLINE]
Free Article
20.

Calibrated tree priors for relaxed phylogenetics and divergence time estimation.

Heled J, Drummond AJ.

Syst Biol. 2012 Jan;61(1):138-49. doi: 10.1093/sysbio/syr087. Epub 2011 Aug 18.

PMID:
21856631
[PubMed - indexed for MEDLINE]
Free PMC Article
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