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Items: 18

1.

Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.

Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ.

PLoS Comput Biol. 2019 Aug 6;15(8):e1007189. doi: 10.1371/journal.pcbi.1007189. eCollection 2019 Aug.

2.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.

PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. eCollection 2019 Apr.

3.

Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling.

Russel PM, Brewer BJ, Klaere S, Bouckaert RR.

Syst Biol. 2019 Mar 1;68(2):219-233. doi: 10.1093/sysbio/syy050.

PMID:
29961836
4.

Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

Duchene S, Bouckaert R, Duchene DA, Stadler T, Drummond AJ.

Syst Biol. 2019 Mar 1;68(2):358-364. doi: 10.1093/sysbio/syy048.

5.

A Bayesian phylogenetic study of the Dravidian language family.

Kolipakam V, Jordan FM, Dunn M, Greenhill SJ, Bouckaert R, Gray RD, Verkerk A.

R Soc Open Sci. 2018 Mar 21;5(3):171504. doi: 10.1098/rsos.171504. eCollection 2018 Mar.

6.

The origin and expansion of Pama-Nyungan languages across Australia.

Bouckaert RR, Bowern C, Atkinson QD.

Nat Ecol Evol. 2018 Apr;2(4):741-749. doi: 10.1038/s41559-018-0489-3. Epub 2018 Mar 12.

PMID:
29531347
7.

Tracing hepatitis B virus (HBV) genotype B5 (formerly B6) evolutionary history in the circumpolar Arctic through phylogeographic modelling.

Bouckaert R, Simons BC, Krarup H, Friesen TM, Osiowy C.

PeerJ. 2017 Aug 31;5:e3757. doi: 10.7717/peerj.3757. eCollection 2017.

8.

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates.

Ogilvie HA, Bouckaert RR, Drummond AJ.

Mol Biol Evol. 2017 Aug 1;34(8):2101-2114. doi: 10.1093/molbev/msx126.

9.

Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes.

Matschiner M, Musilová Z, Barth JM, Starostová Z, Salzburger W, Steel M, Bouckaert R.

Syst Biol. 2017 Jan 1;66(1):3-22. doi: 10.1093/sysbio/syw076.

PMID:
28173588
10.

bModelTest: Bayesian phylogenetic site model averaging and model comparison.

Bouckaert RR, Drummond AJ.

BMC Evol Biol. 2017 Feb 6;17(1):42. doi: 10.1186/s12862-017-0890-6.

11.

Phylogeography by diffusion on a sphere: whole world phylogeography.

Bouckaert R.

PeerJ. 2016 Sep 6;4:e2406. doi: 10.7717/peerj.2406. eCollection 2016.

12.

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.

13.

Species delimitation using genome-wide SNP data.

Leaché AD, Fujita MK, Minin VN, Bouckaert RR.

Syst Biol. 2014 Jul;63(4):534-42. doi: 10.1093/sysbio/syu018. Epub 2014 Mar 12.

14.

Looking for trees in the forest: summary tree from posterior samples.

Heled J, Bouckaert RR.

BMC Evol Biol. 2013 Oct 4;13:221. doi: 10.1186/1471-2148-13-221.

15.

Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods.

Bouckaert R, Alvarado-Mora MV, Pinho JR.

Antivir Ther. 2013;18(3 Pt B):497-503. doi: 10.3851/IMP2656. Epub 2013 Jun 21.

PMID:
23792904
16.

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.

17.

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A.

Mol Biol Evol. 2012 Aug;29(8):1917-32. doi: 10.1093/molbev/mss086. Epub 2012 Mar 14.

18.

DensiTree: making sense of sets of phylogenetic trees.

Bouckaert RR.

Bioinformatics. 2010 May 15;26(10):1372-3. doi: 10.1093/bioinformatics/btq110. Epub 2010 Mar 12.

PMID:
20228129

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