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Items: 1 to 50 of 89

1.

Phylodynamic model adequacy using posterior predictive simulations.

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

Syst Biol. 2018 Jun 25. doi: 10.1093/sysbio/syy048. [Epub ahead of print]

PMID:
29945220
2.

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A.

Virus Evol. 2018 Jun 8;4(1):vey016. doi: 10.1093/ve/vey016. eCollection 2018 Jan.

3.

Posterior summarisation in Bayesian phylogenetics using Tracer 1.7.

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

Syst Biol. 2018 Apr 27. doi: 10.1093/sysbio/syy032. [Epub ahead of print]

PMID:
29718447
4.

The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes.

Stadler T, Gavryushkina A, Warnock RCM, Drummond AJ, Heath TA.

J Theor Biol. 2018 Jun 14;447:41-55. doi: 10.1016/j.jtbi.2018.03.005. Epub 2018 Mar 14.

5.

Bayesian Inference of Species Networks from Multilocus Sequence Data.

Zhang C, Ogilvie HA, Drummond AJ, Stadler T.

Mol Biol Evol. 2018 Feb 1;35(2):504-517. doi: 10.1093/molbev/msx307.

6.

Taming the BEAST-A Community Teaching Material Resource for BEAST 2.

Barido-Sottani J, Bošková V, Plessis LD, Kühnert D, Magnus C, Mitov V, Müller NF, PecErska J, Rasmussen DA, Zhang C, Drummond AJ, Heath TA, Pybus OG, Vaughan TG, Stadler T.

Syst Biol. 2018 Jan 1;67(1):170-174. doi: 10.1093/sysbio/syx060.

7.

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.

8.

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.

Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ.

Syst Biol. 2017 Jan 1;66(1):57-73. doi: 10.1093/sysbio/syw060.

9.

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.

10.

Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.

Vaughan TG, Welch D, Drummond AJ, Biggs PJ, George T, French NP.

Genetics. 2017 Feb;205(2):857-870. doi: 10.1534/genetics.116.193425. Epub 2016 Dec 22.

11.

Bayesian phylogenetic estimation of fossil ages.

Drummond AJ, Stadler T.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20150129. doi: 10.1098/rstb.2015.0129.

12.

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.

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

Mol Biol Evol. 2016 Aug;33(8):2102-16. doi: 10.1093/molbev/msw064. Epub 2016 Apr 9.

13.

The space of ultrametric phylogenetic trees.

Gavryushkin A, Drummond AJ.

J Theor Biol. 2016 Aug 21;403:197-208. doi: 10.1016/j.jtbi.2016.05.001. Epub 2016 May 14.

14.

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods.

Ogilvie HA, Heled J, Xie D, Drummond AJ.

Syst Biol. 2016 May;65(3):381-96. doi: 10.1093/sysbio/syv118. Epub 2016 Jan 28.

15.

Evaluating a multigene environmental DNA approach for biodiversity assessment.

Drummond AJ, Newcomb RD, Buckley TR, Xie D, Dopheide A, Potter BC, Heled J, Ross HA, Tooman L, Grosser S, Park D, Demetras NJ, Stevens MI, Russell JC, Anderson SH, Carter A, Nelson N.

Gigascience. 2015 Oct 6;4:46. doi: 10.1186/s13742-015-0086-1. eCollection 2015.

16.

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

Stadler T, Vaughan TG, Gavryushkin A, Guindon S, Kühnert D, Leventhal GE, Drummond AJ.

Proc Biol Sci. 2015 May 7;282(1806):20150420. doi: 10.1098/rspb.2015.0420.

17.

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.

18.

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.

19.

Calibrated birth-death phylogenetic time-tree priors for bayesian inference.

Heled J, Drummond AJ.

Syst Biol. 2015 May;64(3):369-83. doi: 10.1093/sysbio/syu089. Epub 2014 Nov 14. Erratum in: Syst Biol. 2016 Sep;65(5):943.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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
33.

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.

34.

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.

35.

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
36.

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.

37.

Guided tree topology proposals for Bayesian phylogenetic inference.

Höhna S, Drummond AJ.

Syst Biol. 2012 Jan;61(1):1-11. doi: 10.1093/sysbio/syr074. Epub 2011 Aug 9.

PMID:
21828081
38.

Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo.

Wu CH, Drummond AJ.

Genetics. 2011 May;188(1):151-64. doi: 10.1534/genetics.110.125260. Epub 2011 Mar 8.

39.

A Bayesian phylogenetic method to estimate unknown sequence ages.

Shapiro B, Ho SY, Drummond AJ, Suchard MA, Pybus OG, Rambaut A.

Mol Biol Evol. 2011 Feb;28(2):879-87. doi: 10.1093/molbev/msq262. Epub 2010 Oct 1.

40.

Extinction times in autocatalytic systems.

Drummond PD, Vaughan TG, Drummond AJ.

J Phys Chem A. 2010 Oct 7;114(39):10481-91. doi: 10.1021/jp104471e.

PMID:
20831232
41.

Bayesian random local clocks, or one rate to rule them all.

Drummond AJ, Suchard MA.

BMC Biol. 2010 Aug 31;8:114. doi: 10.1186/1741-7007-8-114.

42.

How accurate and robust are the phylogenetic estimates of Austronesian language relationships?

Greenhill SJ, Drummond AJ, Gray RD.

PLoS One. 2010 Mar 10;5(3):e9573. doi: 10.1371/journal.pone.0009573.

43.

Epidemic dynamics revealed in dengue evolution.

Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Muñoz-Jordán JL, Pybus OG, Holmes EC, Gubler DJ.

Mol Biol Evol. 2010 Apr;27(4):811-8. doi: 10.1093/molbev/msp285. Epub 2009 Dec 4.

44.

Bayesian inference of species trees from multilocus data.

Heled J, Drummond AJ.

Mol Biol Evol. 2010 Mar;27(3):570-80. doi: 10.1093/molbev/msp274. Epub 2009 Nov 11.

45.

Bayesian phylogeography finds its roots.

Lemey P, Rambaut A, Drummond AJ, Suchard MA.

PLoS Comput Biol. 2009 Sep;5(9):e1000520. doi: 10.1371/journal.pcbi.1000520. Epub 2009 Sep 25.

46.

Language phylogenies reveal expansion pulses and pauses in Pacific settlement.

Gray RD, Drummond AJ, Greenhill SJ.

Science. 2009 Jan 23;323(5913):479-83. doi: 10.1126/science.1166858.

47.

Accommodating the effect of ancient DNA damage on inferences of demographic histories.

Rambaut A, Ho SY, Drummond AJ, Shapiro B.

Mol Biol Evol. 2009 Feb;26(2):245-8. doi: 10.1093/molbev/msn256. Epub 2008 Nov 11.

PMID:
19001634
48.

Fully Bayesian tests of neutrality using genealogical summary statistics.

Drummond AJ, Suchard MA.

BMC Genet. 2008 Oct 31;9:68. doi: 10.1186/1471-2156-9-68.

49.

Bayesian inference of population size history from multiple loci.

Heled J, Drummond AJ.

BMC Evol Biol. 2008 Oct 23;8:289. doi: 10.1186/1471-2148-8-289.

50.

Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa.

Atkinson QD, Gray RD, Drummond AJ.

Proc Biol Sci. 2009 Jan 22;276(1655):367-73. doi: 10.1098/rspb.2008.0785.

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