Alexei J Drummond

Summary

Affiliation: University of Auckland
Country: New Zealand

Publications

  1. pmc Bayesian phylogenetic estimation of fossil ages
    Alexei J Drummond
    Department of Computer Science, University of Auckland, Auckland 1010, New Zealand Department of Biosystems Science and Engineering, Eidgenossische Technische Hochschule Zurich, 4058 Basel, Switzerland
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
  2. pmc Bayesian phylogenetics with BEAUti and the BEAST 1.7
    Alexei J Drummond
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 29:1969-73. 2012
  3. pmc Fully Bayesian tests of neutrality using genealogical summary statistics
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Genet 9:68. 2008
  4. pmc Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1
    Charles T T Edwards
    Nuffield Department of Clinical Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
    BMC Evol Biol 6:28. 2006
  5. pmc BEAST: Bayesian evolutionary analysis by sampling trees
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 7:214. 2007
  6. pmc Bayesian random local clocks, or one rate to rule them all
    Alexei J Drummond
    Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    BMC Biol 8:114. 2010
  7. pmc Bayesian selection of nucleotide substitution models and their site assignments
    Chieh Hsi Wu
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 30:669-88. 2013
  8. pmc Bayesian inference of species trees from multilocus data
    Joseph Heled
    Department of Computer Science, University of Auckland, New Zealand
    Mol Biol Evol 27:570-80. 2010
  9. pmc BEAST 2: a software platform for Bayesian evolutionary analysis
    Remco Bouckaert
    Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand
    PLoS Comput Biol 10:e1003537. 2014
  10. pmc Calibrated tree priors for relaxed phylogenetics and divergence time estimation
    Joseph Heled
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Syst Biol 61:138-49. 2012

Collaborators

Detail Information

Publications28

  1. pmc Bayesian phylogenetic estimation of fossil ages
    Alexei J Drummond
    Department of Computer Science, University of Auckland, Auckland 1010, New Zealand Department of Biosystems Science and Engineering, Eidgenossische Technische Hochschule Zurich, 4058 Basel, Switzerland
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
    ..This article is part of the themed issue 'Dating species divergences using rocks and clocks'. ..
  2. pmc Bayesian phylogenetics with BEAUti and the BEAST 1.7
    Alexei J Drummond
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 29:1969-73. 2012
    ..BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk...
  3. pmc Fully Bayesian tests of neutrality using genealogical summary statistics
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Genet 9:68. 2008
    ..Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome...
  4. pmc Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1
    Charles T T Edwards
    Nuffield Department of Clinical Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
    BMC Evol Biol 6:28. 2006
    ..Despite this, the magnitude of this population bottleneck is unclear...
  5. pmc BEAST: Bayesian evolutionary analysis by sampling trees
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 7:214. 2007
    ..A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented...
  6. pmc Bayesian random local clocks, or one rate to rule them all
    Alexei J Drummond
    Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    BMC Biol 8:114. 2010
    ..Thus, including both the global molecular clock and the unconstrained model results, there are a total of 2(2n-2) possible rate models available for averaging with 1, 2, ..., 2n - 2 different rate categories...
  7. pmc Bayesian selection of nucleotide substitution models and their site assignments
    Chieh Hsi Wu
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 30:669-88. 2013
    ..In some instances, this improved modeling of the substitution process can have a measurable effect on downstream inference, including the estimated phylogeny, relative divergence times, and effective population size histories...
  8. pmc Bayesian inference of species trees from multilocus data
    Joseph Heled
    Department of Computer Science, University of Auckland, New Zealand
    Mol Biol Evol 27:570-80. 2010
    ..We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation...
  9. pmc BEAST 2: a software platform for Bayesian evolutionary analysis
    Remco Bouckaert
    Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand
    PLoS Comput Biol 10:e1003537. 2014
    ....
  10. pmc Calibrated tree priors for relaxed phylogenetics and divergence time estimation
    Joseph Heled
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Syst Biol 61:138-49. 2012
    ..Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis...
  11. pmc Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
    Tanja Stadler
    Department of Environmental Systems Science, Eidgenossische Technische Hochschule Zurich, 8092 Zurich, Switzerland
    Proc Natl Acad Sci U S A 110:228-33. 2013
    ..The analysis reveals temporal changes of the effective reproductive number that highlight the effect of past public health interventions...
  12. pmc Mapping the origins and expansion of the Indo-European language family
    Remco Bouckaert
    Department of Computer Science, University of Auckland, Auckland 1142, New Zealand
    Science 337:957-60. 2012
    ..These results highlight the critical role that phylogeographic inference can play in resolving debates about human prehistory...
  13. doi request reprint Phylogenetic and epidemic modeling of rapidly evolving infectious diseases
    Denise Kühnert
    Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
    Infect Genet Evol 11:1825-41. 2011
    ....
  14. pmc Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics
    Wai Lok Sibon Li
    Computational Evolution Group, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 29:751-61. 2012
    ..Our methods are implemented under the BEAST 1.6 software package, available at http://beast-mcmc.googlecode.com...
  15. pmc Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo
    Chieh Hsi Wu
    University of Auckland, Auckland 1001, New Zealand
    Genetics 188:151-64. 2011
    ..Simulated data are used to evaluate our method in terms of accuracy and precision of estimation and also identification of the true mutation model. Finally we apply our method to a red colobus monkey data set as an example...
  16. pmc Simulating gene trees under the multispecies coalescent and time-dependent migration
    Joseph Heled
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 13:44. 2013
    ..Inference of multispecies phylogenies under those conditions is difficult. Indeed even designing simulators which correctly sample gene histories under these conditions is non-trivial...
  17. pmc Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
    Denise Kühnert
    Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland Department of Computer Science, University of Auckland, Auckland, New Zealand Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
    Mol Biol Evol 33:2102-16. 2016
    ..Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group. ..
  18. pmc Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model
    Denise Kühnert
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    J R Soc Interface 11:20131106. 2014
    ..The estimated time of epidemic peak is around 1970. ..
  19. ncbi request reprint Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
    Alexandra Gavryushkina
    Centre for Computational Evolution, University of Auckland, Auckland, New Zealand Department of Computer Science, University of Auckland, Auckland 1010, New Zealand
    Syst Biol . 2016
    ..4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed. [Birth-death process; calibration; divergence times; MCMC; phylogenetics.]...
  20. pmc Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    Alexei J Drummond
    School of Biological Sciences, University of Auckland 1001, Auckland, New Zealand
    Genetics 161:1307-20. 2002
    ..We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences...
  21. pmc Bayesian inference of population size history from multiple loci
    Joseph Heled
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 8:289. 2008
    ..Here we present the Extended Bayesian Skyline Plot, a non-parametric Bayesian Markov chain Monte Carlo algorithm that extends a previous coalescent-based method in several ways, including the ability to analyze multiple loci...
  22. pmc Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models
    Alex Popinga
    Department of Computer Science, University of Auckland, Auckland, New Zealand 1010 Allan Wilson Centre for Molecular Ecology and Evolution, Palmerston North, New Zealand 4442
    Genetics 199:595-607. 2015
    ..However, each of these inference models is shown to have undesirable properties in certain circumstances, especially for epidemic outbreaks with [Formula: see text] close to one or with small effective susceptible populations. ..
  23. pmc A stochastic simulator of birth-death master equations with application to phylodynamics
    Timothy G Vaughan
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 30:1480-93. 2013
    ..Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships...
  24. pmc Recursive algorithms for phylogenetic tree counting
    Alexandra Gavryushkina
    Department of Computer Science, The University of Auckland, Auckland, New Zealand
    Algorithms Mol Biol 8:26. 2013
    ..However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult...
  25. pmc Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration
    Alexandra Gavryushkina
    Department of Computer Science, University of Auckland, Auckland, New Zealand Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    PLoS Comput Biol 10:e1003919. 2014
    ..Such modelling has many advantages as argued in the literature. The sampler is available as an open-source BEAST2 package (https://github.com/CompEvol/sampled-ancestors). ..
  26. pmc Efficient Bayesian inference under the structured coalescent
    Timothy G Vaughan
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North 4442, New Zealand, Institute of Integrative Biology, Swiss Federal Institute of Technology ETH, Zurich 8092, Switzerland and Department of Computer Science, University of Auckland, Auckland 1142, New Zealand
    Bioinformatics 30:2272-9. 2014
    ..However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo (MCMC) sampling algorithms (samplers) capable of efficiently exploring the state space...
  27. pmc How accurate and robust are the phylogenetic estimates of Austronesian language relationships?
    Simon J Greenhill
    Department of Psychology, University of Auckland, Auckland, New Zealand
    PLoS ONE 5:e9573. 2010
    ..The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations...
  28. pmc Calibrated birth-death phylogenetic time-tree priors for bayesian inference
    Joseph Heled
    Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand Department of Computer Science, The University of Auckland, Auckland, New Zealand
    Syst Biol 64:369-83. 2015
    ....