Alexei J Drummond

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Bayesian coestimation of phylogeny and sequence alignment
    Gerton Lunter
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    BMC Bioinformatics 6:83. 2005
  2. 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
  3. 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
  4. 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
  5. 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
  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 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications27

  1. pmc Bayesian coestimation of phylogeny and sequence alignment
    Gerton Lunter
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    BMC Bioinformatics 6:83. 2005
    ..Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both...
  2. 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...
  3. 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...
  4. 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
    ....
  5. 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...
  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 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...
  8. 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...
  9. 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
    ....
  10. 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...
  11. 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. ..
  12. 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...
  13. 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...
  14. 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...
  15. ncbi request reprint Neotenous origins for pelagic octopuses
    Jan Strugnell
    Curr Biol 14:R300-1. 2004
  16. ncbi request reprint mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory
    Quentin D Atkinson
    Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 58A Banbury Rd, Oxford, OX2 6QS, United Kingdom
    Mol Biol Evol 25:468-74. 2008
    ..These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past...
  17. pmc Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus
    Chung Chau Hon
    5N 12, Kadoorie Biological Science Building, The University of Hong Kong, Hong Kong, China
    J Virol 82:1819-26. 2008
    ..This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV...
  18. ncbi request reprint Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
    Simon Y W Ho
    Henry Wellcome Ancient Biomolecules Centre, Oxford, United Kingdom
    Mol Biol Evol 22:1355-63. 2005
    ..If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates...
  19. pmc The molecular population genetics of HIV-1 group O
    Philippe Lemey
    Rega Institute for Medical Research, KULeuven, B 3000 Leuven, Belgium
    Genetics 167:1059-68. 2004
    ..In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome...
  20. ncbi request reprint Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
    Simon Y W Ho
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1561-8. 2005
    ....
  21. pmc Tree measures and the number of segregating sites in time-structured population samples
    Roald Forsberg
    Bioinformatics Research Center, Department of Genetics and Ecology, University of Aarhus, Arhus, Denmark
    BMC Genet 6:35. 2005
    ..Our emphasis is on "measurably evolving populations" i.e. populations from which it is possible to obtain time-structured samples that span a significant interval of evolutionary time...
  22. ncbi request reprint Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    Beth Shapiro
    Mol Biol Evol 23:7-9. 2006
    ....
  23. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006
    ..From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution...
  24. ncbi request reprint Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution
    Oliver G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 24:845-52. 2007
    ..From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses...
  25. pmc Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics
    Philippe Lemey
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 3:e29. 2007
    ....
  26. ncbi request reprint Ancient DNA: would the real Neandertal please stand up?
    Alan Cooper
    Henry Wellcome Ancient Biomolecules Centre and Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Curr Biol 14:R431-3. 2004
    ..This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contribution cannot be resolved at present...
  27. ncbi request reprint Rise and fall of the Beringian steppe bison
    Beth Shapiro
    Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK
    Science 306:1561-5. 2004
    ....