A Rambaut

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006
  2. ncbi request reprint Bi-De: an application for simulating phylogenetic processes
    A Rambaut
    Department of Zoology, University of Oxford, UK
    Comput Appl Biosci 12:469-71. 1996
  3. ncbi request reprint Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    A Rambaut
    Department of Zoology, University of Oxford, UK
    Comput Appl Biosci 13:235-8. 1997
  4. ncbi request reprint Estimating divergence dates from molecular sequences
    A Rambaut
    Department of Zoology, University of Oxford
    Mol Biol Evol 15:442-8. 1998
  5. ncbi request reprint Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
    A Rambaut
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Bioinformatics 16:395-9. 2000
  6. ncbi request reprint Bayesian coalescent inference of past population dynamics from molecular sequences
    A J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1185-92. 2005
  7. ncbi request reprint The epidemic behavior of the hepatitis C virus
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Science 292:2323-5. 2001
  8. ncbi request reprint Phylogenetic evidence for recombination in dengue virus
    E C Holmes
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, U K
    Mol Biol Evol 16:405-9. 1999
  9. pmc An integrated framework for the inference of viral population history from reconstructed genealogies
    O G Pybus
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Genetics 155:1429-37. 2000
  10. ncbi request reprint New inferences from tree shape: numbers of missing taxa and population growth rates
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, UK
    Syst Biol 51:881-8. 2002

Detail Information

Publications20

  1. 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...
  2. ncbi request reprint Bi-De: an application for simulating phylogenetic processes
    A Rambaut
    Department of Zoology, University of Oxford, UK
    Comput Appl Biosci 12:469-71. 1996
    ..Instantaneous mass extinctions can also be simulated. The package allows the tree produced to be used as a template for the simulated evolution of molecular sequence data under a range of different transition models...
  3. ncbi request reprint Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    A Rambaut
    Department of Zoology, University of Oxford, UK
    Comput Appl Biosci 13:235-8. 1997
    ..Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap...
  4. ncbi request reprint Estimating divergence dates from molecular sequences
    A Rambaut
    Department of Zoology, University of Oxford
    Mol Biol Evol 15:442-8. 1998
    ..We believe that the method presented here offers solutions to many of the problems facing molecular dating and provides a platform for future improvements to such analyses...
  5. ncbi request reprint Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
    A Rambaut
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Bioinformatics 16:395-9. 2000
    ..Confidence intervals for these parameters are also estimated...
  6. ncbi request reprint Bayesian coalescent inference of past population dynamics from molecular sequences
    A J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1185-92. 2005
    ....
  7. ncbi request reprint The epidemic behavior of the hepatitis C virus
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Science 292:2323-5. 2001
    ..Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease...
  8. ncbi request reprint Phylogenetic evidence for recombination in dengue virus
    E C Holmes
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, U K
    Mol Biol Evol 16:405-9. 1999
    ..This is the first report of recombination in natural populations of dengue virus...
  9. pmc An integrated framework for the inference of viral population history from reconstructed genealogies
    O G Pybus
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Genetics 155:1429-37. 2000
    ..We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B...
  10. ncbi request reprint New inferences from tree shape: numbers of missing taxa and population growth rates
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, UK
    Syst Biol 51:881-8. 2002
    ..Results of an analysis of the phylogeny of the mosquito-borne flaviviruses suggest that there could be several thousand currently unidentified viruses in this clade...
  11. ncbi request reprint End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences
    A Rambaut
    Department of Zoology, University of Oxford, UK
    Comput Appl Biosci 13:303-6. 1997
    ..Statistical analyses can be performed to test the consistency of the data with various competing hypotheses...
  12. ncbi request reprint Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution
    A Cooper
    Department of Biological Anthropology and Henry Wellcome Ancient Biomolecules Centre, University of Oxford, UK
    Nature 409:704-7. 2001
    ..This first molecular view of the break-up of Gondwana provides a new temporal framework for speciation events within other Gondwanan biota and can be used to evaluate competing biogeographical hypotheses...
  13. pmc Testing the Cambrian explosion hypothesis by using a molecular dating technique
    L Bromham
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 95:12386-9. 1998
    ..The data are not compatible with the Cambrian explosion hypothesis as an explanation for the origin of metazoan phyla, and provide additional support for an extended period of Precambrian metazoan diversification...
  14. ncbi request reprint GENIE: estimating demographic history from molecular phylogenies
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Bioinformatics 18:1404-5. 2002
    ..The methods are based on population genetic models known collectively as coalescent theory...
  15. ncbi request reprint The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach
    O G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 20:381-7. 2003
    ..Because our results are consistent with a demographic scenario specified a priori, they also provide an objective test of inference methods based on the coalescent process...
  16. pmc Widespread intra-serotype recombination in natural populations of dengue virus
    M Worobey
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 96:7352-7. 1999
    ..These findings indicate that recombination may play a very significant role in shaping genetic diversity in dengue virus and, as such, have important implications for its biology and its control...
  17. ncbi request reprint The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa
    P L Davis
    Department of Zoology, University of Oxford, Oxford, UK
    Arch Virol 152:1251-8. 2007
    ..Hence, despite circulating in the same geographic region, these two variants of RABV exhibit striking differences in evolutionary dynamics which are likely to reflect differences in their underlying ecology...
  18. pmc Comparative analyses for adaptive radiations
    P H Harvey
    Department of Zoology, University of Oxford, UK
    Philos Trans R Soc Lond B Biol Sci 355:1599-605. 2000
    ..Alternatively, maximum-likelihood procedures might be used to determine appropriate transformations of phylogenetic branch lengths that accord with particular models of character evolution...
  19. pmc Complete nucleotide sequence and transcriptional analysis of snakehead fish retrovirus
    D Hart
    Department of Veterinary Pathology, University of Glasgow Veterinary School, United Kingdom
    J Virol 70:3606-16. 1996
    ..The snakehead virus is also distinct from a previously characterized complex fish retrovirus, suggesting that discrete groups of these viruses have yet to be identified in the lower vertebrates...
  20. ncbi request reprint Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment
    K Deforche
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    Bioinformatics 24:34-41. 2008
    ..The method was evaluated for recovering 10 random fictive selective pressures in simulation experiments, and for modeling the selective pressure under treatment with the protease inhibitor nelfinavir...