Research Topics
| A RambautSummaryAffiliation: University of Oxford Country: UK Publications
| Collaborators
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Detail Information
Publications
Relaxed phylogenetics and dating with confidenceAlexei 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...
Bi-De: an application for simulating phylogenetic processesA 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...- Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic treesA Rambaut
Department of Zoology, University of Oxford, UK
Comput Appl Biosci 13:235-8. 1997..zoo.ox.ac.uk/Seq-Gen/seq-gen.html++ + or by FTP from ftp:/(/)evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites... - Estimating divergence dates from molecular sequencesA 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... - Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogeniesA 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... - Bayesian coalescent inference of past population dynamics from molecular sequencesA J Drummond
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 22:1185-92. 2005.... - Phylogenetic evidence for recombination in dengue virusE 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... - The epidemic behavior of the hepatitis C virusO 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... - New inferences from tree shape: numbers of missing taxa and population growth ratesO 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... - An integrated framework for the inference of viral population history from reconstructed genealogiesO 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... - End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequencesA Rambaut
Department of Zoology, University of Oxford, UK
Comput Appl Biosci 13:303-6. 1997..AVAILABILITY: End-Epi can be obtained by WWW from http://evolve.zoo.ox.ac.uk/ and by anonymous FTP from ftp://evolve.zoo.ox.ac.uk/packages/End-Epi10.hqx. This file contains the compiled application, the manual and a test tree... - Complete mitochondrial genome sequences of two extinct moas clarify ratite evolutionA 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... - Testing the Cambrian explosion hypothesis by using a molecular dating techniqueL 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... - The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approachO 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... - GENIE: estimating demographic history from molecular phylogeniesO 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. AVAILABILITY: GENIE is available from http://evolve.zoo.ox.ac.uk. All popular operating systems are supported... - The evolutionary dynamics of canid and mongoose rabies virus in Southern AfricaP 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... - Widespread intra-serotype recombination in natural populations of dengue virusM 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... - Comparative analyses for adaptive radiationsP 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... - Complete nucleotide sequence and transcriptional analysis of snakehead fish retrovirusD 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... - Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatmentK 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...