Andrew RambautSummaryAffiliation: University of Edinburgh Country: UK Publications
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Publications
Breeding racehorses: what price good genes?Alastair J Wilson
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
Biol Lett 4:173-5. 2008..Thus, while there are good genes to be bought, a stallion's fees are not an honest signal of his genetic quality and are a poor predictor of a foal's prize winning potential...- Canalization of the evolutionary trajectory of the human influenza virusTrevor Bedford
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
BMC Biol 10:38. 2012..Here, we propose a simple model of antigenic evolution in the influenza virus that accounts for this apparent discrepancy... - Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator IIJohn Archer
Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK
BMC Bioinformatics 13:47. 2012..In particular, error associated with a specific sequencing process must be quantified so that true biological variation may be identified... - BEAST: Bayesian evolutionary analysis by sampling treesAlexei 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... - The genomic and epidemiological dynamics of human influenza A virusAndrew Rambaut
Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK
Nature 453:615-9. 2008..These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions... - Molecular phylodynamics of the heterosexual HIV epidemic in the United KingdomGareth J Hughes
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
PLoS Pathog 5:e1000590. 2009..More effective intervention to restrict the epidemic may therefore be feasible, given effective diagnosis programmes... - Episodic sexual transmission of HIV revealed by molecular phylodynamicsFraser Lewis
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
PLoS Med 5:e50. 2008..The aim of this study was to analyze a high-density sample of an HIV-infected population using recently developed techniques in phylogenetics to infer the short-term dynamics of the epidemic among men who have sex with men (MSM)... - The evolution of genome compression and genomic novelty in RNA virusesRobert Belshaw
Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
Genome Res 17:1496-504. 2007..We suggest that RNA viruses are a good model system for the investigation of general evolutionary relationship between genome attributes such as mutational robustness, mutation rate, and size... - Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1Robert J Gifford
Department of Infection, University College London, London, United Kingdom
J Virol 81:13050-6. 2007..The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods... 
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolutionBeth Shapiro
Department of Zoology, Oxford University, Oxford, United Kingdom
Mol Biol Evol 23:1724-30. 2006..Additionally, many comparative analyses that utilize the phylogenetic relationships among gene sequences assume that mutations represent independent, uncorrelated events. Our results show that this assumption may often be invalid...- Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant formAna B Abecasis
Katholieke Universiteit Leuven, Laboratory for Clinical and Epidemiological Virology, AIDS Reference Laboratory, Rega Institute and University Hospitals, Minderbroedersstraat 10, B 3000 Leuven, Belgium
J Virol 81:8543-51. 2007..We suggest a reanalysis of all pure subtypes and CRFs in order to better understand how high rates of recombination have influenced HIV-1 evolutionary history... - JC virus evolution and its association with human populationsLaura A Shackelton
Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
J Virol 80:9928-33. 2006.... - Heterotachy and tree building: a case study with plastids and eubacteriaPeter Lockhart
The Allan Wilson Centre, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
Mol Biol Evol 23:40-5. 2006..Although homogeneous maximum likelihood inference was found to be robust to model misspecification in our specific example, we caution against assuming that it will always be so... - Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment BChung-Chau Hon
Department of Zoology, The University of Hong Kong, China
J Virol 80:8503-9. 2006..This report reveals the possible mechanisms leading to the emergence and expansion of vvIBDV, which would certainly provide insights into the scope of surveillance and prevention efforts regarding the disease... - Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolutionOliver 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... - Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methodsDimitrios Paraskevis
National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
J Mol Evol 59:709-17. 2004..For patients with known infection dates, the estimated dates of the coalescent events obtained using molecular clock calculations based on a newly developed Bayesian method in gag + env were in agreement with the actual infection dates... - Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virusMichael Worobey
Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
Science 296:211 discussion 211. 2002 - Viral evolution and the emergence of SARS coronavirusEdward C Holmes
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Philos Trans R Soc Lond B Biol Sci 359:1059-65. 2004.... - The molecular population genetics of HIV-1 group OPhilippe 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... - Bayesian estimation of sequence damage in ancient DNASimon Y W Ho
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 24:1416-22. 2007.... - Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequencesAndrew E Armitage
MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
J Virol 82:8743-61. 2008.... - HIV phylogeneticsDeenan Pillay
BMJ 335:460-1. 2007 
Evolutionary genomics of host adaptation in vesicular stomatitis virusSusanna K Remold
Department of Biology, University of Louisville, USA
Mol Biol Evol 25:1138-47. 2008..We discuss the degree to which current genetic architecture is expected to constrain future evolution of complex traits, such as host use by RNA viruses...- The causes and consequences of HIV evolutionAndrew Rambaut
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Nat Rev Genet 5:52-61. 2004 - Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertaintyJoe Parker
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
Infect Genet Evol 8:239-46. 2008..Finally, we re-analyse two existing published data sets as case studies. Our framework aims to provide an improvement over existing methods for this problem... - Reply to Pape et al.: the phylogeography of HIV-1 group M subtype BMichael Worobey
Proc Natl Acad Sci U S A 105:E16. 2008 - Pacing a small cage: mutation and RNA virusesRobert Belshaw
Department of Zoology, University of Oxford, Oxford, UK
Trends Ecol Evol 23:188-93. 2008..We explain the many terms used in investigating RNA viral evolution and highlight the specific experimental and comparative work that needs to be done... - Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivoKoen Deforche
Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
J Comput Biol 14:1105-14. 2007.... - The emergence of HIV/AIDS in the Americas and beyondM Thomas P Gilbert
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
Proc Natl Acad Sci U S A 104:18566-70. 2007..Our results suggest that HIV-1 circulated cryptically in the United States for approximately 12 years before the recognition of AIDS in 1981... - Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamicsPhilippe Lemey
Department of Zoology, University of Oxford, Oxford, United Kingdom
PLoS Comput Biol 3:e29. 2007.... - Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreakTulio de Oliveira
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
Nature 444:836-7. 2006.... - Flight of the dodoBeth Shapiro
Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
Science 295:1683. 2002 - Phylogenetic analysis of a human isolate from the 2000 Israel West Nile virus epidemicThomas Briese
Emerging Diseases Laboratory, Dept of Neurology, Microbiology and Molecular Genetics, 3107 Gillespie Neuroscience Building, University of California at Irvine, Irvine, CA 92697 4292, USA
Emerg Infect Dis 8:528-31. 2002..Phylogenetic analyses indicated a closer relationship of this isolate to 1996 Romanian and 1999 Russian than to 1998-99 Israeli or 1999 New York isolates... - Testing the relationship between morphological and molecular rates of change along phylogeniesLindell Bromham
School of Biological Sciences, University of Sussex, Falmer, Brighton, United Kingdom
Evolution 56:1921-30. 2002..We find no evidence of an association between rates of molecular and morphological rates of change... - Inferring the rate and time-scale of dengue virus evolutionS Susanna Twiddy
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 20:122-9. 2003.... - Inference of viral evolutionary rates from molecular sequencesAlexei Drummond
Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
Adv Parasitol 54:331-58. 2003.... - Origin of AIDS: contaminated polio vaccine theory refutedMichael Worobey
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Nature 428:820. 2004.... - Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other orthobunyavirusesThomas Briese
Jerome L and Dawn Greene Infectious Disease Laboratory, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
J Gen Virol 85:3071-7. 2004..A potential role of motifs that are more similar to CAL than to BUN virus sequences with respect to the serological reaction is discussed. No discernable evidence for reassortment was identified... - Rise and fall of the Beringian steppe bisonBeth Shapiro
Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK
Science 306:1561-5. 2004.... - Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected womanAstrid K N Iversen
AIDS 19:990-3. 2005 - The evolutionary dynamics of endogenous retrovirusesAris Katzourakis
Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
Trends Microbiol 13:463-8. 2005..We hope the model will provide a useful framework for understanding ERV evolution, enabling the testing of evolutionary hypotheses and the estimation of parameters governing ERV proliferation... - Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chainPhilippe Lemey
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
J Virol 79:11981-9. 2005.... - 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... - No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.)Beth Shapiro
Int J Infect Dis 10:334-5; author reply 335-6. 2006 - Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversityRobert Gifford
Department of Infection, University College London, UK
AIDS 20:1521-9. 2006..However, it is not clear how reliable standard genotyping of these sequences is for describing HIV-1 genetic variation and for detecting novel genetic variants and epidemiological trends... - Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequencesBeth Shapiro
Mol Biol Evol 23:7-9. 2006.... - Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trialDavid V Jobes
VaxGen, Inc, South San Francisco, California 94080, USA
AIDS Res Hum Retroviruses 22:968-78. 2006..Our results suggest significant differences on the evolutionary dynamics of these strains. We then discuss the implications of these results for vaccine development... - HIV evolutionary dynamics within and among hostsPhilippe Lemey
Department of Zoology, University of Oxford, Oxford, UK
AIDS Rev 8:125-40. 2006..Characterizing the impact of HIV transmission on viral genetic diversity will be a key factor in reconciling the different population genetic processes within and among hosts... - Inferring confidence sets of possibly misspecified gene treesKorbinian Strimmer
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Proc Biol Sci 269:137-42. 2002..The power of the investigated methods is studied by analysing HIV-1 and mtDNA sequence data as well as simulated sequences. Finally, guidelines for choosing an appropriate method to compare multiple gene trees are provided...