Andrew Rambaut

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. pmc 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
  2. pmc BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics
    Daniel L Ayres
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Syst Biol 61:170-3. 2012
  3. pmc Canalization of the evolutionary trajectory of the human influenza virus
    Trevor Bedford
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Biol 10:38. 2012
  4. pmc Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II
    John Archer
    Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK
    BMC Bioinformatics 13:47. 2012
  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 The genomic and epidemiological dynamics of human influenza A virus
    Andrew Rambaut
    Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK
    Nature 453:615-9. 2008
  7. pmc Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom
    Gareth J Hughes
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
    PLoS Pathog 5:e1000590. 2009
  8. pmc Episodic sexual transmission of HIV revealed by molecular phylodynamics
    Fraser Lewis
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
    PLoS Med 5:e50. 2008
  9. pmc Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form
    Ana 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
  10. pmc Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B
    Chung Chau Hon
    Department of Zoology, The University of Hong Kong, China
    J Virol 80:8503-9. 2006

Collaborators

Detail Information

Publications50

  1. pmc 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...
  2. pmc BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics
    Daniel L Ayres
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Syst Biol 61:170-3. 2012
    ..The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software...
  3. pmc Canalization of the evolutionary trajectory of the human influenza virus
    Trevor 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...
  4. pmc Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II
    John 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...
  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 The genomic and epidemiological dynamics of human influenza A virus
    Andrew 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...
  7. pmc Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom
    Gareth 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...
  8. pmc Episodic sexual transmission of HIV revealed by molecular phylodynamics
    Fraser 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)...
  9. pmc Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form
    Ana 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...
  10. pmc Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B
    Chung 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...
  11. ncbi Heterotachy and tree building: a case study with plastids and eubacteria
    Peter 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...
  12. pmc Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1
    Robert 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...
  13. pmc JC virus evolution and its association with human populations
    Laura 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
    ....
  14. ncbi Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods
    Dimitrios 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...
  15. pmc The evolution of genome compression and genomic novelty in RNA viruses
    Robert 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...
  16. pmc Viral evolution and the emergence of SARS coronavirus
    Edward 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
    ....
  17. 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...
  18. ncbi 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...
  19. ncbi Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus
    Michael Worobey
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Science 296:211 discussion 211. 2002
  20. ncbi A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution
    Beth 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...
  21. pmc HIV phylogenetics
    Deenan Pillay
    BMJ 335:460-1. 2007
  22. 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...
  23. ncbi Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty
    Joe 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...
  24. pmc The emergence of HIV/AIDS in the Americas and beyond
    M 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...
  25. ncbi Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo
    Koen Deforche
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    J Comput Biol 14:1105-14. 2007
    ....
  26. doi Pacing a small cage: mutation and RNA viruses
    Robert 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...
  27. pmc Reply to Pape et al.: the phylogeography of HIV-1 group M subtype B
    Michael Worobey
    Proc Natl Acad Sci U S A 105:E16. 2008
  28. doi Evolutionary genomics of host adaptation in vesicular stomatitis virus
    Susanna 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...
  29. pmc Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences
    Andrew E Armitage
    MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
    J Virol 82:8743-61. 2008
    ....
  30. ncbi Bayesian estimation of sequence damage in ancient DNA
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 24:1416-22. 2007
    ....
  31. 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
    ....
  32. ncbi Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other orthobunyaviruses
    Thomas 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...
  33. ncbi Origin of AIDS: contaminated polio vaccine theory refuted
    Michael Worobey
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Nature 428:820. 2004
    ....
  34. ncbi Inference of viral evolutionary rates from molecular sequences
    Alexei Drummond
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Adv Parasitol 54:331-58. 2003
    ....
  35. ncbi The causes and consequences of HIV evolution
    Andrew Rambaut
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nat Rev Genet 5:52-61. 2004
  36. ncbi Inferring the rate and time-scale of dengue virus evolution
    S Susanna Twiddy
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 20:122-9. 2003
    ....
  37. ncbi Testing the relationship between morphological and molecular rates of change along phylogenies
    Lindell 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...
  38. pmc Phylogenetic analysis of a human isolate from the 2000 Israel West Nile virus epidemic
    Thomas 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...
  39. ncbi Flight of the dodo
    Beth Shapiro
    Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
    Science 295:1683. 2002
  40. ncbi 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
    ....
  41. ncbi Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman
    Astrid K N Iversen
    AIDS 19:990-3. 2005
  42. ncbi Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak
    Tulio de Oliveira
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Nature 444:836-7. 2006
    ....
  43. ncbi HIV evolutionary dynamics within and among hosts
    Philippe 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...
  44. pmc 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 trial
    David 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...
  45. ncbi Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity
    Robert 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...
  46. ncbi 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
  47. ncbi Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    Beth Shapiro
    Mol Biol Evol 23:7-9. 2006
    ....
  48. pmc Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain
    Philippe Lemey
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    J Virol 79:11981-9. 2005
    ....
  49. ncbi The evolutionary dynamics of endogenous retroviruses
    Aris 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...
  50. pmc Inferring confidence sets of possibly misspecified gene trees
    Korbinian 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...