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Papers authored by Rambaut A

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Bayesian phylogeography finds its roots.

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Lemey P, Rambaut A, Drummond AJ, and Suchard MA

PLoS computational biology 5(9):e1000520, 2009 Sep - Who cited this? | PubMed ID: 19779555 | Fulltext

Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom.

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Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A, Leigh Brown AJ, and UK HIV Drug Resistance Collaboration

PLoS pathogens 5(9):e1000590, 2009 Sep - Who cited this? | PubMed ID: 19779560 | Fulltext

Evolutionary analysis of the dynamics of viral infectious disease.

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Pybus OG and Rambaut A

Nature reviews. Genetics 10(8):540-50, 2009 Aug - Who cited this? | PubMed ID: 19564871 | Fulltext

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.

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Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, and Rambaut A

Nature 459(7250):1122-5, 2009 Jun 25 - Who cited this? | PubMed ID: 19516283 | Fulltext

Pandemic potential of a strain of influenza A (H1N1): early findings.

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Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM,

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Science (New York, N.Y.) 324(5934):1557-61, 2009 Jun 19 - Who cited this? | PubMed ID: 19433588 | Fulltext

Many-core algorithms for statistical phylogenetics.

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Suchard MA and Rambaut A

Bioinformatics (Oxford, England) 25(11):1370-6, 2009 Jun 1 - Who cited this? | PubMed ID: 19369496 | Fulltext

Accommodating the effect of ancient DNA damage on inferences of demographic histories.

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Rambaut A, Ho SY, Drummond AJ, and Shapiro B

Molecular biology and evolution 26(2):245-8, 2009 Feb - Who cited this? | PubMed ID: 19001634 | Fulltext

The RNA virus database.

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Belshaw R, de Oliveira T, Markowitz S, and Rambaut A

Nucleic acids research 37(Database issue):D431-5, 2009 Jan - Who cited this? | PubMed ID: 18948277 | Fulltext

Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences.

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Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, and Iversen AK

Journal of virology, 2008 Jun 18 - Who cited this? | PubMed ID: 18562517 | Fulltext

Evolutionary genomics of host adaptation in vesicular stomatitis virus.

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Remold SK, Rambaut A, and Turner PE

Molecular biology and evolution 25(6):1138-47, 2008 Jun - Who cited this? | PubMed ID: 18353798 | Fulltext

The genomic and epidemiological dynamics of human influenza A virus.

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Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, and Holmes EC

Nature 453(7195):615, 2008 May 29 - Who cited this? | PubMed ID: 18418375 | Fulltext

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty.

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Parker J, Rambaut A, and Pybus OG

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 8(3):239-46, 2008 May - Who cited this? | PubMed ID: 17921073 | Fulltext

Breeding racehorses: what price good genes?.

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Wilson AJ and Rambaut A

Biology letters 4(2):173-5, 2008 Apr 23 - Who cited this? | PubMed ID: 18089517 | Fulltext

Pacing a small cage: mutation and RNA viruses.

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Belshaw R, Gardner A, Rambaut A, and Pybus OG

Trends in ecology & evolution (Personal edition) 23(4):188-93, 2008 Apr - Who cited this? | PubMed ID: 18295930 | Fulltext

Reply to Pape et al.: the phylogeography of HIV-1 group M subtype B.

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Worobey M, Pitchenik AE, Gilbert MT, Wlasiuk G, and Rambaut A

Proceedings of the National Academy of Sciences of the United States of America 105(12):E16, 2008 Mar 25 - Who cited this? | PubMed ID: 18337514 | Fulltext

Episodic sexual transmission of HIV revealed by molecular phylodynamics.

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Lewis F, Hughes GJ, Rambaut A, Pozniak A, and Leigh Brown AJ

PLoS medicine 5(3), 2008 Mar 18 - Who cited this? | PubMed ID: 18351795 | Fulltext

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment.

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Deforche K, Camacho R, Van Laethem K, Lemey P, Rambaut A, Moreau Y, and Vandamme AM

Bioinformatics (Oxford, England) 24(1):34, 2008 Jan 1 - Who cited this? | PubMed ID: 18024973 | Fulltext

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.

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Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D, and

Journal of virology 81(23):13050, 2007 Dec - Who cited this? | PubMed ID: 17898057 | Fulltext

The emergence of HIV/AIDS in the Americas and beyond.

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Gilbert MT, Rambaut A, Wlasiuk G, Spira TJ, Pitchenik AE, and Worobey M

Proceedings of the National Academy of Sciences of the United States of America 104(47):18566-70, 2007 Nov 20 - Who cited this? | PubMed ID: 17978186 | Fulltext

The evolution of genome compression and genomic novelty in RNA viruses.

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Belshaw R, Pybus OG, and Rambaut A

Genome research 17(10):1496, 2007 Oct - Who cited this? | PubMed ID: 17785537 | Fulltext

Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo.

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Deforche K, Camacho R, Laethem KV, Shapiro B, Moreau Y, Rambaut A, Vandamme AM, and Lemey P

Journal of computational biology : a journal of computational molecular cell biology 14(8):1105-14, 2007 Oct - Who cited this? | PubMed ID: 17985990 | Fulltext

HIV phylogenetics.

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Pillay D, Rambaut A, Geretti AM, and Brown AJ

BMJ (Clinical research ed.) 335(7618):460-1, 2007 Sep 8 - Who cited this? | PubMed ID: 17823148 | Fulltext

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form.

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Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, and Vandamme AM

Journal of virology 81(16):8543-51, 2007 Aug - Who cited this? | PubMed ID: 17553886 | Fulltext

Bayesian estimation of sequence damage in ancient DNA.

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Ho SY, Heupink TH, Rambaut A, and Shapiro B

Molecular biology and evolution 24(6):1416-22, 2007 Jun - Who cited this? | PubMed ID: 17395598 | Fulltext

Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.

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Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, and Holmes EC

Molecular biology and evolution 24(3):845, 2007 Mar - Who cited this? | PubMed ID: 17218639 | Fulltext

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

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Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, and Rambaut A

PLoS computational biology 3(2):e29, 2007 Feb 16 - Who cited this? | PubMed ID: 17305421 | Fulltext

BEAST: Bayesian evolutionary analysis by sampling trees.

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Drummond AJ and Rambaut A

BMC evolutionary biology 7:214, 2007 - Who cited this? | PubMed ID: 17996036 | Fulltext

The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa.

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Davis PL, Rambaut A, Bourhy H, and Holmes EC

Archives of virology 152(7):1251-8, 2007 - Who cited this? | PubMed ID: 17401615 | Fulltext

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak.

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de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D'Arrigo R, Amicosante M, Perrin L, Colizzi V, Perno CF, and Benghazi Study Group

Nature 444(7121):836-7, 2006 Dec 14 - Who cited this? | PubMed ID: 17171825 | Fulltext

JC virus evolution and its association with human populations.

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Shackelton LA, Rambaut A, Pybus OG, and Holmes EC

Journal of virology 80(20):9928-33, 2006 Oct - Who cited this? | PubMed ID: 17005670 | Fulltext

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.

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Jobes DV, Daoust M, Nguyen VT, Padua A, Sinangil F, Pérez-Losada M, Crandall KA, Oliphant T, Posada D, Rambaut A, Fuchs J, and Berman PW

AIDS research and human retroviruses 22(10):968-78, 2006 Oct - Who cited this? | PubMed ID: 17067266 | Fulltext

A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.

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Shapiro B, Rambaut A, Pybus OG, and Holmes EC

Molecular biology and evolution 23(9):1724-30, 2006 Sep - Who cited this? | PubMed ID: 16774976 | Fulltext

Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B.

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Hon CC, Lam TY, Drummond A, Rambaut A, Lee YF, Yip CW, Zeng F, Lam PY, Ng PT, and Leung FC

Journal of virology 80(17):8503-9, 2006 Sep - Who cited this? | PubMed ID: 16912300 | Fulltext

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity.

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Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, Pillay D, and UK Collaborative Group on HIV Drug Resistance

AIDS (London, England) 20(11):1521-9, 2006 Jul 13 - Who cited this? | PubMed ID: 16847407 | Fulltext

No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.).

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Shapiro B, Rambaut A, and Gilbert MT

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 10(4):334-5; author reply 335-6, 2006 Jul - Who cited this? | PubMed ID: 16730469 | Fulltext

Relaxed phylogenetics and dating with confidence.

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Drummond AJ, Ho SY, Phillips MJ, and Rambaut A

PLoS biology 4(5), 2006 May - Who cited this? | PubMed ID: 16683862 | Fulltext

Heterotachy and tree building: a case study with plastids and eubacteria.

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Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, and Larkum T

Molecular biology and evolution 23(1):40, 2006 Jan - Who cited this? | PubMed ID: 16151191 | Fulltext

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.

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Shapiro B, Rambaut A, and Drummond AJ

Molecular biology and evolution 23(1):7, 2006 Jan - Who cited this? | PubMed ID: 16177232 | Fulltext

HIV evolutionary dynamics within and among hosts.

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Lemey P, Rambaut A, and Pybus OG

AIDS reviews 8(3):125-40, 2006 - Who cited this? | PubMed ID: 17078483 | Fulltext

The evolutionary dynamics of endogenous retroviruses.

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Katzourakis A, Rambaut A, and Pybus OG

Trends in microbiology 13(10):463-8, 2005 Oct - Who cited this? | PubMed ID: 16109487 | Fulltext

Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain.

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Lemey P, Derdelinckx I, Rambaut A, Van Laethem K, Dumont S, Vermeulen S, Van Wijngaerden E, and Vandamme AM

Journal of virology 79(18):11981-9, 2005 Sep - Who cited this? | PubMed ID: 16140774 | Fulltext

Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman.

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Iversen AK, Learn GH, Skinhøj P, Mullins JI, McMichael AJ, and Rambaut A

AIDS (London, England) 19(9):990-3, 2005 Jun 10 - Who cited this? | PubMed ID: 15905685 | Fulltext

Bayesian coalescent inference of past population dynamics from molecular sequences.

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Drummond AJ, Rambaut A, Shapiro B, and Pybus OG

Molecular biology and evolution 22(5):1185-92, 2005 May - Who cited this? | PubMed ID: 15703244 | Fulltext

Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth.

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Walker PR, Pybus OG, Rambaut A, and Holmes EC

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 5(3):199-208, 2005 Apr - Who cited this? | PubMed ID: 15737910 | Fulltext

Rise and fall of the Beringian steppe bison.

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Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, Driver JC,

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Science (New York, N.Y.) 306(5701):1561-5, 2004 Nov 26 - Who cited this? | PubMed ID: 15567864 | Fulltext

Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods.

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Paraskevis D, Magiorkinis E, Magiorkinis G, Kiosses VG, Lemey P, Vandamme AM, Rambaut A, and Hatzakis A

Journal of molecular evolution 59(5):709-17, 2004 Nov - Who cited this? | PubMed ID: 15693627 | Fulltext

Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other orthobunyaviruses.

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Briese T, Rambaut A, and Lipkin WI

The Journal of general virology 85(Pt 10):3071, 2004 Oct - Who cited this? | PubMed ID: 15448370 | Fulltext

Viral evolution and the emergence of SARS coronavirus.

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Holmes EC and Rambaut A

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 359(1447):1059-65, 2004 Jul 29 - Who cited this? | PubMed ID: 15306390 | Fulltext

The molecular population genetics of HIV-1 group O.

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Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M, and Vandamme AM

Genetics 167(3):1059-68, 2004 Jul - Who cited this? | PubMed ID: 15280223 | Fulltext

Origin of AIDS: contaminated polio vaccine theory refuted.

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Worobey M, Santiago ML, Keele BF, Ndjango JB, Joy JB, Labama BL, Dhed'A BD, Rambaut A, Sharp PM, Shaw GM, and Hahn BH

Nature 428(6985):820, 2004 Apr 22 - Who cited this? | PubMed ID: 15103367 | Fulltext

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