Andrew Rambaut

Research Interests

The evolution of emerging human viral pathogens, in particular, fast evolving RNA viruses that have been sampled through time. Inferring evolutionary and population dynamic processes from molecular sequence data. Models of molecular evolution for phylogenetic reconstruction using maximum likelihood and Bayesian inference. Molecular clock techniques including auto-correlated clocks and over-dispersed clocks. Developing computational methods for phylogenetic and evolutionary analysis, primarily using Bayesian MCMC.


Total publications: 140
Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak.
Dudas G & Rambaut A (2014) PLoS Currents: Outbreaks May 2, Edition 1.
The genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus.
Worobey M, Han G-Z & Rambaut A (2014) Proc Natl Acad Sci USA In press
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.
Bouckaert R, Heled J, Kühnert D, Vaughan, Wu C-H, Xie D, Suchard MA, Rambaut A & Drummond AJ (2014) PLoS Comput Biol 10, e1003537.
Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.
Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D & Suchard MA (2014) PLoS Pathogens 10, e1003932.
Spread, circulation and evolution of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV).
Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Swee Hoe Ong, Al Rabeeah AA, Alhakeem RF, Assiri A, Al-Tawfiq JA, Albarrak A, Barry M, Shibl A, Alrabeah FA, Hajjar S, Balkhy HH, Flemban H, Rambaut A, Kellam P & Memish ZA (2014) MBio 5, e01062-13.
A synchronized global sweep of the internal genes of modern avian influenza virus.
Worobey M, Han G-Z & Rambaut A (2014) Nature 508, 254-257.
Integrating influenza antigenic dynamics with molecular evolution.
Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ & Rambaut A (2014) eLife 3, e01914.
The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.
Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme A-M, Van Laethem K & Lemey P (2014) PLoS Comput Biol 10, e1003505.
Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility.
Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enouf V, van der Werf Sylvie & Ferguson NM (2014) The Lancet Infectious Diseases 14
Transmission and Evolution of the Middle East Respiratory Syndrome Coronavirus in Saudi Arabia - a descriptive prospective genomic genomic study.
Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ, Assiri A, Al-Tawfiq JA, Alhakeem RF, Madani H, AlRabiah FA; Al Hajjar S, Albarrak A, Flemban H,  Balkhy HH, Alsubaie S, Palser AL, Gall A, Bashford-Rogers R, Rambaut A, Zumla AI & Memish ZA (2013) The Lancet 382, 1993-2002.
Reconstructing geographical movements and host species transitions of foot-and-mouth disease virus serotype SAT 2.
Hall MD, Knowles NJ, Wadsworth J, Rambaut A & Woolhouse M (2013) MBio 4, e00591-13.
Multiple introductions of Salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture.
Karlsen M, Gjerset B, Hansen T & Rambaut A (2013) J Gen Virol 95, 52-59.
The genesis and source of the H7N9 influenza viruses causing human infections in China.
Lam TT-Y, Wang J, Shen Y, Zhou B, Duan L, Cheung C-L, Ma C, Lycett SJ, Leung CY-H, Chen X, Li L, Hong W, Chai Y, Zhou L, Liang H, Ou Z, Liu Y, Farooqui A, Kelvin DJ, Poon LLM, Smith DK, Pybus OG, Leung GM, Shu Y, Webster RG, Webby RJ, Peiris JSM, Rambaut A, Zhu H & Guan Y (2013) Nature 502, 241-244.
Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection.
Drosten C, Seilmaier M, Corman VM, Hartmann W, Scheible G, Sack S, Guggemos W, Kallies R, Muth D, Junglen S, Müller MA, Haas W, Guberina H, Röhnisch T, Schmid-Wendtner M, Aldabbagh S, Dittmer U, Gold H, Graf P, Bonin F, Rambaut A & Wendtner C-M (2013) The Lancet Infectious Diseases 13, 745-751.
Real-time characterization of the molecular epidemiology of an influenza pandemic.
Hedge J, Lycett SJ & Rambaut A (2013) Biology Letters 9
Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.
Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A, Guan Y, Pillay D, Kellam P & Nastouli E (2013) Emerg Infect Dis 19, 736-742.
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.
Faria NR, Suchard MA, Rambaut A, Streicker DG & Lemey P (2013) Phil Trans Royal Soc B 368, 20120196.
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.
Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B & Suchard MA (2013) Mol Biol Evol 30, 713-724.
Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny.
Thomas JA, Trueman JW, Rambaut A & Welch JJ (2012) Syst Biol 62, 285-297.
Unifying the spatial epidemiology and evolution of emerging epidemics.
Pybus OG, Suchard MA, Lemey P, Bernardin FJ, Rambaut A, Crawford FW, Gray RR, Arinaminpathy N, Stramer S, Busch MP & Delwart EL (2012) Proc Natl Acad Sci USA 109, 15066-15071.
Estimating divergence dates and substitution rates in the Drosophila phylogeny.
Obbard DJ, Maclennan J, Kim K-W, Rambaut A, O?Grady PM & Jiggins FM (2012) Mol Biol Evol 29, 3459-3473.
Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus.
McAdam PR, Templeton KE, Edwards GF, Holden MTG, Feil EJ, Aanensen DM, Bargawi HJA, Spratt BG, Bentley SD, Parkhill J, Enright MC, Holmes A, Girvan EK, Godfrey PA, Feldgarden M, Kearns AM, Rambaut A, Robinson DA & Fitzgerald JR (2012) Proc Natl Acad Sci USA 109, 9107-9112.
Canalization of the evolutionary trajectory of the human influenza virus.
Bedford T, Rambaut A & Pascual M (2012) BMC Biol 10, 38.
Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication.
Weinert LA, Welch JJ, Suchard MA, Lemey P, Rambaut A & Fitzgerald JR (2012) Biology Letters 8, 829-832.
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.
Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A & Robertson DL (2012) BMC Bioinformatics 13, 47.
APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete "All or Nothing" Phenomenon. .
Armitage AE, Deforche K, Chang C-H, Wee E, Kramer B, Welch JJ, Gerstoft J, Fugger L, McMichael A, Rambaut A & Iversen AKN (2012) PLoS Genetics 8, e1002550.
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.
Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA & Alekseyenko AV (2012) Mol Biol Evol 29, 2157-2167.
Bayesian phylogenetics with BEAUti and the BEAST 1.7.
Drummond AJ, Suchard MA, Dong Xie & Rambaut A (2012) Mol Biol Evol 29, 1969-1973.
Origin and Fate of A/H1N1 Influenza in Scotland during 2009.
Lycett S, McLeish NJ, Robertson C, Carman W, Baillie G, McMenamin J, Rambaut A, Simmonds P, Woolhouse M & Leigh Brown AJ (2012) J Gen Virol 93, 1253-1260.
Phylogeography and Population Dynamics of Dengue Viruses in the Americas.
Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A & Carrington CVF (2012) Mol Biol Evol 29, 1533-1543.
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans.
Bahl J, Nelson MI, Chan KH, Chen RB, Vijaykrishna D, Halpin RA, Stockwell TB, Lin XD, Wentworth DE, Ghedin E, Guan Y, Peiris JSM, Riley S, Rambaut A, Holmes EC & Smith GJD (2011) Proc Natl Acad Sci USA 108, 19359-19364.
The origin and evolution of the unique HCV circulating recombinant form 2k/1b.
Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A & Pybus OG (2012) J Virol 86, 2212-2220.
Toward a quantitative understanding of viral phylogeography.
Faria NR, Suchard MA, Rambaut A & Lemey P (2011) Current Opinion in Virology 1, 423-429.
BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics.
Ayres D, Darling A, Zwickl D, Beerli P, Holder M, Lewis P, Huelsenbeck JP, Ronquist F, Swofford D, Cummings MP, Rambaut A & Suchard MA (2012) Syst Biol 61, 170-173.
Evolutionary Dynamics of Local Pandemic H1N1/09 Influenza Lineages Revealed by Whole Genome Analysis.
Baillie G, Galiano M, Agapow P-M, Myers R, Chiam R, Gall A, Palser A, Watson S, Hedge J, Underwood A, Platt S, Mclean E, Pebody R, Rambaut A, Green J, Daniels R, Pybus O & Kellam P and Zambon M (2012) J Virol 86, 11-18.
SPREAD: Spatial phylogenetic reconstruction of evolutionary dynamics.
Bielejec F, Rambaut A, Suchard MA & Lemey P (2011) Bioinformatics 27, 2910-2912.
Multiple hybridizations between ancient brown and polar bears and an Irish origin for the modern polar bear matriline.
Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, WIllerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG & Shapiro B (2011) Current Biology 15, 1251-1258.
Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.
Raghwani J, Rambaut A, Holmes EC, Vu Ty Hang, Tran Tinh Hien, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR & Simmons CP (2011) PLoS Pathog 7, e1002064.
Spatial Dynamics of Human-origin H1 Influenza A Virus in North American Swine.
Nelson MI, Lemey P, Yi Tan, Vincent A, Tsan-Yuk Lam, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC & Gramer M (2011) PLoS Pathog 7, e1002077.
Genomic analysis of Hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation.
Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Sapuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A & Shapiro B (2011) Viruses 3, 83-101.
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach.
Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M & Robertson DL (2010) PLoS Comput Biol 6, e1001022.
A Bayesian phylogenetic method to estimate unknown sequence ages.
Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG & Rambaut A (2010) Mol Biol Evol 28, 879-887.
Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus.
Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Jalal N, Faouzi A, Echevarría JE, Morón SV, Rambaut A, Campiz N, Tatem AJ, Holmes EC & Bourhy H (2010) PLoS Pathog 6, e1001166.
Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation.
Guinane CM, Zakour NLB, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay J, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penades J & Fitzgerald JR (2010) Genome Biology and Evolution 2, 454-466.
Phylodynamic Reconstruction Reveals Norovirus GII. 4 Epidemic Expansions and their Molecular Determinants.
Siebenga JJ, Lemey P, Pond SLK, Rambaut A, Vennema H & Koopmans M (2010) PLoS Pathog 6, e1000884.
Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses.
Firth C, Kitchen A, Shapiro A, Suchard MA, Holmes EC & Rambaut A (2010) Mol Biol Evol 27, 2038-2051.
Phylogeography takes a relaxed random walk in continuous space and time.
Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol 27, 1877-1886.
Recent human to poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus.
Lowder BV, Guinane CM, Zakour NLB, Weinert L, Conway-Morris A, Cartwright RA, Simpson AJ, Rambaut A, Nübel U, & Fitzgerald JR (2009) Proc Natl Acad Sci USA 106, 19545-19550.
Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom.
Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A & Leigh Brown AJ (2009) PLoS Pathog 5, e1000590.
Making Privileged Data Public: Influenza - Response.
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, Rambaut A & Ferguson NM (2009) Science 325, 1072 - 1073.
Bayesian Phylogeography Finds Its Roots.
Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Comput Biol 5, e1000520.
Evolutionary analysis of the dynamics of viral infectious disease.
Pybus OG & Rambaut A (2009) Nature Reviews Genetics 10, 540-550.
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.
Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JSM, Guan Y & Rambaut A (2009) Nature 459, 1122-1125.
Pandemic Potential of a Strain of Influenza A (H1N1) : Early Findings.
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, Rambaut A, Pybus OG, Lopez-Gatell H, Apluche-Aranda CM, Chapela IB, Zavala EP, Guevara DME, Checchi E, Garcia E, Hugonnet S, Roth C & and The WHO Rapid Pandemic Assessment Collaboration. 2009. (2009) Science 324, 1557-1561.
Many-Core Algorithms for Statistical Phylogenetics.
Suchard MA & Rambaut A (2009) Bioinformatics 25, 1370-1376.
Accommodating the effect of ancient DNA damage on inferences of demographic histories.
Rambaut A, Ho SYW, Drummond AJ & Shapiro B (2008) Mol Biol Evol 26, 245-248.
The RNA Virus Database.
Belshaw R, de Oliveira T, Markowitz S & Rambaut A (2009) Nucleic Acids Research 37, D431-D435.
Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences.
Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A & Iversen AKN (2008) J Virol 82, 8743-8761.
The Genomic and Epidemiological Dynamics of Human Influenza A Virus.
Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK & Holmes EC (2008) Nature 453, 615-619.
Reply to Pape et al.: The phylogeography of HIV-1 group M subtype B.
Worobey M, Pitchenik AE, Gilbert MTP, Wlasiuk G & Rambaut A (2008) Proc Natl Acad Sci USA 105, E16.
Evolutionary genomics of host adaptation in vesicular stomatitis virus (VSV).
Remold SK, Rambaut A & Turner PE (2008) Mol Biol Evol 25, 1138-1147.
Pacing a small cage: mutation and RNA viruses.
Belshaw R, Gardner A, Rambaut A & Pybus OG (2008) Trends Ecol Evol 23, 188-193.
Episodic sexual transmission of HIV revealed by molecular phylodynamics.
Lewis FI, Hughes GJ, Rambaut A, Pozniak A & Leigh Brown AJ (2008) PLoS Med 5, e50.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Parker J, Rambaut A & Pybus OG (2008) Infect Genet Evol 8, 239-246.
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo.
Deforche K, Camacho R, Van Laethem K, Shapiro B, Moreau Y, Rambaut A, & Vandamme AM (2007) J Comput Biol 14, 1105-1114.
Breeding racehorses: what price good genes?.
Wilson AJ & Rambaut A (2008) Biology Letters 4, 173-175.
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment.
Deforche K, Camacho R, Van Laethem K, Lemey P, Rambaut A, Moreau Y, & Vandamme AM (2007) Bioinformatics 24, 34-41.
BEAST: Bayesian Evolutionary Analysis Sampling Trees.
Drummond AJ & Rambaut A (2007) BMC Evolutionary Biology 7, 214.
The Emergence of HIV/AIDS in the Americas and Beyond.
Gilbert MTP, Rambaut A, Wlasiuk G, Spira TJ, Pitchenik AE & Worobey M (2007) Proc Natl Acad Sci USA 104, 18566-18570.
Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of HIV-1.
Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme A-M, Kellam P & Pillay D (2007) J Virol 81, 13050-13056.
The use of HIV phylogenetics: Virological evidence within HIV criminalisation cases is of limited value in proving transmission.
Pillay D, Rambaut A, Geretti AM & Leigh Brown A (2007) British Medical Journal 335, 460-461.
The evolution of genome compression and genomic novelty in RNA Viruses.
Belshaw R, Pybus OG & Rambaut A (2007) Genome Res 17, 1496-1504.
Recombination is confounding the early evolutionary history of HIV-1: subtype G is a circulating recombinant form.
Abecasis A, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A & Vandamme A-M (2007) J Virol 81, 8543-8551.
Bayesian estimation of sequence damage in ancient DNA.
Ho SYW, Heupink TH, Rambaut A & and Shapiro B (2007) Mol Biol Evol 24, 1416-1422.
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.
Lemey P, Kosakovsky Pond S, Drummond AJ, Pybus OG, Shapiro B, Taveira N & Rambaut A (2006) PLoS Comput Biol 3, 282-292 (e29).
The evolutionary dynamics of canid and mongoose rabies virus in southern Africa.
Davis PL, Rambaut A, Bourhy H & Holmes EC (2007) Archives in Virology 152, 1251-1258.
Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.
Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ & Holmes EC (2007) Mol Biol Evol 24, 845-852.
Molecular Epidemiology: HIV-1 and HCV sequences from Libyan outbreak.
deOliveira 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 (2006) Nature 444, 836-837.
JC virus evolution and its association with human populations.
Shackelton LA, Rambaut A, Pybus OG & Holmes EC (2006) J Virol 80, 9928-9933.
HIV evolutionary dynamics within and among hosts.
Lemey P, Rambaut A & Pybus OG (2006) AIDS Reviews 8, 125-140.
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.
Shapiro B, Rambaut A, Pybus OG & Holmes EC (2006) Mol Biol Evol 23, 1724-1730.
Phylogenetic analysis reveals correlation between the expansion of very virulent Infectious Bursal Disease Virus and the reassortment of its genome segment B.
Hon C-C, Lam T-Y, Drummond AJ, Rambaut A, Lee Y-F, Yip C-W, Zeng F, Lam P-Y, Ng PTW & Leung FCC (2006) J Virol 80, 8503-8509.
Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity.
Gifford R, deOliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P & Pillay D (2006) AIDS 20, 1521-1529.
No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al).
Shapiro B, Rambaut A & Gilbert TP (2006) Internat J Infect Disease 10, 334-335.
Relaxed Phylogenetics and Dating with Confidence.
Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.
Shapiro B, Rambaut A & Drummond AJ (2006) Mol Biol Evol 23, 7-9.
The nature of heterotachy.
Lockhart P, Novis P, Milligan B, Riden J, Rambaut A & Larkum T (2006) Mol Biol Evol 23, 40-45.
The evolutionary dynamics of endogenous retroviruses.
Katzourakis A, Rambaut A, & Pybus OG (2005) Trends in Microbiology 13, 463-468.
Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain.
Lemey P, Derdelinckx I, Rambaut A, Van Laethem K, Dumont S, Vermeulen S, Van Wijngaerden E & Vandamme A-M (2005) J Virol 79, 11981-11989.
Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually-infected woman.
Iversen AKN, Learn GH, Skinhoj P, Mullins JI, McMichael AJ & Rambaut A (2005) AIDS 19, 990-993.
Bayesian coalescent inference of past population dynamics from molecular sequences.
Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.
Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth.
Walker PR, Pybus OG, Rambaut A & Holmes EC (2005) Infect Genet Evol 5, 199-208.
Rise and fall of the Beringian steppe bison.
Shapiro B, Drummond AJ, Rambaut A, Wilson M, Sher A, Pybus OG, Gilbert MTP, Barnes I, Binladen J, Willerslev E, Hansen A, Baryshnikov GF, Burns J, Davydov S, Driver J, Gubin SV, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson R, Storer J, Tedford R, Vorobiev A, Zimov S & Cooper A (2004) Science 306, 1561-1565.
Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other Bunyaviruses.
Briese T, Rambaut A & Lipkin WI (2004) J Gen Virol 85, 3071-3077.
The molecular population genetics of HIV-1 group O.
Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M & Vandamme A-M (2004) Genetics 167, 1059-1068.
Viral evolution and the emergence of SARS coronavirus.
Holmes EC & Rambaut A (2004) Phil Trans R Soc Lond B 359, 1059-1065.
Origin of AIDS: Contaminated polio vaccine theory refuted.
Worobey M, Santiago ML, Keele BF, Ndjango J-BN, Joy JB, Labama BL, Dhed'a BD, Rambaut A, Sharp PM, Shaw GM & Hahn BH (2004) Nature 428, 820.
The causes and consequences of HIV evolution.
Rambaut A, Posasa D, Crandall KA & Holmes EC (2004) Nature Reviews Genetics 5, 52-61.
Inference of viral evolutionary rates from molecular sequences.
Drummond A, Pybus OG & Rambaut A (2003) Adv Parasitology 54, 331-358.
Measurably evolving populations.
Drummond AJ, Pybus OG, Rambaut A, Forsberg R & Rodrigo AG (2003) Trends Ecol Evol 18, 481-488.
Sexual transmission of HIV in Africa.
Walker PR, Worobey M, Rambaut A, Holmes EC & Pybus OG (2003) Nature 422, 679.
The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach.
Pybus OG, Drummond AJ, Nakano T, Robertson BH & Rambaut A (2003) Mol Biol Evol 20, 381-387.
Inferring the rate and time-scale of dengue virus evolution.
Twiddy SS, Holmes EC & Rambaut A (2003) Mol Biol Evol 20, 122-129.
New inferences from tree shape: numbers of missing taxa and population growth rates.
Pybus OG, Rambaut A, Holmes EC & Harvey PH (2002) Syst Biol 51, 881-888.
Testing the relationship between morphological and molecular rates of change along phylogenies.
Bromham L, Woolfit M, Lee MS & Rambaut A (2002) Evolution 56, 1921-1930.
GENIE: estimating demographic history from molecular phylogenies.
Pybus OG & Rambaut A (2002) Bioinformatics 18, 1404-1405.
Phylogenetic analysis of a human isolate from the 2000 Israel West Nile virus epidemic.
Briese T, Rambaut A, Pathmajeyan M, Bishara J, Weinberger M, Pitlik S & Lipkin WI (2002) Emerg Infect Dis 8, 528-531.
Questioning the evidence for genetic recombination in the 1918 'Spanish flu' virus.
Worobey M, Rambaut A, Pybus OG & Robertson DL (2002) Science 296, 211.
Flight of the dodo.
Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Bininda-Emonds OR, Lee PL & Cooper A (2002) Science 295, 1683.
Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.
Jenkins GM, Rambaut A, Pybus OG & Holmes EC (2002) J Mol Evol 54, 156-165.
Inferring confidence sets of possibly misspecified gene trees.
Strimmer K & Rambaut A (2002) Proc Roy Soc B 269, 137-142.
The epidemic behavior of the hepatitis C virus.
Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC & Harvey PH (2001) Science 292, 2323-2325.
Human origins and ancient human DNA.
Cooper A, Rambaut A, Macaulay V, Willerslev E, Hansen AJ & Stringer C (2001) Science 292, 1655-1656.
Phylogeny and the origin of HIV-1.
Rambaut A, Robertson DL, Pybus OG, Peeters M & Holmes EC (2001) Nature 410, 1047-1048.
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution.
Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J & Ward R (2001) Nature 409, 704-707.
Evolutionary rate differences in trypanosomes.
Stevens J & Rambaut A (2001) Infect Genet Evol 1, 143-150.
Comparative analyses for adaptive radiations.
Harvey PH & Rambaut A (2000) Phil Trans Roy Soc B 355, 1599-1605.
An integrated framework for the inference of viral population history from reconstructed genealogies.
Pybus OG, Rambaut A & Harvey PH (2000) Genetics 155, 1429-1437.
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies.
Rambaut A (2000) Bioinformatics 16, 395-399.
The power of relative rates tests depends on the data.
Bromham L, Penny D, Rambaut A & Hendy MD (2000) J Mol Evol 50, 296-301.
Testing the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta virus.
Jenkins GM, Woelk CH, Rambaut A & Holmes EC (2000) J Mol Evol 50, 98-102.
Genetic analysis of West Nile New York 1999 encephalitis virus.
Jia XY, Briese T, Jordan I, Rambaut A, Chi HC, Mackenzie JS, Hall RA, Scherret J & Lipkin WI (1999) Lancet 354, 1971-1972.
Widespread intra-serotype recombination in natural populations of dengue virus.
Worobey M, Rambaut A & Holmes EC (1999) Proc Natl Acad Sci USA 96, 7352-7357.
Phylogenetic evidence for recombination in dengue virus.
Holmes EC, Worobey M & Rambaut A (1999) Mol Biol Evol 16, 405-409.
Testing the Cambrian explosion hypothesis by using a molecular dating technique.
Bromham L, Rambaut A, Fortey R, Cooper A & Penny D (1998) Proc Natl Acad Sci USA 95, 12386-12389.
Estimating divergence dates from molecular sequences.
Rambaut A & Bromham L (1998) Mol Biol Evol 15, 442-448.
Phylogenetic extinction rates and comparative methodology.
Harvey PH & Rambaut A (1998) Proc Roy Soc B 265, 1691-1696.
PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees.
Grassly NC, Adachi J & Rambaut A (1997) Comput Appl Biosci 13, 559-560.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A & Grassly NC (1997) Comput Appl Biosci 13, 235-238.
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences.
Rambaut A, Harvey PH & Nee S (1997) Comput Appl Biosci 13, 303-306.
Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees.
Ong CK, Nee S, Rambaut A, Bernard HU & Harvey PH (1997) J Mol Evol 44, 199-206.
Determinants of rate variation in mammalian DNA sequence evolution.
Bromham L, Rambaut A & Harvey PH (1996) J Mol Evol 43, 610-621.
Bi-De: an application for simulating phylogenetic processes.
Rambaut A, Grassly NC, Nee S & Harvey PH (1996) Comput Appl Biosci 12, 469-471.
Inferring the population history of an epidemic from a phylogenetic tree.
Ong CK, Nee S, Rambaut A & Harvey PH (1996) J Theor Biol 182, 173-178.
Complete nucleotide sequence and transcriptional analysis of snakehead fish retrovirus.
Hart D, Frerichs GN, Rambaut A & Onions DE (1996) J Virol 70, 3606-3616.
Isolation and sequence analysis of a cDNA encoding the c subunit of a vacuolar-type H(+)-ATPase from the CAM plant Kalanchoe daigremontiana.
Bartholomew DM, Rees DJ, Rambaut A & Smith JA (1996) Plant Mol Biol 31, 435-442.
Recombination between sequences of hepatitis B virus from different genotypes.
Bollyky PL, Rambaut A, Harvey PH & Holmes EC (1996) J Mol Evol 42, 97-102.
Revealing the history of infectious disease epidemics through phylogenetic trees.
Holmes EC, Nee S, Rambaut A, Garnett GP & Harvey PH (1995) Phil Trans Roy Soc B 349, 33-40.
Inferring population history from molecular phylogenies.
Nee S, Holmes EC, Rambaut A & Harvey PH (1995) Phil Trans Roy Soc B 349, 25-31.
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data.
Purvis A & Rambaut A (1995) Comput Appl Biosci 11, 247-251.
Andrew Rambaut, 2007