Phylogeography takes a relaxed random walk in continuous space and time.

Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol In press

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) PNAS doi: 10.1073/pnas.0909285106

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 Pathogens 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.

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) PNAS 105, E16.

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.

Estimation of 2Nes from temporal allele frequency data.

Bollback JP, York T & Nielsen R (2008) Genetics In press

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.

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) PNAS 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 Research 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.

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.

Genes under positive selection in Escherichia coli.

Petersen L, Bollback JP, Dimmic M, Hubisz M & Nielsen R (2007) Genome Res 17, 1336-1343.

Clonal interference is alleviated by high mutation rates in large populations.

Bollback JP & Huelsenbeck JP (2007) Mol Biol Evol 24, 1397-1406.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R & Willerslev E (2007) PLoS One 2, e197.

Estimating the history of mutations on a phylogeny.

Bollback JJ, Gardner PP & Nielsen R (2007) In "Ancestral Sequence Reconstruction", Oxford Univ. Press CH. 6, 69-79.

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

Freyhult EK, Bollback JP & Gardner PP (2007) Genome Res 17, 117-125.

Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system.

Reynolds SM, Dryer K, Bollback JP, Uy JAC, Patricelli GL, Robson T, Borgia G & Braun MJ (2007) Auk 124, 857-867.

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.

Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution.

Betancourt AJ & Bollback JP (2006) Curr Opin Genet Dev 16, 618-623.

SIMMAP: stochastic character mapping of discrete traits on phylogenies.

Bollback JP (2006) BMC Bioinformatics 7, 88.

Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil.

Conn JE, Vineis JH, Bollback JP, Onyabe DY, Wilkerson RC & Povoa MM (2006) Am J Trop Med Hyg 74, 798-806.

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.

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.

Posterior mapping and predictive distributions.

Bollback JP (2005) In "Statistical methods in Molecular Evolution", Springer-Verlag

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.

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.

True and false gharials: a nuclear gene phylogeny of crocodylia.

Harshman J, Huddleston CJ, Bollback JP, Parsons TJ & Braun MJ (2003) Syst Biol 52, 386-402.

Stochastic mapping of morphological characters.

Huelsenbeck JP, Nielsen R & Bollback JP (2003) Syst Biol 52, 131-158.

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.

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 the root of a phylogenetic tree.

Huelsenbeck JP, Bollback JP & Levine AM (2002) Syst Biol 51, 32-43.

Bayesian model adequacy and choice in phylogenetics.

Bollback JP (2002) Mol Biol Evol 19, 1171-1180.

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.

Phylogeny and the origin of HIV-1.

Rambaut A, Robertson DL, Pybus OG, Peeters M & Holmes EC (2001) Nature 410, 1047-1048.

Evolutionary rate differences in trypanosomes.

Stevens J & Rambaut A (2001) Infect Genet Evol 1, 143-150.

Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi.

Conn JE, Bollback JP, Onyabe DY, Robinson TN, Wilkerson RC & Povoa MM (2001) Mol Ecol Notes 1, 223-225.

Empirical and hierarchical Bayesian estimation of ancestral states.

Huelsenbeck JP & Bollback JP (2001) Syst Biol 50, 351-366.

Application of the likelihood function in phylogenetic analysis.

Huelsenbeck JP & Bollback JP (2001) In "Handbook of Statistical Genetics", John Wiley and Sons CH. 15, 415-439.

Bayesian inference of phylogeny and its impact on evolutionary biology.

Huelsenbeck JP, Ronquist F, Nielsen R & Bollback JP (2001) Science 294, 2310-2314.

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.

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.

Complete nucleotide sequence and transcriptional analysis of snakehead fish retrovirus.

Hart D, Frerichs GN, Rambaut A & Onions DE (1996) J Virol 70, 3606-3616.

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.