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.

Publications

Total publications: 93

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, N�bel 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.

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) PNAS 105, E16.

Evolutionary genomics of host adaptation in vesicular stomatitis virus (VSV).: Remold SK, Rambaut A & Turner PE (2008) MBE 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) 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.

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.