This site is for the research, software and publications of Andrew Rambaut and members of his research group.

News

The BEAST software package has its own website: http://beast.bio.ed.ac.uk

We now have a site for posting analyses and news about emerging infectious diseases: http://epidemic.bio.ed.ac.uk/. This includes a new section on the novel human 2c genotype coronavirus.

 
A special issue of Phil. Trans. Roy. Soc. B on “Next Generation Molecular & Evolutionary Epidemiology of Infectious Disease” is now available: http://rstb.royalsocietypublishing.org/content/368/

 
Recent publications
The hidden history of HIV-1: establishment and early spread of the AIDS pandemic.
Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG & Lemey P (2014) Science 346, 56-61.
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.
Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang P-P, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JLB, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH & Sabeti PC. (2014) Science Advanced access
Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak.
Dudas G & Rambaut A (2014) PLoS Currents: Outbreaks 6
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 111, 8107-8112.
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.
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.
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.
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.
Real-time characterization of the molecular epidemiology of an influenza pandemic.
Hedge J, Lycett SJ & Rambaut A (2013) Biology Letters 9

Latest software
2014-09-20 - BEAST
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
2014-07-09 - FigTree
Produce high-quality figures of phylogenetic trees
2013-12-11 - Tracer
A program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes
2013-04-23 - Path-O-Gen
Explore temporal signal and clocklikeness in trees
2011-10-28 - Seq-Gen
An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phyloge(...)
2008-11-29 - TreeStat
A program that calculates summary statistics of a set of trees
2002-12-01 - Phylogen
2002-10-04 - TreeEdit

 
Andrew Rambaut, 2007