OutbreakTools: a new platform for disease outbreak analysis using the R software.
Jombart T, Aanensen D, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut1 A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R & Ferguson N (2014) Epidemics 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.
Bayesian phylogenetics with BEAUti and the BEAST 1.7.
Drummond AJ, Suchard MA, Dong Xie & Rambaut A (2012) Mol Biol Evol 29, 1969-1973.
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.
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.
A generation time effect on the rate of molecular evolution in invertebrates.
Thomas JA, Welch JJ, Lanfear R & Bromham L (2010) Mol Biol Evol 27, 1173-1180.
Quantifying adaptive evolution in the Drosophila immune system: a high throughput approach.
Obbard DJ, Welch JJ, Kim K-W & Jiggins FM (2009) PLoS Genetics 5, e1000698.
Bayesian Phylogeography Finds Its Roots.
Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Comput Biol 5, e1000520.
Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally.
Weinert, LA, Welch JJ & Jiggins FM (2009) Proc Roy Soc B 276, 3619-3627.
Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors.
Obbard DJ, Welch JJ & Little TJ (2009) Malaria Journal 8, 117.
Many-Core Algorithms for Statistical Phylogenetics.
Suchard MA & Rambaut A (2009) Bioinformatics 25, 1370-1376.
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.
Molecular dates for the "Cambrian explosion": the influence of prior assumptions.
Welch JJ, Fontanillas E & Bromham L (2005) Syst Biol 54, 672-678.
Molecular dating when rates vary.
Welch JJ & Bromham L (2005) Trends Ecol Evol 20, 320-327.
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.
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.
GENIE: estimating demographic history from molecular phylogenies.
Pybus OG & Rambaut A (2002) Bioinformatics 18, 1404-1405.
Inferring confidence sets of possibly misspecified gene trees.
Strimmer K & Rambaut A (2002) Proc Roy Soc B 269, 137-142.
An integrated framework for the inference of viral population history from reconstructed genealogies.
Pybus OG, Rambaut A & Harvey PH (2000) Genetics 155, 1429-1437.
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.
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.
Watching the Clock: Studying variation in rates of molecular evolution between species.
Lanfear R, Welch JJ & Bromham L (2010) Trends Ecol Evol 25, 495-503.
Testing the Island Rule: Primates as a case study.
Welch JJ (2009) Proc Roy Soc B 276, 675-682.
Calculating Independent Contrasts for the Comparative Study of Substitution Rates.
Welch JJ & Waxman D (2008) J Theor Biol 251, 667-678.
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.
Comparative analyses for adaptive radiations.
Harvey PH & Rambaut A (2000) Phil Trans Roy Soc B 355, 1599-1605.
Phylogenetic extinction rates and comparative methodology.
Harvey PH & Rambaut A (1998) Proc Roy Soc B 265, 1691-1696.
Bi-De: an application for simulating phylogenetic processes.
Rambaut A, Grassly NC, Nee S & Harvey PH (1996) Comput Appl Biosci 12, 469-471.
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.
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.
The "island rule" and deep-sea gastropods: Re-examining the evidence.
Welch JJ (2010) PLoS One 5, e8776.
Breeding racehorses: what price good genes?.
Wilson AJ & Rambaut A (2008) Biology Letters 4, 173-175.
Fisher's Microscope and Haldane's Ellipse.
Waxman D & Welch JJ (2005) Am Nat 166, 447-457.
The nk Model and Population Genetics.
Welch JJ & Waxman D (2005) J Theor Biol 234, 329-340.
Accumulating Dobzhansky-Muller incompatibilities: reconciling theory with data.
Welch JJ (2004) Evolution 58, 1145-1156.
Adaptation and Species Range.
Peck JR & Welch JJ (2004) Evolution 58, 211-221.
Modularity and the Cost of Complexity.
Welch JJ & Waxman D (2003) Evolution 57, 1723-1734.
Non-equivalent loci and mutation-selection balance.
Waxman D & Welch JJ (2003) Theor Pop Biol 63, 339-345.
Non-equivalent loci and the distribution of mutant effects.
Welch JJ & Waxman D (2002) Genetics 161, 897-904.
Andrew Rambaut, 2007