Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic.
Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC & Luban J (2016) Cell 167, 1088-1098.
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.
Dudas G, Carvalho LM, Trevor Bedford, Andrew J Tatem, Guy Baele, Nuno Faria, Daniel Park, Jason Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah Caddy, Matt Cotten, Jonathan Dambrozio, Simon Dellicour, Antonino Di Caro, Joseph Diclaro, Sophie Duraffour, Mike Elmore, Lawrence Fakoli, Merle Gilbert, Sahr M Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald Grant, Bart Haagmans, Julian Hiscox, Umaru Jah, Brima Kargbo, Jeffrey Kugelman, Di Liu, Jia Lu, Christine Malboeuf, Suzanne Mate, David Matthews, Christian Matranga, Luke Meredith, James Qu, Joshua Quick, Susan Pas, My Phan, Georgios Poliakis, Chantal Reusken, Mariano Sanchez-Lockhart, Stephen Schaffner, John Schieffelin, Rachel Sealfon, Etienne Simon-Loriere, Saskia Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed Vandi, Simon Watson, Kendra West, Shannon Whitmer, Michael Wiley, Sarah Winnicki, Shirlee Wohl, Roman Wölfel, Nathan Yozwiak, Kristian Andersen, Sylvia Blyden, Fatorma Bolay, Bernice Dahn, Miles Carroll, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George Gao, Robert Garry, Ian Goodfellow, Stephan Günther, Christian Happi, Edward Holmes, Brima Kargbo, Paul Kellam, Marion Koopmans, Nicholas Loman, N'Faly Magassouba, Dhamari Naidoo, Stuart Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver Pybus, Pardis Sabeti, Amadou Sall, Keïta Sakoba, Ute Ströeher, Isatta Wurie, Marc Suchard, Philippe Lemey & Rambaut A (2016) bioRxiv 071779
The Evolution of Ebola virus: Insights from the 2013-2016 Epidemic.
Holmes EC, Dudas G, Rambaut A & Andersen KG (2016) Nature 538, 193-200.
Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences".
Rambaut A, Dudas G, Carvalho LM, Park DJ, Yozwiak NL, Holmes EC & Andersen KG (2016) Science 353, 658.
SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A & Lemey P (2016) Mol Biol Evol 33, 2167-2169.
Origins of the 2009 H1N1 influenza pandemic in swine in Mexico.
Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, Castro-Peralta F, Cunha LF, Trovão NS, Lozano-Dubernard B, Rambaut A, van Bakel H & García-Sastre A (2016) eLife 5, e16777.
Emerging concepts of data integration in pathogen phylodynamics.
Baele G, Suchard MA, Rambaut A & Lemey P (2016) Systematic Biology In press
Exploring the temporal structure of heterochronous sequences using TempEst.
Rambaut A, Lam TT, Carvalho LM & Pybus OG (2016) Virus Evolution 2, vew007.
Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting.
Bourhy H, Emmanuel Nakouné, Matthew Hall, Pierre Nouvellet, Anthony Lepelletier, Chiraz Talbi, Laurence Watier, Edward C. Holmes, Simon Cauchemez, Philippe Lemey, Christl A. Donnelly & Rambaut A (2016) PLoS Pathogens 12, e1005525.
Using genomics data to reconstruct transmission trees during disease outbreaks.
Hall MD, Woolhouse MEJ & Rambaut A (2016) Revue scientifique et technique-Office international des epizooties 35, 287-296.
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