Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.

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Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.

Campbell K, Gifford RJ, Singer J, Hill V, O'Toole Á, Rambaut A, Hampson K & Brunker K (2022) PLoS Pathogens 18, e1010023.

Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.

Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun RM, Jackson B, Orton R, Nielsen M, Hsu NS, Harrison EM, De Silva TI, Rambaut A, Peacock SJ, Robertson DL & Carabelli AM (2022) Virus Evolution 8, veac023.

Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number.

Keeling MJ, Dyson L, Guyver-Fletcher G, Holmes A, Semple MG, Tildesley MJ, Hill EM, Brito A, Earnest R, Fauver J, Kalinich C, Petrone M, Rothman J, Vogels C, Watkins A, Ferguson D, Schulz W, Kerantzas N, Landry M, Peaper D, Baillie JK, Openshaw PJM, Carson G, Alex B, Bach B, Barclay WS, Bogaert D, Chand M, Cooke GS, Docherty AB, Dunning J, da Silva Filipe A, Fletcher T, Green CA, Harrison EM, Hiscox JA, Ho AYW, Horby PW, Ijaz S, Khoo S, Klenerman P, Lim WS, Mentzer AJ, Merson L, Meynert AM, Noursadeghi M, Palmarini M, Paxton WA, Pollakis G, Price N, Rambaut A, Robertson DL, Russell CD, Sancho-Shimizu V, Scott JT, Sigfrid L, Solomon T, Sriskandan S, Stuart D, Summers C, Tedder RS, Thomson EC, Thwaites RS, Turtle LCW, Zambon M, Hardwick H, Donohue C, Ewins J, Oosthuyzen W, Griffiths F, Norman L, Pius R, Drake TM, Fairfield CJ, Knight S, Mclean KA, Murphy D, Shaw CA, Dalton J, Girvan M, Saviciute E, Harrison SRJ, Marsh L, Connor M, Leeming G, Law A, Hendry R, Greenhalf W, Shaw V, Ahmed KA, Armstrong JA, Ashworth M, Asiimwe IG, Bakshi S, Barlow SL, Booth L, Brennan B, Bullock K, Catterall BWA, Clark JJ, Clarke EA, Cole S, Cooper L, Cox H, Davis C, Dincarslan O, Dunn C, Dyer P, Elliott A, Evans A, Fisher L, Foster T, Garcia-Dorival I, Greenhalf W, Gunning P, Hartley C, Ho A, Jensen RL, Jones CB, Jones TR, Khandaker S, King K, Kiy RT, Koukorava C, Lake A, Lant S, Latawiec D, Lavelle-Langham L, Lefteri D, Lett L, Livoti LA, Mancini M, McDonald S, McEvoy L, McLauchlan J, Metelmann S, Miah NS, Middleton J, Mitchell J, Moore SC, Murphy EG, Penrice-Randal R, Pilgrim J, Prince T, Reynolds W, Ridley PM, Sales D, Shaw VE, Shears RK, Small B, Subramaniam KS, Szemiel A, Taggart A, Tanianis J, Thomas J, Trochu E, van Tonder L, Wilcock E, Zhang JE, Adeniji K, Agranoff D, Agwuh K, Ail D, Alegria A, Angus B, Ashish A, Atkinson D, Bari S, Barlow G, Barnass S, Barrett N, Bassford C, Baxter D, Beadsworth M, Bernatoniene J, Berridge J, Best N, Bothma P, Brealey D, Brittain-Long R, Bulteel N, Burden T, Burtenshaw A, Caruth V, Chadwick D, Chambler D, Chee N, Child J, Chukkambotla S, Clark T, Collini P, Cosgrove C, Cupitt J, Cutino-Moguel M-T, Dark P, Dawson C, Dervisevic S, Donnison P, Douthwaite S, DuRand I, Dushianthan A, Dyer T, Evans C, Eziefula C, Fegan C, Finn A, Fullerton D, Garg S, Garg A, Godden J, Goldsmith A, Graham C, Hardy E, Hartshorn S, Harvey D, Havalda P, Hawcutt DB, Hobrok M, Hodgson L, Holme A, Hormis A, Jacobs M, Jain S, Jennings P, Kaliappan A, Kasipandian V, Kegg S, Kelsey M, Kendall J, Kerrison C, Kerslake I, Koch O, Koduri G, Koshy G, Laha S, Larkin S, Leiner T, Lillie P, Limb J, Linnett V, Little J, MacMahon M, MacNaughton E, Mankregod R, Masson H, Matovu E, McCullough K, McEwen R, Meda M, Mills G, Minton J, Mirfenderesky M, Mohandas K, Mok Q, Moon J, Moore E, Morgan P, Morris C, Mortimore K, Moses S, Mpenge M, Mulla R, Murphy M, Nagel M, Nagarajan T, Nelson M, Otahal I, Pais M, Panchatsharam S, Paraiso H, Patel B, Pepperell J, Peters M, Phull M, Pintus S, Pooni JS, Post F, Price D, Prout R, Rae N, Reschreiter H, Reynolds T, Richardson N, Roberts M, Roberts D, Rose A, Rousseau G, Ryan B, Saluja T, Shah A, Shanmuga P, Sharma A, Shawcross A, Sizer J, Smith R, Snelson C, Spittle N, Staines N, Stambach T, Stewart R, Subudhi P, Szakmany T, Tatham K, Thomas J, Thompson C, Thompson R, Tridente A, Tupper-Carey D, Twagira M, Ustianowski A, Vallotton N, Vincent-Smith L, Visuvanathan S, Vuylsteke A, Waddy S, Wake R, Walden A, Welters I, Whitehouse T, Whittaker P, Whittington A, Wijesinghe M, Williams M, Wilson L, Wilson S, Winchester S, Wiselka M, Wolverson A, Wooton DG, Workman A, Yates B, Young P & ISARIC4C Investigators (2022) Statistical Methods in Medical Research

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.

Thomson EC, Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, Davis C, Piccoli L, Pascall DJ, Dillen J, Lytras S, Czudnochowski N, Shah R, Meury M, Jesudason N, De Marco A, Li K, Bassi J, O'Toole A, Pinto D, Colquhoun RM, Culap K, Jackson B, Zatta F, Rambaut A, Jaconi S, Sreenu VB, Nix J, Zhang I, Jarrett RF, Glass WG, Beltramello M, Nomikou K, Pizzuto M, Tong L, Cameroni E, Croll TI, Johnson N, Di Iulio J, Wickenhagen A, Ceschi A, Harbison AM, Mair D, Ferrari P, Smollett K, Sallusto F, Carmichael S, Garzoni C, Nichols J, Galli M, Hughes J, Riva A, Ho A, Schiuma M, Semple MG, Openshaw PJM, Fadda E, Baillie JK, Chodera JD, Rihn SJ, Lycett SJ, Virgin HW, Telenti A, Corti D, Robertson DL, Snell G, The ISARIC4C Investigators & the COVID-19 Genomics UK (COG-UK) Consortium (2021) Cell 184, 1171-1187.

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A & Pybus OG (2021) Science 371, 708-712.

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, Rey SM, Nicholls SM, Colquhoun RM, da Silva Filipe A, Shepherd J, Pascall DJ, Shah R, Jesudason N, Li K, Jarrett R, Pacchiarini N, Bull M, Geidelberg L, Siveroni I, COG-UK Consortium, Goodfellow I, Loman NJ, Pybus OG, Robertson DL, Thomson EC, Rambaut A & Connor TR (2021) Cell 184, 64-75.

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling.

Holbrook AJ, Lemey P, Baele G, Dellicour S, Brockmann D, Rambaut A & Suchard MA (2021) Journal of Computational and Graphical Statistics 30, 24-Nov.

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.

Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O'Toole Á, Amato R, Ragonnet-Cronin M, Harrison I, Jackson B, Ariani CV, Boyd O, Loman NJ, McCrone JT, Gon?alves S, Jorgensen D, Myers R, Hill V, Jackson DK, Gaythorpe K, Groves N, Sillitoe J, Kwiatkowski DP, Flaxman S, Ratmann O, Bhatt S, Hopkins S, Gandy A, Rambaut A, Ferguson NM & The COVID-19 Genomics UK (COG-UK) consortium (2021) Nature

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

da Silva Filipe A, Shepherd JG, Williams T, Hughes J, Aranday-Cortes E, Asamaphan P, Ashraf S, Balcazar C, Brunker K, Campbell A, Carmichael S, Davis C, Dewar R, Gallagher MD, Gunson R, Hill V, Ho A, Jackson B, James E, Jesudason N, Johnson N, McWilliam Leitch EC, Li K, MacLean A, Mair D, McAllister DA, McCrone JT, McDonald SE, McHugh MP, Morris AK, Nichols J, Niebel M, Nomikou K, Orton RJ, O'Toole Á, Palmarini M, Parcell BJ, Parr YA, Rambaut A, Rooke S, Shaaban S, Shah R, Singer JB, Smollett K, Starinskij I, Tong L, Sreenu VB, Wastnedge E, Holden MTG, Robertson DL, Templeton K, Thomson EC & The COVID-19 Genomics UK (COG-UK) Consortium (2021) Nature Microbiology 6, 112-122.

Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.

Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L & Pybus OG (2021) Nature microbiology 6, 415.

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.

Baele G, Lemey P, Rambaut A & Suchard, MA (2017) Bioinformatics 33, 1798?1805.

Exploring the temporal structure of heterochronous sequences using TempEst.

Rambaut A, Lam TT, Carvalho LM & Pybus OG (2016) Virus Evolution 2, vew007.

The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study.

Hall MD, Woolhouse M & Rambaut A (2016) Virus Evolution 2, vew003.

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A & Suchard MA (2014) BMC Bioinfomatics 15, 133.

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.

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.

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.