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

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Massive Parallelization Boosts Big Bayesian Multidimensional Scaling.

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Andersen KG, Rambaut A, Lipkin WI, Holmes EC & Garry RF (2020) Nature Medicine

Outcome of hospitalization for COVID-19 in patients with interstitial lung disease an international multicenter study.

Drake TM, Docherty AB, Harrison EM, Quint JK, Adamali H, Agnew S, Babu S, Barber CM, Barratt S, Bendstrup E, Bianchi S, Villegas DC, Chaudhuri N, Chua F, Coker R, Chang W, Crawshaw A, Crowley LE, Dosanjh D, Fiddler CA, Forrest IA, George PM, Gibbons MA, Groom K, Haney S, Hart SP, Heiden E, Henry M, Ho L-P, Hoyles RK, Hutchinson J, Hurley K, Jones M, Jones S, Kokosi M, Kreuter M, MacKay LS, Mahendran S, Margaritopoulos G, Molina-Molina M, Molyneaux PL, O'Brien A, O'Reilly K, Packham A, Parfrey H, Poletti V, Porter JC, Renzoni E, Rivera-Ortega P, Russell A-M, Saini G, Spencer LG, Stella GM, Stone H, Sturney S, Thickett D, Thillai M, Wallis T, Ward K, Wells AU, West A, Wickremasinghe M, Woodhead F, Hearson G, Howard L, Baillie JK, Openshaw PJM, Semple MG, Stewart I, Jenkins RG, Alex GCB, Bach B, Barclay WS, Bogaert D, Chand M, Cooke GS, Dunning J, da Silva Filipe A, Fletcher T, Green CA, Hiscox JA, Ho AYW, Horby PW, Ijaz S, Khoo S, Klenerman P, Law A, Lim WS, Mentzer AJ, Merson L, Meynert AM, Noursadeghi M, Moore SC, Palmarini M, Paxton WA, Pollakis G, Price N, Rambaut A, Robertson DL, Russell CD, Sancho-Shimizu V, Scott JT, de Silva T, Sigfrid L, Solomon T, Sriskandan S, Stuart D, Summers C, Tedder RS, Thomson EC, Thompson AAR, Thwaites RS, Turtle LCW, Zambon M, Hardwick H, Donohue C, Lyons R, Griffiths F, Oosthuyzen W, Norman L, Pius R, Fairfield CJ, Knight S, Mclean KA, Murphy D, Shaw CA, Dalton J, Girvan M, Saviciute E, Roberts S, Harrison J, Marsh L, Connor M, Halpin S, Jackson C, Gamble C, Leeming G, Law A, Wham M, Clohisey S, Hendry R, Scott-Brown J, Greenhalf W, Shaw V, McDonald S, Keating S, 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, Finch L, Fisher LWS, 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-Hughes 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 S, Garg A, Gkrania-Klotsas E, 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, Laird 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, Shankar-Hari M, 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 (2020) American Journal of Respiratory and Critical Care Medicine 202, 1656-1665.

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.

Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A & Suchard MA (2020) Nature Communications 11, 5110.

Mapping of HIV-1C transmission networks reveals extensive spread of viral lineages across villages in Botswana treatment-as-prevention trial.

Novitsky V, Zahralban-Steele M, Moyo S, Nkhisang T, Maruapula D, McLane MF, Leidner J, Bennett K, Wirth KE, Gaolathe T, Kadima E, Chakalisa U, Holme MP, Lockman S, Mmalane M, Makhema J, Gaseitsiwe S, DeGruttola V, Essex M, Abeler-Dorner L, Bonsall D, Fraser C, Golubchik T, Ayles H, Bowden R, Calvez V, Fidler S, Grabowski K, Kagaayi J, Hayes R, Seeley J, Herbeck J, Lingappa J, Kaleebu P, Ssemwanga D, Pillay D, Tanser F, Quinn T, Rambaut A, Leigh-Brown A, Ratmann O, Wawer M, Cohen M, Dennis A, D'Oliveira T, Frampton D, Hoppe A, Kellam P, Kityo C, Paton N & PANGEA Consortium (2020) Journal of Infectious Diseases 222, 1670-1680.

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic.

Boni MF, Lemey P, Jiang X, Lam TT-Y, Perry BW, Castoe TA, Rambaut A & Robertson DL (2020) Nature Microbiology 5, 1408-1417.

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 (2020) Nature Microbiology 5, 1403-1407.

Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19.

Biggerstaff M, Cowling BJ, Cucunub? ZM, Dinh L, Ferguson NM, Gao H, Hill V, Imai N, Johansson MA, Kada S, Morgan O, Pastore Y Piontti A, Polonsky JA, Prasad PV, Quandelacy TM, Rambaut A, Tappero JW, Vandemaele KA, Vespignani A, Warmbrod KL, Wong JY & WHO COVID-19 Modelling Parameters Group (2020) Emerging infectious diseases 26, e1-e14.

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study.

Sikkema RS, Pas SD, Nieuwenhuijse DF, O'Toole Á, Verweij JJ, van der Linden A, Chestakova I, Schapendonk C, Pronk M, Lexmond P, Bestebroer T, Overmars RJ, van Nieuwkoop S, van den Bijllaardt W, Bentvelsen RG, van Rijen MML, Buiting AGM, van Oudheusden AJG, Diederen BM, Bergmans AMC, van der Eijk A, Molenkamp R, Rambaut A, Timen A, Kluytmans JAJW, Oude Munnink BB, Kluytmans van den Bergh MFQ & Koopmans MPG (2020) The Lancet Infectious Diseases 20, 1273-1280.

Author Correction: Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands (Nature Medicine, (2020), 26, 9, (1405-1410), 10.1038/s41591-020-0997-y).

Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M, Oudehuis GJAPM, Schinkel J, Kluytmans J, Kluytmans-van den Bergh M, van den Bijllaardt W, Berntvelsen RG, van Rijen MML, Schneeberger P, Pas S, Diederen BM, Bergmans AMC, van der Eijk PAV, Verweij JJ, Buiting AGN, Streefkerk R, Aldenkamp AP, de Man P, Koelemal JGM, Ong D, Paltansing S, Veassen N, Sleven J, Bakker L, Brockhoff H, Rietveld A, Slijkerman Megelink F, Cohen Stuart J, de Vries A, van der Reijden W, Ros A, Lodder E, Verspui-van der Eijk E, Huijskens I, Kraan EM, van der Linden MPM, Debast SB, Naiemi NA, Kroes ACM, Damen M, Dinant S, Lekkerkerk S, Pontesilli O, Smit P, van Tienen C, Godschalk PCR, van Pelt J, Ott A, van der Weijden C, Wertheim H, Rahamat-Langendoen J, Reimerink J, Bodewes R, Duizer E, van der Veer B, Reusken C, Lutgens S, Schneeberger P, Hermans M, Wever P, Leenders A, ter Waarbeek H, Hoebe C & The Dutch-Covid-19 response team (2020) Nature Medicine 26, 1802.

The emergence of SARS-CoV-2 in Europe and North America.

Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO & Lemey P (2020) Science 370, 564-570.

Gradients do grow on trees: A linear-time O(N)-dimensional gradient for statistical phylogenetics.

Ji X, Zhang Z, Holbrook A, Nishimura A, Baele G, Rambaut A, Lemey P & Suchard MA (2020) Molecular Biology and Evolution 37, 3047-3060.

Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020.

Thompson CP, Grayson NE, Paton RS, Bolton JS, Louren?o J, Penman BS, Lee LN, Odon V, Mongkolsapaya J, Chinnakannan S, Dejnirattisai W, Edmans M, Fyfe A, Imlach C, Kooblall K, Lim N, Liu C, L?pez-Camacho C, McInally C, McNaughton AL, Ramamurthy N, Ratcliff J, Supasa P, Sampson O, Wang B, Mentzer AJ, Turner M, Semple MG, Baillie K, Harvala H, Screaton GR, Temperton N, Klenerman P, Jarvis LM, Gupta S, Simmonds P, 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, Law A, Lim WS, Merson L, Meynert AM, Noursadeghi M, Moore SC, Palmarini M, Paxton WA, Pollakis G, Price N, Rambaut A, Robertson DL, Russell CD, Sancho-Shimizu V, Scott JT, de Silva T, Sigfrid L, Solomon T, Sriskandan S, Stuart D, Summers C, Tedder RS, Thomson EC, Roger Thompson AA, Thwaites RS, Turtle LCW, Zambon M, Hardwick H, Donohue C, Lyons R, Griffiths F, Oosthuyzen W, Norman L, Pius R, Drake TM, Fairfield CJ, Knight S, McLean KA, Murphy D, Shaw CA, Dalton J, Lee J, Plotkin D, Girvan M, Saviciute E, Roberts S, Harrison J, Marsh L, Connor M, Halpin S, Jackson C, Gamble C, Leeming G, Law A, Wham M, Clohisey S, Hendry R, Scott-Brown J, Greenhalf W, Shaw V, McDonald S, Keating S, 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, Finch L, Fisher LWS, 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-Hughes 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 S, Garg A, Gkrania-Klotsas E, Godden J, Goldsmith A, Graham C, Hardy E, Hartshorn S, Harvey D, Havalda P, Hawcutt DB, Hobrok M, Hodgson L, 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, Laird 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, Pattison N, 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, Shankar-Hari M, 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 (2020) Eurosurveillance 25, 2000685.

Evolution and epidemic spread of SARS-CoV-2 in Brazil.

Candido DS, Claro IM, de Jesus JG, Souza WM, Moreira FRR, Dellicour S, Mellan TA, du Plessis L, Pereira RHM, Sales FCS, Manuli ER, Th?z? J, Almeida L, Menezes MT, Voloch CM, Fumagalli MJ, Coletti TM, da Silva CAM, Ramundo MS, Amorim MR, Hoeltgebaum HH, Mishra S, Gill MS, Carvalho LM, Buss LF, Prete CA, Jr, Ashworth J, Nakaya HI, Peixoto PS, Brady OJ, Nicholls SM, Tanuri A, Rossi ?D, Braga CKV, Gerber AL, de Guimar?es APC, Gaburo N, Jr, Alencar CS, Ferreira ACS, Lima CX, Levi JE, Granato C, Ferreira GM, Francisco RS, Jr, Granja F, Garcia MT, Moretti ML, Perroud MW, Jr, Casti?eiras TMPP, Lazari CS, Hill SC, de Souza Santos AA, Simeoni CL, Forato J, Sposito AC, Schreiber AZ, Santos MNN, de S? CZ, Souza RP, Resende-Moreira LC, Teixeira MM, Hubner J, Leme PAF, Moreira RG, Nogueira ML, Ferguson NM, Costa SF, Proenca-Modena JL, Vasconcelos ATR, Bhatt S, Lemey P, Wu C-H, Rambaut A, Loman NJ, Aguiar RS, Pybus OG, Sabino EC, Faria NR, Brazil-UK Centre for Arbovirus Discovery, Diagnosis & Genomics and Epidemiology (CADDE) Genomic Network (2020) Science 369, 1255-1260.

Identification of common deletions in the spike protein of severe acute respiratory syndrome coronavirus 2.

Liu Z, Zheng H, Lin H, Li M, Yuan R, Peng J, Xiong Q, Sun J, Li B, Wu J, Yi L, Peng X, Zhang H, Zhang W, Hulswit RJG, Loman N, Rambaut A, Ke C, Bowden TA, Pybus OG & Lu J (2020) Journal of Virology 94, e00790-20.

Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples by use of nanopore sequencing.

Shaw AG, Majumdar M, Troman C, O'Toole Á, Benny B, Abraham D, Praharaj I, Kang G, Sharif S, Alam MM, Shaukat S, Angez M, Khurshid A, Mahmood N, Arshad Y, Rehman L, Mujtaba G, Akthar R, Salman M, Klapsa D, Hajarha Y, Asghar H, Bandyopadhyay A, Rambaut A, Martin J & Grassly N (2020) Journal of Clinical Microbiology 58, e00920.

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands.

Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M, Oudehuis GJAPM, Schinkel J, Kluytmans J, Kluytmans-van den Bergh M, van den Bijllaardt W, Berntvelsen RG, van Rijen MML, Schneeberger P, Pas S, Diederen BM, Bergmans AMC, van der Eijk PAV, Verweij J, Buiting AGN, Streefkerk R, Aldenkamp AP, de Man P, Koelemal JGM, Ong D, Paltansing S, Veassen N, Sleven J, Bakker L, Brockhoff H, Rietveld A, Slijkerman Megelink F, Cohen Stuart J, de Vries A, van der Reijden W, Ros A, Lodder E, Verspui-van der Eijk E, Huijskens I, Kraan EM, van der Linden MPM, Debast SB, Naiemi NA, Kroes ACM, Damen M, Dinant S, Lekkerkerk S, Pontesilli O, Smit P, van Tienen C, Godschalk PCR, van Pelt J, Ott A, van der Weijden C, Wertheim H, Rahamat-Langendoen J, Reimerink J, Bodewes R, Duizer E, van der Veer B, Reusken C, Lutgens S, Schneeberger P, Hermans M, Wever P, Leenders A, ter Waarbeek H, Hoebe C & The Dutch-Covid-19 response team (2020) Nature Medicine 26, 1405-1410.

Temporal signal and the phylodynamic threshold of SARS-CoV-2.

Duchene S, Featherstone L, Haritopoulou-Sinanidou M, Rambaut A, Lemey P & Baele G (2020) Virus Evolution 6, veaa061.

Determinants of dengue virus dispersal in the americas.

Allicock OM, Sahadeo N, Lemey P, Auguste AJ, Suchard MA, Rambaut A & Carrington CVF (2020) Virus Evolution 6, veaa074.

Online bayesian phylodynamic inference in BEAST with application to epidemic reconstruction.

Gill MS, Lemey P, Suchard MA, Rambaut A & Baele G (2020) Molecular Biology and Evolution 37, 1832-1842.

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.

Lu J, du Plessis L, Liu Z, Hill V, Kang M, Lin H, Sun J, François S, Kraemer MUG, Faria NR, McCrone JT, Peng J, Xiong Q, Yuan R, Zeng L, Zhou P, Liang C, Yi L, Liu J, Xiao J, Hu J, Liu T, Ma W, Li W, Su J, Zheng H, Peng B, Fang S, Su W, Li K, Sun R, Bai R, Tang X, Liang M, Quick J, Song T, Rambaut A, Loman N, Raghwani J, Pybus OG & Ke C (2020) Cell 181, 997-1003.

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.

Ratmann O, Kagaayi J, Hall M, Golubchick T, Kigozi G, Xi X, Wymant C, Nakigozi G, Abeler-D?rner L, Bonsall D, Gall A, Hoppe A, Kellam P, Bazaale J, Kalibbala S, Laeyendecker O, Lessler J, Nalugoda F, Chang LW, de Oliveira T, Pillay D, Quinn TC, Reynolds SJ, Spencer SEF, Ssekubugu R, Serwadda D, Wawer MJ, Gray RH, Fraser C, Grabowski MK, Ayles H, Bowden R, Calvez V, Cohen M, Dennis A, Essex M, Fidler S, Frampton D, Hayes R, Herbeck J, Kaleebu P, Kityo C, Lingappa J, Novitsky V, Paton N, Rambaut A, Seeley J, Ssemwanga D, Tanser F, Lutalo T, Galiwango R, Makumbi F, Sewankambo NK, Nabukalu D, Ndyanabo A, Ssekasanvu J, Nakawooya H, Nakukumba J, Kigozi GN, Nantume BS, Resty N, Kambasu J, Nalugemwa M, Nakabuye R, Ssebanobe L, Nankinga J, Kayiira A, Nanfuka G, Ahimbisibwe R, Tomusange S, Galiwango RM, Nakalanzi M, Otobi JO, Ankunda D, Ssembatya JL, Ssemanda JB, Kato E, Kairania R, Kisakye A, Batte J, Ludigo J, Nampijja A, Watya S, Nehemia K, Anyokot SM, Mwinike J, Kibumba G, Ssebowa P, Mondo G, Wasswa F, Nantongo A, Kakembo R, Galiwango J, Ssemango G, Redd AD, Santelli J, Kennedy CE, Wagman J, Tobian A & Rakai Health Sciences Program and the Pangea HIV Consortium (2020) The Lancet HIV 7, e173-e183.

Importation and early local transmission of covid-19 in brazil, 2020.

de Jesus JG, Sacchi C, Candido DDS, Claro IM, Sales FCS, Manuli ER, da Silva DBB, de Paiva TM, Pinho MAB, Santos KCO, Hill SC, Aguiar RS, Romero F, Dos Santos FCP, Gon?alves CR, Timenetsky MDC, Quick J, Croda JHR, de Oliveira W, Rambaut A, Pybus OG, Loman NJ, Sabino EC & Faria NR (2020) Revista do Instituto de Medicina Tropical de Sao Paulo 62, e30.

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020.

Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D & The WHO European Region sequencing laboratories and GISAID EpiCoV group (2020) Eurosurveillance 25, 2001410.

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-D?rner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, Ayles H, Bowden R, Calvez V, Cohen M, Dennis A, Essex M, Fidler S, Frampton D, Hayes R, Herbeck JT, Kaleebu P, Kityo C, Lingappa J, Novitsky V, Paton N, Rambaut A, Seeley J, Ssemwanga D, Tanser F, Nakigozi G, Ssekubugu R, Nalugoda F, Lutalo T, Galiwango R, Makumbi F, Sewankambo NK, R?Tobian AA, Reynolds SJ, Chang LW, Nabukalu D, Ndyanabo A, Ssekasanvu J, Nakawooya H, Nakukumba J, Kigozi GN, Nantume BS, Resty N, Kambasu J, Nalugemwa M, Nakabuye R, Ssebanobe L, Nankinga J, Kayiira A, Nanfuka G, Ahimbisibwe R, Tomusange S, Galiwango RM, Kalibbali S, Nakalanzi M, Otobi JO, Ankunda D, Ssembatya JL, Ssemanda JB, Kairania R, Kato E, Kisakye A, Batte J, Ludigo J, Nampijja A, Watya S, Nehemia K, Anyokot M, Sr, Mwinike J, Kibumba G, Ssebowa P, Mondo G, Wasswa F, Nantongo A, Kakembo R, Galiwango J, Ssemango G, Redd AD, Santelli J, Kennedy CE, Wagman J & PANGEA Consortium and Rakai Health Sciences Program (2019) Nature Communications 10, 1411.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A & Suchard MA (2019) Systematic Biology 68, 1052-1061.

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates.

Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P & Thorne J (2019) Molecular Biology and Evolution 36, 1793-1803.

PANGEA-HIV 2: Phylogenetics and Networks for Generalised Epidemics in Africa.

Abeler-Dörner L, Grabowski MK, Rambaut A, Pillay D & Fraser C (2019) Current Opinion in HIV and AIDS 14, 173-180.

SANTA-SIM: Simulating viral sequence evolution dynamics under selection and recombination.

Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen FA, IV & Theys K (2019) Virus Evolution 5, vez003.

Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building.

Nelson MI, Lloyd-Smith JO, Simonsen L, Rambaut A, Holmes EC, Chowell G, Miller MA, Spiro DJ, Grenfell B & Viboud C (2019) Epidemics 26, 116-127.

High-performance computing in bayesian phylogenetics and phylodynamics using BEAGLE.

Baele G, Ayres DL, Rambaut A, Suchard MA & Lemey P (2019) Methods in Molecular Biology 1910, 691-722.

Tracking virus outbreaks in the twenty-first century.

Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC & Andersen KG (2019) Nature Microbiology 4, 44488.

Metagenomic next-generation sequencing of the 2014 ebola virus disease outbreak in the democratic republic of the Congo.

Li T, Mbala-Kingebeni P, Naccache SN, Th?z? J, Bouquet J, Federman S, Somasekar S, Yu G, Martin CS-S, Achari A, Schneider BS, Rimoin AW, Rambaut A, Nsio J, Mulembakani P, Ahuka-Mundeke S, Kapetshi J, Pybus OG, Muyembe-Tamfum J-J & Chiu CY (2019) Journal of Clinical Microbiology 57, e00827-19.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Bouckaert R, Vaughan TG, Barido-Sottani J, Duch?ne S, Fourment M, Gavryushkina A, Heled J, Jones G, K?hnert D, De Maio N, Matschiner M, Mendes FK, M?ller NF, Ogilvie HA, Du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu C-H, Xie D, Zhang C, Stadler T & Drummond AJ (2019) PLoS Computational Biology 15, e1006650.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak.

Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A & Lemey P (2018) Nature Communications 9, 2222.

Posterior summarization in Bayesian phylogenetics using Tracer 1.7.

Rambaut A, Drummond AJ, Xie D, Baele G & Suchard MA (2018) Systematic Biology 67, 901-904.

Pandemics: Spend on surveillance, not prediction comment.

Holmes EC, Rambaut A & Andersen KG (2018) Nature 558, 180-182.

Erratum: Correction: MERS-CoV spillover at the camel-human interface (eLife (2018) 7 PII: e37324).

Dudas G, Carvalho LM, Rambaut A & Bedford T (2018) eLife 7

MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity.

Chu DKW, Hui KPY, Perera RAPM, Miguel E, Niemeyer D, Zhao J, Channappanavar R, Dudas G, Oladipo JO, Traor? A, Fassi-Fihri O, Ali A, Demissi? GF, Muth D, Chan MCW, Nicholls JM, Meyerholz DK, Kuranga SA, Mamo G, Zhou Z, So RTY, Hemida MG, Webby RJ, Roger F, Rambaut A, Poon LLM, Perlman S, Drosten C, Chevalier V & Peiris M (2018) Proceedings of the National Academy of Sciences of the United States of America 115, 3144-3149.

Detection and characterization of homologues of human hepatitis viruses and pegiviruses in rodents and bats in Vietnam.

Van Nguyen D, Van Nguyen C, Bonsall D, Ngo TT, Carrique-Mas J, Pham AH, Bryant JE, Thwaites G, Baker S, Woolhouse M, Simmonds P, Kiet BT, Berto A, Boni MF, Bryant JE, Phu BD, Campbell JI, Hung DM, Huong DT, Oanh DT, Day JN, Tan DV, van Doorn HR, Han DA, Farrar JJ, Trang HTT, Nghia HDT, Long HB, Duong HV, Thu HTK, Cuong LC, Hung LM, Phuong LT, Phuc LT, Phuong LT, Luat LX, Ha LTT, Chuong LV, Loan MTP, Nadjm B, Bao NT, Hoa NT, Tue NT, Tu NC, Thuan ND, Dong N, Chuyen NK, An NN, Vinh NN, Hung NQ, Dung NT, Minh NT, Binh NT, Tham NTH, Tien NTH, Chuc NTK, Ngoc NTL, Ha NTL, Lien NTN, Diep NTN, Nhung NT, Chau NTS, Chi NTY, Trinh NT, Van NT, Cuong NV, Hung NV, Kinh NV, Hoang NVM, My NV, Thang NV, Thanh NV, Chau NVV, Xang NV, My PH, Anh PH, Khoa PTM, Tam PTT, Lao PV, Minh PV, Bay PVB, Rabaa MA, Rahman M, Thompson C, Ngan TTD, Nhu TDH, Chau THM, Toan TK, Phuc TM, Hong TTK, Dung TTN, Thanh TTT, Minh TTT, Nguyen TT, Hien TT, Tri TQ, Hien VB, Tai VN, Cuong VQ, Phat VV, Huong VTL, Hang VTT, Wertheim H, Bogaardt C, Brierley L, Chase-Topping M, Ivens A, Lu L, Nguyen D, Rambaut A, Cotten M, Munnink BBO, Kellam P, Phan MVT, van der Hoek L, Deijs M, Jebbink MF, Farsani SMJ, Saylors K & Wolfe N (2018) Viruses 10, 102.

Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs.

Berto A, Pham HA, Thao TTN, Vy NHT, Caddy SL, Hiraide R, Tue NT, Goodfellow I, Carrique-Mas JJ, Thwaites GE, Baker S, Boni MF, the VIZIONS consortium, Kiet BT, Bryant JE, Phu BD, Campbell JI, Hung DM, Huong DT, Oanh DT, Day JN, Van Tan D, van Doorn HR, Han DA, Farrar JJ, Trang HTT, Nghia HDT, Long HB, Van Duong H, Thu HTK, Cuong LC, Hung M, Phuong T, Phuc T, Phuong T, Luat X, Ha LTT, Van Chuong L, Loan MTP, Nadjm B, Bao NT, Hoa NT, Tu NC, Thuan ND, Dong N, Chuyen NK, An NN, Vinh NN, Hung NQ, Dung NT, Minh NT, Binh NT, Tham NTH, Tien NTH, Chuc NTK, Le Ngoc NT, Ha NTL, Lien NTN, Diep NTN, Nhung NT, Chau NTS, Chi NTY, Trinh NT, Van NT, Van Cuong N, Van Hung N, Van Kinh N, Van Minh Hoang N, Van My N, Van Thang N, Van Thanh N, Van Vinh Chau N, Van Xang N, My PH, Khoa PTM, Tam PTT, Van Lao P, Van Minh P, Van Be Bay P, Rabaa MA, Rahman M, Thompson C, Ngan TTD, Nhu TDH, Chau THM, Toan TK, Phuc TM, Hong TTK, Dung TTN, Thanh TTT, Minh TTT, Nguyen TT, Hien TT, Tri TQ, Hien VB, Tai VN, Cuong VQ, Phat VV, Huong VTL, Hang VTT, Wertheim H, Bogaardt C, Chase-Topping M, Ivens A, Lu L, Ngyuen D, Rambaut A, Simmonds P, Woolhouse M, Cotten M, Oude Munnink BB, Kellam P, Phan MVT, van der Hoek L, Deijs M, Jebbink MF, Farsani SMJ, Saylors K & Wolfe N (2018) Zoonoses and Public Health 65, 43-50.

Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam.

Berto A, Anh PH, Carrique-Mas JJ, Simmonds P, Van Cuong N, Tue NT, Van Dung N, Woolhouse ME, Smith I, Marsh GA, Bryant JE, Thwaites GE, Baker S, Rabaa MA, the VIZIONS consortium, Kiet BT, Boni MF, Phu BD, Campbell JI, Hung DM, Huong DT, Oanh DT, Day JN, Van Tan D, van Doorn HR, Han DA, Farrar JJ, Trang HTT, Nghia HDT, Long HB, Van Duong H, Thu HTK, Cuong LC, Hung M, Phuong T, Phuc T, Phuong T, Luat X, Ha LTT, Van Chuong L, Loan MTP, Nadjm B, Bao NT, Tu NC, Thuan ND, Dong N, Chuyen NK, An NN, Vinh NN, Hung NQ, Dung NT, Minh NT, Binh NT, Tham NTH, Tien NTH, Chuc NTK, Le Ngoc NT, Ha NTL, Lien NTN, Diep NTN, Nhung NT, Chau NTS, Chi NTY, Trinh NT, Van NT, Van Hung N, Van Kinh N, Van Minh Hoang N, Van My N, Van Thang N, Van Thanh N, Van Vinh Chau N, Van Xang N, My PH, Khoa PTM, Tam PTT, Van Lao P, Van Minh P, Van Be Bay P, Rahman M, Thompson C, Ngan TTD, Nhu TDH, Chau THM, Toan TK, Phuc TM, Hong TTK, Dung TTN, Thanh TTT, Minh TTT, Nguyen TT, Hien TT, Tri TQ, Hien VB, Tai VN, Cuong VQ, Phat VV, Huong VTL, Hang VTT, Wertheim H, Bogaardt C, Brierley L, Chase-Topping M, Ivens A, Lu L, Rambaut A, Woolhouse M, Cotten M, Oude Munnink BB, Kellam P, Phan MVT, van der Hoek L, Deijs M, Jebbink MF, Farsani SMJ, Saylors K & Wolfe N (2018) Zoonoses and Public Health 65, 30-42.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P & Suchard MA (2018) Statistics in Medicine 37, 195-206.

Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors.

Whitmer SLM, Ladner JT, Wiley MR, Patel K, Dudas G, Rambaut A, Sahr F, Prieto K, Shepard SS, Carmody E, Knust B, Naidoo D, Deen G, Formenty P, Nichol ST, Palacios G, Str?her U & Ebola Virus Persistence Study Group (2018) Cell Reports 22, 1159-1168.

MERS-CoV spillover at the camel-human interface.

Dudas G, Carvalho LM, Rambaut A & Bedford T (2018) eLife 7, e31257.

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Faria NR, Quick J, Morales I, Theze J, ..., Rambaut A, Bedford T, ..., Loman N. & Pybus OG (2017) Nature 546, 406-410.

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, ..., Rambaut A, ..., Bedford T, Pybus OG, Isern S, Palacios GF & Andersen KG (2017) Nature 546, 401-405.

Genome sequencing reveals Zika virus diversity and spread in the Americas.

Metsky HC, Matranga CB, Wohl S, Schaffner SF, ..., Rambaut A, ..., Yozwiak NL, MacInnis BL & Sabeti PC (2017) Nature 546, 411?415.

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, ..., Suchard MA, Lemey P & Rambaut A (2017) Nature 2017/04/12/online

Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P & Watson SJ (2017) PLoS pathogens 13, e1006749.

Emerging concepts of data integration in pathogen phylodynamics.

Baele G, Suchard MA, Rambaut A & Lemey P (2017) Systematic Biology 66, e47-e65.

Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam [version 1; referees: 2 approved].

Thi Ty Hang V, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, Thao Huong D, Dang Trung Nghia H, Tran Anh Vu N, Thi Hong Phuong P, Van Xang N, Dong N, Nhu Hiep P, Van Hung N, Tinh Hien T, Rabaa M, Thwaites GE, Baker S, Van Tan L, van Doorn HR, Berto A, Boni MF, Bryant JE, Phu BD, Campbell JI, Carrique-Mas J, Hung DM, Huong DT, Oanh DT, Day JN, Tan DV, Han DA, Farrar JJ, Trang HTT, Long HB, Duong HV, Thu HTK, Cuong LC, Hung LM, Phuong LT, Phuc LT, Phuong LT, Luat LX, Ha LTT, Chuong LV, Loan MTP, Nadjm B, Bao NT, Hoa NT, Tue NT, Tu NC, Thuan ND, Chuyen NK, An NN, Vinh NN, Hung NQ, Dung NT, Minh NT, Binh NT, Tham NTH, Tien NTH, Chuc NTK, Ngoc NTL, Ha NTL, Lien NTN, Diep NTN, Nhung NT, Chau NTS, Chi NTY, Trinh NT, Van NT, Van Cuong N, Van Kinh NV, Van Minh Hoang N, Van My N, Van Thang N, Van Thanh N, Van Vinh Chau N, Ha My P, Hong Anh P, Thi Minh Khoa P, Van Lao PV, Van Minh P, Van Be Bay P, Rahman M, Thompson C, Thi Dieu Ngan TTD, Do Hoang Nhu T, Hoang Minh Chau THM, Toan TK, Thi Kim Hong T, Thi Ngoc Dung T, Thi Thanh Thanh T, Thi Thuy Minh T, Thua Nguyen TT, Tri TQ, Be Hien V, Tai VN, Cuong VQ, Phat VV, Wertheim H, Bogaardt C, Chase-Topping M, Ivens A, Lu L, Nyugen D, Rambaut A, Simmonds P, Woolhouse M, Cotten M, Oude Munnink BB, Kellam P, Tra Phan MVT, Deijs M, van der Hoek L, Jebbink MF, Farsani SMJ, Saylors K, Wolfe N & VIZIONS consortium (2017) Wellcome Open Research 2, 80.

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.

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.

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.

Reduced evolutionary rate in reemerged Ebola virus transmission chains.

Blackley DJ, Michael R. Wiley, Jason T. Ladner, Mosoka Fallah, Terrence Lo, Merle L. Gilbert, Christopher Gregory, Jonathan D?ambrozio, Stewart Coulter, Suzanne Mate, Zephaniah Balogun, Jeffrey Kugelman, William Nwachukwu, Karla Prieto, Adolphus Yeiah, Fred Amegashie, Brian Kearney, Meagan Wisniewski, John Saindon, Gary Schroth, Lawrence Fakoli, Joseph W. Diclaro II, Jens H. Kuhn, Lisa E. Hensley, Peter B. Jahrling, Ute Ströher, Stuart T. Nichol, Moses Massaquoi, Francis Kateh, Peter Clement, Alex Gasasira, Fatorma Bolay, Stephan S. Monroe, Rambaut A, Mariano Sanchez-Lockhart, A. Scott Laney, Tolbert Nyenswah, Athalia Christie & Palacios G (2016) Science Advances 2, e1600378.

Persistent HIV-1 replication maintains the tissue reservoir during therapy.

Lorenzo-Redondo R, Fryer HR, Bedford T, Kim E, Archer J, Kosakovsky Pond, SL, Chung Y, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR & Wolinsky SM (2016) Nature 530, 51-56.

MERS-CoV recombination: implications about the reservoir and potential for adaptation.

Dudas G & Rambaut A (2016) Virus Evolution 2, vev023.

Real-time, portable genome sequencing for Ebola surveillance.

Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JHJ, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sánchez Á, Carter LL, Doerrbecker J, Enkirch T, Dorival IG, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallasch E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Racine T, Bello A, Sall AA, Faye O, Faye O, Magassouba NF, Williams CV, Amburgey V Winona L Davis E Gerlach J Washington F Monteil V Jourdain M Bererd M Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P J., Turner D, Pollakis G, Hiscox JA, Matthews DA, Shea MKO, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Wölfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keïta S, Rambaut A, Formenty P, Günther S & Carroll MW (2016) Nature 530, 228-232.

Epidemic history and iatrogenic transmission of blood-borne viruses in mid-20th century Kinshasa .

Hogan C, Iles J, Frost EH, Giroux G, Cassar O, Gessain A, Dion M-J, Ilunga V, Rambaut A, Yengo-ki-Ngimbi A-E, Behets F, Pybus OG & Pépin J (2016) The Journal of Infectious Diseases 214, 353-360.

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

Arias A, Watson SJ, Danny Asogun, Ekaete Alice Tobin, Jia Lu, My V. T. Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno R. Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr Gevao, Daniel Cooper, Matthew Newport, Peter Horby, Jake Dunning, Foday Sahr, Tim Brooks, Andrew J.H. Simpson, Elisabetta Groppelli, Guoying Liu, Nisha Mulakken, Kate Rhodes, James Akpablie, Zabulon Yoti, Margaret Lamunu, Esther Vitto, Patrick Otim, Collins Owilli, Isaac Boateng, Lawrence Okoror, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Ighodalo Yemisis, Donatus Adomeh, Solomon Ehikhiametalor, Patience Akhilomen, Chris Aire, Andreas Kurth, Nicola Cook, Jan Baumann, Martin Gabriel, Roman Wölfel, Antonino Di Caro, Miles W. Carroll, Stephan Günther, John Redd, Dhamari Naidoo, Oliver G. Pybus, Rambaut A, Kellam P, Goodfellow I & Cotten M (2016) Virus Evolution 2, vew016.

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set .

Hall M, Woolhouse M & Rambaut A (2015) PLOS Comput Biol 11, e1004613.

Evolution and Spread of Ebola Virus in Liberia, 2014-2015.

Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, Nagle ER, Beitzel B, Gilbert ML, Fakoli L, Diclaro JW, Schoepp RJ, Fair J, Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A, Sanchez-Lockhart M, Bolay FK, Kugelman JR & Palacios, G (2015) Cell Host and Microbe 18, 659-669.

Relationship between Haemagglutination Inhibition titre and immunity to influenza in ferrets.

Wikramaratna, P & Rambaut A (2015) Vaccine 33, 33, 41, p. 5380-5385.

Lessons from Ebola: improving infectious disease surveillance to inform outbreak management.

Woolhouse M, Rambaut A & Kellam P (2015) Science Translational Medicine 7, 307.

Real-time digital pathogen surveillance - the time is now.

Gardy J, Loman NJ & Rambaut A (2015) Genome Biology 16, 155.

Testing for temporal signal in molecular dating.

Murray G, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A & Welch JJ (2015) Methods in Ecology and Evolution 7, 80?89.

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone.

Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF & Sabeti PC (2015) Cell 161, 1516-1526.

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.

Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman EN, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Capobianchi MR, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CE, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Van Herp M, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Av?i?-?upanc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P & Günther S (2015) Nature 524, 97-101.

Global Migration of Influenza A Viruses in Swine.

Nelson M, Viboud C, Vincent A, Culhane M, Detmer S, Wentworth D, Rambaut A, Suchard MA, Holmes EC & Lemey P (2015) Nature Communications 6, 6696.

Global circulation patterns of seasonal influenza viruses vary with antigenic drift.

Bedford T, Riley S, Barr I, Broor S, Chadha M, Cox N, Daniels R, Gunasekaran C, Hurt A, Kelso A, Klimov A, Lewis N, Li X, McCauley J, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith D, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P & Russell C (2015) Nature 523, 217-220.

An Observational, Laboratory-Based Study of Outbreaks of Middle East Respiratory Syndrome Coronavirus in Jeddah and Riyadh, Kingdom of Saudi Arabia, 2014.

Drosten C, Muth D, Corman VM, Hussain R, Al Masri M, HajOmar W, Landt O, Assiri A, Eckerle I, Al Shangiti A, Al-Tawfig JA, Albarrak A, Zumla A, Rambaut A & Memish ZA (2015) Clinical Infectious Diseases 60, 369-377.

Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1-PB2-HA Gene Complex.

Dudas G, Bedford T, Lycett S & Rambaut A (2015) Mol Biol Evol 32, 162-172.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: Applications to viral and host phenotypic evolution.

Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF & Suchard MA (2015) Methods in Ecology and Evolution 6, 67-82.

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 345, 1369-1372.

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.

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 7, 28-34.

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.

Multiple introductions of Salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture.

Karlsen M, Gjerset B, Hansen T & Rambaut A (2013) J Gen Virol 95, 52-59.

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.

Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection.

Drosten C, Seilmaier M, Corman VM, Hartmann W, Scheible G, Sack S, Guggemos W, Kallies R, Muth D, Junglen S, Müller MA, Haas W, Guberina H, Röhnisch T, Schmid-Wendtner M, Aldabbagh S, Dittmer U, Gold H, Graf P, Bonin F, Rambaut A & Wendtner C-M (2013) The Lancet Infectious Diseases 13, 745-751.

Real-time characterization of the molecular epidemiology of an influenza pandemic.

Hedge J, Lycett SJ & Rambaut A (2013) Biology Letters 9

Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.

Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A, Guan Y, Pillay D, Kellam P & Nastouli E (2013) Emerg Infect Dis 19, 736-742.

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.

Faria NR, Suchard MA, Rambaut A, Streicker DG & Lemey P (2013) Phil Trans Royal Soc B 368, 20120196.

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.

Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B & Suchard MA (2013) Mol Biol Evol 30, 713-724.

Unifying the spatial epidemiology and evolution of emerging epidemics.

Pybus OG, Suchard MA, Lemey P, Bernardin FJ, Rambaut A, Crawford FW, Gray RR, Arinaminpathy N, Stramer S, Busch MP & Delwart EL (2012) Proc Natl Acad Sci USA 109, 15066-15071.

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus.

McAdam PR, Templeton KE, Edwards GF, Holden MTG, Feil EJ, Aanensen DM, Bargawi HJA, Spratt BG, Bentley SD, Parkhill J, Enright MC, Holmes A, Girvan EK, Godfrey PA, Feldgarden M, Kearns AM, Rambaut A, Robinson DA & Fitzgerald JR (2012) Proc Natl Acad Sci USA 109, 9107-9112.

Canalization of the evolutionary trajectory of the human influenza virus.

Bedford T, Rambaut A & Pascual M (2012) BMC Biol 10, 38.

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication.

Weinert LA, Welch JJ, Suchard MA, Lemey P, Rambaut A & Fitzgerald JR (2012) Biology Letters 8, 829-832.

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A & Robertson DL (2012) BMC Bioinformatics 13, 47.

APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete "All or Nothing" Phenomenon. .

Armitage AE, Deforche K, Chang C-H, Wee E, Kramer B, Welch JJ, Gerstoft J, Fugger L, McMichael A, Rambaut A & Iversen AKN (2012) PLoS Genetics 8, e1002550.

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.

Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA & Alekseyenko AV (2012) Mol Biol Evol 29, 2157-2167.

Origin and Fate of A/H1N1 Influenza in Scotland during 2009.

Lycett S, McLeish NJ, Robertson C, Carman W, Baillie G, McMenamin J, Rambaut A, Simmonds P, Woolhouse M & Leigh Brown AJ (2012) J Gen Virol 93, 1253-1260.

Phylogeography and Population Dynamics of Dengue Viruses in the Americas.

Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A & Carrington CVF (2012) Mol Biol Evol 29, 1533-1543.

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans.

Bahl J, Nelson MI, Chan KH, Chen RB, Vijaykrishna D, Halpin RA, Stockwell TB, Lin XD, Wentworth DE, Ghedin E, Guan Y, Peiris JSM, Riley S, Rambaut A, Holmes EC & Smith GJD (2011) Proc Natl Acad Sci USA 108, 19359-19364.

The origin and evolution of the unique HCV circulating recombinant form 2k/1b.

Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A & Pybus OG (2012) J Virol 86, 2212-2220.

Toward a quantitative understanding of viral phylogeography.

Faria NR, Suchard MA, Rambaut A & Lemey P (2011) Current Opinion in Virology 1, 423-429.

Evolutionary Dynamics of Local Pandemic H1N1/09 Influenza Lineages Revealed by Whole Genome Analysis.

Baillie G, Galiano M, Agapow P-M, Myers R, Chiam R, Gall A, Palser A, Watson S, Hedge J, Underwood A, Platt S, Mclean E, Pebody R, Rambaut A, Green J, Daniels R, Pybus O & Kellam P and Zambon M (2012) J Virol 86, 11-18.

SPREAD: Spatial phylogenetic reconstruction of evolutionary dynamics.

Bielejec F, Rambaut A, Suchard MA & Lemey P (2011) Bioinformatics 27, 2910-2912.

Evolutionary history of rabies in ghana.

Hayman DT, Johnson N, Horton DL, Hedge J, Wakeley PR, Banyard AC, Zhang S, Alhassan A & Fooks AR (2011) PLoS Negl Trop Dis. 5, e1001.

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

Raghwani J, Rambaut A, Holmes EC, Vu Ty Hang, Tran Tinh Hien, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR & Simmons CP (2011) PLoS Pathog 7, e1002064.

Spatial Dynamics of Human-origin H1 Influenza A Virus in North American Swine.

Nelson MI, Lemey P, Yi Tan, Vincent A, Tsan-Yuk Lam, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC & Gramer M (2011) PLoS Pathog 7, e1002077.

Genomic analysis of Hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation.

Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Sapuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A & Shapiro B (2011) Viruses 3, 83-101.

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach.

Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M & Robertson DL (2010) PLoS Comput Biol 6, e1001022.

A Bayesian phylogenetic method to estimate unknown sequence ages.

Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG & Rambaut A (2010) Mol Biol Evol 28, 879-887.

Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus.

Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Jalal N, Faouzi A, Echevarría JE, Morón SV, Rambaut A, Campiz N, Tatem AJ, Holmes EC & Bourhy H (2010) PLoS Pathog 6, e1001166.

Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation.

Guinane CM, Zakour NLB, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay J, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penades J & Fitzgerald JR (2010) Genome Biology and Evolution 2, 454-466.

Phylodynamic Reconstruction Reveals Norovirus GII. 4 Epidemic Expansions and their Molecular Determinants.

Siebenga JJ, Lemey P, Pond SLK, Rambaut A, Vennema H & Koopmans M (2010) PLoS Pathog 6, e1000884.

Emergence, dominance, and possible decline of CXCR4 infection.

Meehan CJ, Hedge JA, Robertson DL, McCormack GP & Travers SA (2010) J Med Virol 82, 2004-2012.

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, Nübel U, & Fitzgerald JR (2009) Proc Natl Acad Sci USA 106, 19545-19550.

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 Pathog 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.

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.

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) Proc Natl Acad Sci USA 105, E16.

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.

Estimation of 2Nes from temporal allele frequency data.

Bollback JP, York T & Nielsen R (2008) Genetics 179, 497?502.

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.

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 Evol Biol 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) Proc Natl Acad Sci USA 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 Res 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.

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.

Genes under positive selection in Escherichia coli.

Petersen L, Bollback JP, Dimmic M, Hubisz M & Nielsen R (2007) Genome Res 17, 1336-1343.

Clonal interference is alleviated by high mutation rates in large populations.

Bollback JP & Huelsenbeck JP (2007) Mol Biol Evol 24, 1397-1406.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R & Willerslev E (2007) PLoS One 2, e197.

Estimating the history of mutations on a phylogeny.

Bollback JJ, Gardner PP & Nielsen R (2007) In "Ancestral Sequence Reconstruction", Oxford Univ. Press CH. 6, 69-79.

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

Freyhult EK, Bollback JP & Gardner PP (2007) Genome Res 17, 117-125.

Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system.

Reynolds SM, Dryer K, Bollback JP, Uy JAC, Patricelli GL, Robson T, Borgia G & Braun MJ (2007) Auk 124, 857-867.

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.

Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution.

Betancourt AJ & Bollback JP (2006) Curr Opin Genet Dev 16, 618-623.

SIMMAP: stochastic character mapping of discrete traits on phylogenies.

Bollback JP (2006) BMC Bioinformatics 7, 88.

Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil.

Conn JE, Vineis JH, Bollback JP, Onyabe DY, Wilkerson RC & Povoa MM (2006) Am J Trop Med Hyg 74, 798-806.

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.

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.

Posterior mapping and predictive distributions.

Bollback JP (2005) In "Statistical methods in Molecular Evolution", Springer-Verlag

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.

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.

True and false gharials: a nuclear gene phylogeny of crocodylia.

Harshman J, Huddleston CJ, Bollback JP, Parsons TJ & Braun MJ (2003) Syst Biol 52, 386-402.

Stochastic mapping of morphological characters.

Huelsenbeck JP, Nielsen R & Bollback JP (2003) Syst Biol 52, 131-158.

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.

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 the root of a phylogenetic tree.

Huelsenbeck JP, Bollback JP & Levine AM (2002) Syst Biol 51, 32-43.

Bayesian model adequacy and choice in phylogenetics.

Bollback JP (2002) Mol Biol Evol 19, 1171-1180.

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.

Phylogeny and the origin of HIV-1.

Rambaut A, Robertson DL, Pybus OG, Peeters M & Holmes EC (2001) Nature 410, 1047-1048.

Evolutionary rate differences in trypanosomes.

Stevens J & Rambaut A (2001) Infect Genet Evol 1, 143-150.

Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi.

Conn JE, Bollback JP, Onyabe DY, Robinson TN, Wilkerson RC & Povoa MM (2001) Mol Ecol Notes 1, 223-225.

Empirical and hierarchical Bayesian estimation of ancestral states.

Huelsenbeck JP & Bollback JP (2001) Syst Biol 50, 351-366.

Application of the likelihood function in phylogenetic analysis.

Huelsenbeck JP & Bollback JP (2001) In "Handbook of Statistical Genetics", John Wiley and Sons CH. 15, 415-439.

Bayesian inference of phylogeny and its impact on evolutionary biology.

Huelsenbeck JP, Ronquist F, Nielsen R & Bollback JP (2001) Science 294, 2310-2314.

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.

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.

Complete nucleotide sequence and transcriptional analysis of snakehead fish retrovirus.

Hart D, Frerichs GN, Rambaut A & Onions DE (1996) J Virol 70, 3606-3616.

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.