Virus and Pathogen Evolution
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.
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.
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.
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.
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.
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.
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.
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.
 
Andrew Rambaut, 2007