Andrew Rambaut, Ph.D. - Publications

Affiliations: 
Institute of Evolutionary Biology University of Edinburgh, Edinburgh, Scotland, United Kingdom 
Website:
http://tree.bio.ed.ac.uk/

208 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Mbala-Kingebeni P, Pratt C, Mutafali-Ruffin M, Pauthner MG, Bile F, Nkuba-Ndaye A, Black A, Kinganda-Lusamaki E, Faye M, Aziza A, Diagne MM, Mukadi D, White B, Hadfield J, Gangavarapu K, ... ... Rambaut A, et al. Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease. The New England Journal of Medicine. 384: 1240-1247. PMID 33789012 DOI: 10.1056/NEJMoa2024670  0.52
2021 Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, ... ... Rambaut A, et al. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Medrxiv : the Preprint Server For Health Sciences. PMID 33688664 DOI: 10.1101/2021.02.26.21252554  0.64
2021 Dellicour S, Gill MS, Faria NR, Rambaut A, Pybus OG, Suchard MA, Lemey P. Relax, keep walking-a practical guide to continuous phylogeographic inference with BEAST. Molecular Biology and Evolution. PMID 33528560 DOI: 10.1093/molbev/msab031  0.64
2021 Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology. PMID 33514928 DOI: 10.1038/s41564-021-00872-5  0.8
2021 du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, ... ... Rambaut A, et al. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science (New York, N.Y.). PMID 33419936 DOI: 10.1126/science.abf2946  0.64
2020 Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, Rey SM, Nicholls SM, Colquhoun RM, da Silva Filipe A, Shepherd J, ... ... Rambaut A, et al. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell. PMID 33275900 DOI: 10.1016/j.cell.2020.11.020  0.64
2020 Candido DS, Claro IM, de Jesus JG, Souza WM, Moreira FRR, Dellicour S, Mellan TA, du Plessis L, Pereira RHM, Sales FCS, Manuli ER, Thézé J, Almeida L, Menezes MT, Voloch CM, ... ... Rambaut A, et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science (New York, N.Y.). PMID 32703910 DOI: 10.1126/science.abd2161  0.64
2020 Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology. PMID 32669681 DOI: 10.1038/s41564-020-0770-5  0.8
2020 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, ... ... Rambaut A, et al. Identification of common deletions in the spike protein of SARS-CoV-2. Journal of Virology. PMID 32571797 DOI: 10.1128/JVI.00790-20  0.64
2020 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, ... ... Rambaut A, et al. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell. PMID 32359424 DOI: 10.1016/j.cell.2020.04.023  0.64
2020 Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nature Medicine. 26: 450-452. PMID 32284615 DOI: 10.1038/s41591-020-0820-9  0.8
2019 Li T, Mbala-Kingebeni P, Naccache SN, Thézé J, Bouquet J, Federman S, Somasekar S, Yu G, Sanchez-San Martin C, Achari A, Schneider BS, Rimoin AW, Rambaut A, Nsio J, Mulembakani P, et al. Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo. Journal of Clinical Microbiology. PMID 31315955 DOI: 10.1128/JCM.00827-19  0.64
2019 Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG. Tracking virus outbreaks in the twenty-first century. Nature Microbiology. 4: 10-19. PMID 30546099 DOI: 10.1038/s41564-018-0296-2  0.8
2018 Nelson MI, Lloyd-Smith JO, Simonsen L, Rambaut A, Holmes EC, Chowell G, Miller MA, Spiro DJ, Grenfell B, Viboud C. Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building. Epidemics. PMID 30446431 DOI: 10.1016/j.epidem.2018.10.004  0.8
2018 Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nature Communications. 9: 2222. PMID 29884821 DOI: 10.1038/s41467-018-03763-2  0.64
2018 Holmes EC, Rambaut A, Andersen KG. Pandemics: spend on surveillance, not prediction. Nature. 558: 180-182. PMID 29880819 DOI: 10.1038/d41586-018-05373-w  0.8
2018 Dudas G, Carvalho LM, Rambaut A, Bedford T. Correction: MERS-CoV spillover at the camel-human interface. Elife. 7. PMID 29669683 DOI: 10.7554/eLife.37324  0.52
2018 Chu DKW, Hui KPY, Perera RAPM, Miguel E, Niemeyer D, Zhao J, Channappanavar R, Dudas G, Oladipo JO, Traoré A, Fassi-Fihri O, Ali A, Demissié GF, Muth D, Chan MCW, ... ... Rambaut A, et al. MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507189 DOI: 10.1073/pnas.1718769115  0.52
2018 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, et al. Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors. Cell Reports. 22: 1159-1168. PMID 29386105 DOI: 10.1016/j.celrep.2018.01.008  0.52
2018 Dudas G, Carvalho LM, Rambaut A, Bedford T. MERS-CoV spillover at the camel-human interface. Elife. 7. PMID 29336306 DOI: 10.7554/eLife.31257  0.52
2017 Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels R, Russell C, Pybus OG, McCauley J, Kellam P, Watson SJ. Genome-wide evolutionary dynamics of influenza B viruses on a global scale. Plos Pathogens. 13: e1006749. PMID 29284042 DOI: 10.1371/journal.ppat.1006749  0.64
2017 Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Pond SLK, Chung YS, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, et al. Lorenzo-Redondo et al. reply. Nature. 551: E10. PMID 29168807 DOI: 10.1038/nature24635  0.52
2017 Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, ... ... Rambaut A, et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. PMID 28538727 DOI: 10.1038/nature22401  0.8
2017 Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, ... ... Rambaut A, et al. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature. PMID 28538723 DOI: 10.1038/nature22400  0.64
2017 Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, ... ... Rambaut A, et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. PMID 28405027 DOI: 10.1038/nature22040  0.8
2017 Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA. Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza. Statistics in Medicine. PMID 28098392 DOI: 10.1002/sim.7196  0.52
2016 Arias A, Watson SJ, Asogun D, Tobin EA, Lu J, Phan MVT, Jah U, Wadoum REG, Meredith L, Thorne L, Caddy S, Tarawalie A, Langat P, Dudas G, Faria NR, ... ... Rambaut A, et al. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evolution. 2: vew016. PMID 28694998 DOI: 10.1093/ve/vew016  0.64
2016 Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evolution. 2: vew007. PMID 27774300 DOI: 10.1093/ve/vew007  0.64
2016 Dudas G, Rambaut A. MERS-CoV recombination: implications about the reservoir and potential for adaptation. Virus Evolution. 2: vev023. PMID 27774293 DOI: 10.1093/ve/vev023  0.52
2016 Holmes EC, Dudas G, Rambaut A, Andersen KG. The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature. 538: 193-200. PMID 27734858 DOI: 10.1038/nature19790  0.8
2016 Rambaut A, Dudas G, de Carvalho LM, Park DJ, Yozwiak NL, Holmes EC, Andersen KG. Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences". Science (New York, N.Y.). 353: 658. PMID 27516592 DOI: 10.1126/science.aaf3823  1
2016 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. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. Elife. 5. PMID 27350259 DOI: 10.7554/eLife.16777  1
2016 Bourhy H, Nakouné E, Hall M, Nouvellet P, Lepelletier A, Talbi C, Watier L, Holmes EC, Cauchemez S, Lemey P, Donnelly CA, Rambaut A. Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. Plos Pathogens. 12: e1005525. PMID 27058957 DOI: 10.1371/journal.ppat.1005525  1
2016 Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Kosakovsky Pond SL, Chung YS, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature. PMID 26814962 DOI: 10.1038/nature16933  1
2016 Hogan C, Iles J, Frost EH, Giroux G, Cassar O, Gessain A, Dion MJ, Ilunga V, Rambaut A, Yengo-Ki-Ngimbi AÉ, Behets F, Pybus OG, Pépin J. Epidemic history and iatrogenic transmission of blood-borne viruses in mid-20th century Kinshasa. The Journal of Infectious Diseases. PMID 26768251 DOI: 10.1093/infdis/jiw009  1
2015 Hall M, Woolhouse M, Rambaut A. Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. Plos Computational Biology. 11: e1004613. PMID 26717515 DOI: 10.1371/journal.pcbi.1004613  1
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, ... ... Rambaut A, et al. Evolution and Spread of Ebola Virus in Liberia, 2014-2015. Cell Host & Microbe. 18: 659-669. PMID 26651942 DOI: 10.1016/j.chom.2015.11.008  1
2015 Woolhouse ME, Rambaut A, Kellam P. Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management. Science Translational Medicine. 7: 307rv5. PMID 26424572 DOI: 10.1126/scitranslmed.aab0191  1
2015 Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HD, Cuong NV, Pham HA, Berto A, Phat VV, Dung TT, Bao LH, Hoa NT, ... ... Rambaut A, et al. The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases. Ecohealth. PMID 26403795 DOI: 10.1007/s10393-015-1061-0  1
2015 Wikramaratna PS, Rambaut A. Relationship between haemagglutination inhibition titre and immunity to influenza in ferrets. Vaccine. 33: 5380-5. PMID 26342848 DOI: 10.1016/j.vaccine.2015.08.065  1
2015 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, ... ... Rambaut A, et al. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. 161: 1516-26. PMID 26091036 DOI: 10.1016/j.cell.2015.06.007  1
2015 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, et al. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature. PMID 26083749 DOI: 10.1038/nature14594  1
2015 Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, Klimov A, Lewis NS, Li X, McCauley JW, Odagiri T, ... ... Rambaut A, et al. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 523: 217-20. PMID 26053121 DOI: 10.1038/nature14460  1
2015 Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P. Global migration of influenza A viruses in swine. Nature Communications. 6: 6696. PMID 25813399 DOI: 10.1038/ncomms7696  1
2015 Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA. Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution. Methods in Ecology and Evolution / British Ecological Society. 6: 67-82. PMID 25780554 DOI: 10.1111/2041-210X.12293  0.52
2015 Dudas G, Bedford T, Lycett S, Rambaut A. Reassortment between influenza B lineages and the emergence of a coadapted PB1-PB2-HA gene complex. Molecular Biology and Evolution. 32: 162-72. PMID 25323575 DOI: 10.1093/molbev/msu287  0.52
2015 Gardy J, Loman NJ, Rambaut A. Real-time digital pathogen surveillance - the time is now Genome Biology. 16. DOI: 10.1186/s13059-015-0726-x  1
2015 Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ. The effect of genetic structure on molecular dating and tests for temporal signal Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12466  1
2015 Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA. Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: Applications to viral and host phenotypic evolution Methods in Ecology and Evolution. 6: 67-82. DOI: 10.1111/2041-210X.12293  1
2015 Dudas G, Bedford T, Lycett S, Rambaut A. Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1-PB2-HA Gene Complex Molecular Biology and Evolution. 32: 162-172. DOI: 10.1093/molbev/msu287  1
2015 Drosten C, Muth D, Corman VM, Hussain R, Al Masri M, HajOmar W, Landt O, Assiri A, Eckerle I, Al Shangiti A, Al-Tawfiq JA, Albarrak A, Zumla A, Rambaut A, Memish ZA. An observational, laboratory-based study of outbreaks of middle east respiratory syndrome coronavirus in Jeddah and Riyadh, Kingdom of Saudi Arabia, 2014 Clinical Infectious Diseases. 60: 369-377. DOI: 10.1093/cid/ciu812  1
2014 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. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science (New York, N.Y.). 346: 56-61. PMID 25278604 DOI: 10.1126/science.1256739  1
2014 Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, ... ... Rambaut A, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science (New York, N.Y.). 345: 1369-72. PMID 25214632 DOI: 10.1126/science.1259657  1
2014 Jombart T, Aanensen DM, 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, ... ... Rambaut A, et al. OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics. 7: 28-34. PMID 24928667 DOI: 10.1016/j.epidem.2014.04.003  1
2014 Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA. πBUSS: A parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios Bmc Bioinformatics. 15. PMID 24885610 DOI: 10.1186/1471-2105-15-133  1
2014 Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. Plos Currents. 6. PMID 24860690 DOI: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d  0.52
2014 Worobey M, Han GZ, Rambaut A. Genesis and pathogenesis of the 1918 pandemic H1N1 influenza a virus Proceedings of the National Academy of Sciences of the United States of America. 111: 8107-8112. PMID 24778238 DOI: 10.1073/pnas.1324197111  1
2014 Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis Plos Computational Biology. 10. PMID 24722319 DOI: 10.1371/journal.pcbi.1003537  1
2014 Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P. The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates Plos Computational Biology. 10. PMID 24699231 DOI: 10.1371/journal.pcbi.1003505  1
2014 Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: From sequence substitution to phylogeography Systematic Biology. 63: 493-504. PMID 24627184 DOI: 10.1093/sysbio/syu015  1
2014 Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D, Suchard MA. Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. Plos Pathogens. 10: e1003932. PMID 24586153 DOI: 10.1371/journal.ppat.1003932  1
2014 Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, Al Rabeeah AA, Alhakeem RF, Assiri A, Al-Tawfiq JA, Albarrak A, Barry M, Shibl A, Alrabiah FA, Hajjar S, ... ... Rambaut A, et al. Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. Mbio. 5. PMID 24549846 DOI: 10.1128/mBio.01062-13  1
2014 Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A. Integrating influenza antigenic dynamics with molecular evolution. Elife. 3: e01914. PMID 24497547 DOI: 10.7554/eLife.01914  1
2014 Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enouf V, van der Werf S, Ferguson NM. Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. The Lancet. Infectious Diseases. 14: 50-6. PMID 24239323 DOI: 10.1016/S1473-3099(13)70304-9  1
2014 Karlsen M, Gjerset B, Hansen T, Rambaut A. Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture. The Journal of General Virology. 95: 52-9. PMID 24062534 DOI: 10.1099/vir.0.057455-0  1
2014 Armitage AE, Deforche K, Welch JJ, Van Laethem K, Camacho R, Rambaut A, Iversen AKN. Possible footprints of APOBEC3F and/or other APOBEC3 deaminases, but not APOBEC3G, on HIV-1 from patients with acute/early and chronic infections Journal of Virology. 88: 12882-12894. DOI: 10.1128/JVI.01460-14  1
2014 Worobey M, Han GZ, Rambaut A. A synchronized global sweep of the internal genes of modern avian influenza virus Nature. DOI: 10.1038/nature13016  1
2013 Hall MD, Knowles NJ, Wadsworth J, Rambaut A, Woolhouse MEJ. Reconstructing geographical movements and host species transitions of foot-and-mouth disease virus serotype SAT 2 Mbio. 4. PMID 24149511 DOI: 10.1128/mBio.00591-13  1
2013 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, Al-nassir WN, Albarrak A, Flemban H, Balkhy HH, ... ... Rambaut A, et al. Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet. 382: 1993-2002. PMID 24055451 DOI: 10.1016/S0140-6736(13)61887-5  1
2013 Collins S, Rambaut A, Bridgett SJ. Fold or hold: Experimental evolution in vitro Journal of Evolutionary Biology. 26: 2123-2134. PMID 24003997 DOI: 10.1111/jeb.12233  1
2013 Lam TT, Wang J, Shen Y, Zhou B, Duan L, Cheung CL, Ma C, Lycett SJ, Leung CY, Chen X, Li L, Hong W, Chai Y, Zhou L, Liang H, ... ... Rambaut A, et al. The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature. 502: 241-4. PMID 23965623 DOI: 10.1038/nature12515  1
2013 Spoor LE, McAdam PR, Weinert LA, Rambaut A, Hasman H, Aarestrup FM, Kearns AM, Larsen AR, Skov RL, Ross Fitzgerald J. Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus Mbio. 4. PMID 23943757 DOI: 10.1128/mBio.00356-13  1
2013 Hedge J, Lycett SJ, Rambaut A. Real-time characterization of the molecular epidemiology of an influenza pandemic. Biology Letters. 9: 20130331. PMID 23883574 DOI: 10.1098/rsbl.2013.0331  1
2013 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, ... ... Rambaut A, et al. Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection. The Lancet. Infectious Diseases. 13: 745-51. PMID 23782859 DOI: 10.1016/S1473-3099(13)70154-3  1
2013 Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A, Guan Y, Pillay D, Kellam P, Nastouli E. Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerging Infectious Diseases. 19: 736-42B. PMID 23693015 DOI: 10.3201/eid1905.130057  1
2013 Faria NR, Suchard MA, Rambaut A, Streicker DG, Lemey P. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120196. PMID 23382420 DOI: 10.1098/rstb.2012.0196  1
2013 Pybus OG, Fraser C, Rambaut A. Evolutionary epidemiology: preparing for an age of genomic plenty. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120193. PMID 23382418 DOI: 10.1098/rstb.2012.0193  1
2013 Ward MJ, Lycett SJ, Kalish ML, Rambaut A, Leigh Brown AJ. Estimating the rate of intersubtype recombination in early HIV-1 group M strains. Journal of Virology. 87: 1967-73. PMID 23236072 DOI: 10.1128/JVI.02478-12  1
2013 Thomas JA, Trueman JW, Rambaut A, Welch JJ. Relaxed phylogenetics and the palaeoptera problem: resolving deep ancestral splits in the insect phylogeny. Systematic Biology. 62: 285-97. PMID 23220768 DOI: 10.1093/sysbio/sys093  1
2013 Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Molecular Biology and Evolution. 30: 713-24. PMID 23180580 DOI: 10.1093/molbev/mss265  1
2012 Pybus OG, Suchard MA, Lemey P, Bernardin FJ, Rambaut A, Crawford FW, Gray RR, Arinaminpathy N, Stramer SL, Busch MP, Delwart EL. Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proceedings of the National Academy of Sciences of the United States of America. 109: 15066-71. PMID 22927414 DOI: 10.1073/pnas.1206598109  1
2012 Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM. Estimating divergence dates and substitution rates in the Drosophila phylogeny. Molecular Biology and Evolution. 29: 3459-73. PMID 22683811 DOI: 10.1093/molbev/mss150  1
2012 Weinert LA, Welch JJ, Suchard MA, Lemey P, Rambaut A, Fitzgerald JR. Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication Biology Letters. 8: 829-832. PMID 22628096 DOI: 10.1098/rsbl.2012.0290  1
2012 McAdam PR, Templeton KE, Edwards GF, Holden MT, Feil EJ, Aanensen DM, Bargawi HJ, Spratt BG, Bentley SD, Parkhill J, Enright MC, Holmes A, Girvan EK, Godfrey PA, Feldgarden M, ... ... Rambaut A, et al. Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proceedings of the National Academy of Sciences of the United States of America. 109: 9107-12. PMID 22586109 DOI: 10.1073/pnas.1202869109  1
2012 Bedford T, Rambaut A, Pascual M. Canalization of the evolutionary trajectory of the human influenza virus. Bmc Biology. 10: 38. PMID 22546494 DOI: 10.1186/1741-7007-10-38  1
2012 Armitage AE, Deforche K, Chang CH, Wee E, Kramer B, Welch JJ, Gerstoft J, Fugger L, McMichael A, Rambaut A, Iversen AK. APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon. Plos Genetics. 8: e1002550. PMID 22457633 DOI: 10.1371/journal.pgen.1002550  1
2012 Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, Robertson DL. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. Bmc Bioinformatics. 13: 47. PMID 22443413 DOI: 10.1186/1471-2105-13-47  1
2012 Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Molecular Biology and Evolution. 29: 2157-67. PMID 22403239 DOI: 10.1093/molbev/mss084  1
2012 Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology and Evolution. 29: 1969-1973. PMID 22367748 DOI: 10.1093/molbev/mss075  1
2012 Lycett S, Mcleish NJ, Robertson C, Carman W, Baillie G, McMenamin J, Rambaut A, Simmonds P, Woolhouse M, Leigh Brown AJ. Origin and fate of A/H1N1 influenza in scotland during 2009 Journal of General Virology. 93: 1253-1260. PMID 22337637 DOI: 10.1099/vir.0.039370-0  1
2012 Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CVF. Phylogeography and population dynamics of dengue viruses in the Americas Molecular Biology and Evolution. 29: 1533-1543. PMID 22319149 DOI: 10.1093/molbev/msr320  1
2012 Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A, Pybus OG. Origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b Journal of Virology. 86: 2212-2220. PMID 22114341 DOI: 10.1128/JVI.06184-11  1
2012 Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, Palser AL, Watson SJ, Hedge J, Underwood A, Platt S, McLean E, Pebody RG, Rambaut A, Green J, et al. Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis. Journal of Virology. 86: 11-8. PMID 22013031 DOI: 10.1128/JVI.05347-11  1
2012 Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology. 61: 170-3. PMID 21963610 DOI: 10.1093/sysbio/syr100  1
2011 Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography Current Opinion in Virology. 1: 423-429. PMID 22440846 DOI: 10.1016/j.coviro.2011.10.003  1
2011 Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris JSM, Riley S, Rambaut A, Holmes EC, et al. Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans Proceedings of the National Academy of Sciences of the United States of America. 108: 19359-19364. PMID 22084096 DOI: 10.1073/pnas.1109314108  1
2011 Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: Spatial phylogenetic reconstruction of evolutionary dynamics Bioinformatics. 27: 2910-2912. PMID 21911333 DOI: 10.1093/bioinformatics/btr481  1
2011 Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Supuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A, Shapiro B. Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses. 3: 83-101. PMID 21765983 DOI: 10.3390/v3020083  1
2011 Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, et al. Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology : Cb. 21: 1251-8. PMID 21737280 DOI: 10.1016/j.cub.2011.05.058  1
2011 Nelson MI, Lemey P, Tan Y, Vincent A, LamTommy TTY, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC, Gramer M. Spatial dynamics of human-origin H1 influenza a virus in north american swine Plos Pathogens. 7. PMID 21695237 DOI: 10.1371/journal.ppat.1002077  1
2011 Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP. Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission Plos Pathogens. 7. PMID 21655108 DOI: 10.1371/journal.ppat.1002064  1
2011 Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A bayesian phylogenetic method to estimate unknown sequence ages Molecular Biology and Evolution. 28: 879-887. PMID 20889726 DOI: 10.1093/molbev/msq262  1
2010 Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL. The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. Plos Computational Biology. 6: e1001022. PMID 21187908 DOI: 10.1371/journal.pcbi.1001022  1
2010 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. Phylodynamics and Human-mediated dispersal of a zoonotic virus Plos Pathogens. 6. PMID 21060816 DOI: 10.1371/journal.ppat.1001166  1
2010 Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay JA, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penadés JR, et al. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution. 2: 454-66. PMID 20624747 DOI: 10.1093/gbe/evq031  1
2010 Siebenga JJ, Lemey P, Kosakovsky Pond SL, Rambaut A, Vennema H, Koopmans M. Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. Plos Pathogens. 6. PMID 20463813 DOI: 10.1371/journal.ppat.1000884  1
2010 Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses Molecular Biology and Evolution. 27: 2038-2051. PMID 20363828 DOI: 10.1093/molbev/msq088  1
2010 Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time Molecular Biology and Evolution. 27: 1877-1885. PMID 20203288 DOI: 10.1093/molbev/msq067  1
2009 Lowder BV, Guinane CM, Ben Zakour NL, Weinert LA, Conway-Morris A, Cartwright RA, Simpson AJ, Rambaut A, Nübel U, Fitzgerald JR. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proceedings of the National Academy of Sciences of the United States of America. 106: 19545-50. PMID 19884497 DOI: 10.1073/pnas.0909285106  1
2009 Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots Plos Computational Biology. 5. PMID 19779555 DOI: 10.1371/journal.pcbi.1000520  1
2009 Pybus OG, Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease Nature Reviews Genetics. 10: 540-550. PMID 19564871 DOI: 10.1038/nrg2583  1
2009 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. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic Nature. 459: 1122-1125. PMID 19516283 DOI: 10.1038/nature08182  1
2009 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, et al. Pandemic potential of a strain of influenza A (H1N1): early findings. Science (New York, N.Y.). 324: 1557-61. PMID 19433588 DOI: 10.1126/science.1176062  1
2009 Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics Bioinformatics. 25: 1370-1376. PMID 19369496 DOI: 10.1093/bioinformatics/btp244  1
2009 Rambaut A, Ho SYW, Drummond AJ, Shapiro B. Accommodating the effect of ancient DNA damage on inferences of demographic histories Molecular Biology and Evolution. 26: 245-248. PMID 19001634 DOI: 10.1093/molbev/msn256  1
2009 Belshaw R, de Oliveira T, Markowitz S, Rambaut A. The RNA Virus Database Nucleic Acids Research. 37: D431-D435. PMID 18948277 DOI: 10.1093/nar/gkn729  1
2009 Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A, Leigh Brown AJ. Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom Plos Pathogens. 5. DOI: 10.1371/journal.ppat.1000590  1
2009 Lemey P, Suchard M, Rambaut A. Reconstructing the initial global spread of a human influenza pandemic Plos Currents. DOI: 10.1371/currents.RRN1031  1
2009 Rambaut A, Holmes E. The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic Plos Currents. DOI: 10.1371/currents.RRN1003  1
2009 Christophe Fraser, Christl AD, 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, et al. Response Science. 325: 1072-1073.  1
2008 Armitage AE, Katzourakis A, De Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AKN. Conserved footprints of APOBEC3G on hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences Journal of Virology. 82: 8743-8761. PMID 18562517 DOI: 10.1128/JVI.00584-08  1
2008 Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus Nature. 453: 615-619. PMID 18418375 DOI: 10.1038/nature06945  1
2008 Remold SK, Rambaut A, Turner PE. Evolutionary genomics of host adaptation in vesicular stomatitis virus. Molecular Biology and Evolution. 25: 1138-47. PMID 18353798 DOI: 10.1093/molbev/msn059  1
2008 Lewis F, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ. Episodic sexual transmission of HIV revealed by molecular phylodynamics Plos Medicine. 5: 0392-0402. PMID 18351795 DOI: 10.1371/journal.pmed.0050050  1
2008 Worobey M, Pitchenik AE, Gilbert MTP, Wlasiuk G, Rambaut A. Reply to Pape et al.: The phylogeography of HIV-1 group M subtype B Proceedings of the National Academy of Sciences of the United States of America. 105: E16. PMID 18337514 DOI: 10.1073/pnas.0712128105  1
2008 Belshaw R, Gardner A, Rambaut A, Pybus OG. Pacing a small cage: mutation and RNA viruses Trends in Ecology and Evolution. 23: 188-193. PMID 18295930 DOI: 10.1016/j.tree.2007.11.010  1
2008 Wilson AJ, Rambaut A. Breeding racehorses: what price good genes? Biology Letters. 4: 173-5. PMID 18089517 DOI: 10.1098/rsbl.2007.0588  1
2008 Deforche K, Camacho R, Van laethem K, Lemey P, Rambaut A, Moreau Y, Vandamme AM. Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment Bioinformatics. 24: 34-41. PMID 18024973 DOI: 10.1093/bioinformatics/btm540  1
2008 Parker J, Rambaut A, Pybus OG. Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty Infection, Genetics and Evolution. 8: 239-246. PMID 17921073 DOI: 10.1016/j.meegid.2007.08.001  1
2007 Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees Bmc Evolutionary Biology. 7. PMID 17996036 DOI: 10.1186/1471-2148-7-214  1
2007 Deforche K, Camacho R, Laethem KV, Shapiro B, Moreau Y, Rambaut A, Vandamme AM, Lemey P. Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo Journal of Computational Biology. 14: 1105-1114. PMID 17985990 DOI: 10.1089/cmb.2007.0073  1
2007 Gilbert MTP, Rambaut A, Wlasiuk G, Spira TJ, Pitchenik AE, Worobey M. The emergence of HIV/AIDS in the Americas and beyond Proceedings of the National Academy of Sciences of the United States of America. 104: 18566-18570. PMID 17978186 DOI: 10.1073/pnas.0705329104  1
2007 Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. Journal of Virology. 81: 13050-6. PMID 17898057 DOI: 10.1128/JVI.00889-07  1
2007 Pillay D, Rambaut A, Geretti AM, Brown AJL. HIV phylogenetics British Medical Journal. 335: 460-461. PMID 17823148 DOI: 10.1136/bmj.39315.398843.BE  1
2007 Belshaw R, Pybus OG, Rambaut A. The evolution of genome compression and genomic novelty in RNA viruses Genome Research. 17: 1496-1504. PMID 17785537 DOI: 10.1101/gr.6305707  1
2007 Abecasis AB, Lemey P, Vidal N, De Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM. Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form Journal of Virology. 81: 8543-8551. PMID 17553886 DOI: 10.1128/JVI.00463-07  1
2007 Davis PL, Rambaut A, Bourhy H, Holmes EC. The evolutionary dynamics of canid and mongoose rabies virus in southern Africa Archives of Virology. 152: 1251-1258. PMID 17401615 DOI: 10.1007/s00705-007-0962-9  1
2007 Ho SY, Heupink TH, Rambaut A, Shapiro B. Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution. 24: 1416-22. PMID 17395598 DOI: 10.1093/molbev/msm062  1
2007 Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, Rambaut A. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. Plos Computational Biology. 3: e29. PMID 17305421 DOI: 10.1371/journal.pcbi.0030029  1
2007 Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, Holmes EC. Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Molecular Biology and Evolution. 24: 845-52. PMID 17218639 DOI: 10.1093/molbev/msm001  1
2007 Holmes EC, Rambaut A. Evolutionary genetics and the emergence of SARS Coronavirus Sars: a Case Study in Emerging Infections. DOI: 10.1093/acprof:oso/9780198568193.003.0003  1
2007 Cooper A, Grassly N, Rambaut A. Using Molecular Data to Estimate Divergence Times Palaeobiology Ii. 532-534. DOI: 10.1002/9780470999295ch.132  1
2006 de Oliveira 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. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature. 444: 836-7. PMID 17171825 DOI: 10.1038/444836a  1
2006 Lemey P, Rambaut A, Pybus OG. HIV evolutionary dynamics within and among hosts. Aids Reviews. 8: 125-40. PMID 17078483  1
2006 Jobes DV, Daoust M, Nguyen VT, Padua A, Sinangil F, Pérez-Losada M, Crandall KA, Oliphant T, Posada D, Rambaut A, Fuchs J, Berman PW. Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. Aids Research and Human Retroviruses. 22: 968-78. PMID 17067266 DOI: 10.1089/aid.2006.22.968  1
2006 Shackelton LA, Rambaut A, Pybus OG, Holmes EC. JC virus evolution and its association with human populations. Journal of Virology. 80: 9928-33. PMID 17005670 DOI: 10.1128/JVI.00441-06  1
2006 Hon CC, Lam TY, Drummond A, Rambaut A, Lee YF, Yip CW, Zeng F, Lam PY, Ng PT, Leung FC. Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B. Journal of Virology. 80: 8503-9. PMID 16912300 DOI: 10.1128/JVI.00585-06  1
2006 Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, Pillay D. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. Aids (London, England). 20: 1521-9. PMID 16847407 DOI: 10.1097/01.aids.0000237368.64488.ae  1
2006 Shapiro B, Rambaut A, Pybus OG, Holmes EC. A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Molecular Biology and Evolution. 23: 1724-30. PMID 16774976 DOI: 10.1093/molbev/msl037  1
2006 Shapiro B, Rambaut A, Gilbert MT. No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.). International Journal of Infectious Diseases : Ijid : Official Publication of the International Society For Infectious Diseases. 10: 334-5; author reply . PMID 16730469 DOI: 10.1016/j.ijid.2006.02.006  1
2006 Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. Plos Biology. 4: e88. PMID 16683862 DOI: 10.1371/journal.pbio.0040088  1
2006 Shapiro B, Rambaut A, Drummond AJ. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Molecular Biology and Evolution. 23: 7-9. PMID 16177232 DOI: 10.1093/molbev/msj021  1
2006 Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, Larkum T. Heterotachy and tree building: a case study with plastids and eubacteria. Molecular Biology and Evolution. 23: 40-5. PMID 16151191 DOI: 10.1093/molbev/msj005  1
2005 Lemey P, Derdelinckx I, Rambaut A, Van Laethem K, Dumont S, Vermeulen S, Van Wijngaerden E, Vandamme AM. Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain Journal of Virology. 79: 11981-11989. PMID 16140774 DOI: 10.1128/JVI.79.18.11981-11989.2005  1
2005 Katzourakis A, Rambaut A, Pybus OG. The evolutionary dynamics of endogenous retroviruses Trends in Microbiology. 13: 463-468. PMID 16109487 DOI: 10.1016/j.tim.2005.08.004  1
2005 Iversen AKN, Learn GH, Skinhøf P, Mullins JI, McMichael AJ, Rambaut A. Preferential detection of HIV subtype C′ over subtype A in cervical cells from a dually infected woman [2] Aids. 19: 990-993. PMID 15905685  1
2005 Walker PR, Pybus OG, Rambaut A, Holmes EC. Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth Infection, Genetics and Evolution. 5: 199-208. PMID 15737910 DOI: 10.1016/j.meegid.2004.06.011  1
2005 Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences Molecular Biology and Evolution. 22: 1185-1192. PMID 15703244 DOI: 10.1093/molbev/msi103  1
2004 Paraskevis D, Magiorkinis E, Magiorkinis G, Kiosses VG, Lemey P, Vandamme AM, Rambaut A, Hatzakis A. Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods Journal of Molecular Evolution. 59: 709-717. PMID 15693627 DOI: 10.1007/s00239-004-2651-6  1
2004 Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, et al. Rise and fall of the Beringian steppe bison. Science (New York, N.Y.). 306: 1561-5. PMID 15567864 DOI: 10.1126/science.1101074  1
2004 Briese T, Rambaut A, Lipkin WI. Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other orthobunyaviruses Journal of General Virology. 85: 3071-3077. PMID 15448370 DOI: 10.1099/vir.0.80122-0  1
2004 Holmes EG, Rambaut A. Viral evolution and the emergence of SARS coronavirus Philosophical Transactions of the Royal Society B: Biological Sciences. 359: 1059-1065. PMID 15306390 DOI: 10.1098/rstb.2004.1478  1
2004 Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M, Vandamme AM. The molecular population genetics of HIV-1 group O. Genetics. 167: 1059-68. PMID 15280223 DOI: 10.1534/genetics.104.026666  1
2004 Worobey M, Santiago ML, Keele BF, Ndjango JBN, Joy JB, Labama BL, Dhed'a BD, Rambaut A, Sharp PM, Shaw GM, Hahn BH. Contaminated polio vaccine theory refuted Nature. 428: 820. PMID 15103367 DOI: 10.1038/428820a  1
2004 Rambaut A, Posada D, Crandall KA, Holmes EC. The causes and consequences of HIV evolution. Nature Reviews. Genetics. 5: 52-61. PMID 14708016 DOI: 10.1038/nrg1246  1
2003 Drummond A, Pybus OG, Rambaut A. Inference of Viral Evolutionary Rates from Molecular Sequences Advances in Parasitology. 54: 331-358. PMID 14711090 DOI: 10.1016/S0065-308X(03)54008-8  1
2003 Walker PR, Worobey M, Rambaut A, Holmes EC, Pybus OG. Epidemiology: Sexual transmission of HIV in Africa. Nature. 422: 679. PMID 12700750 DOI: 10.1038/422679a  1
2003 Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A. The epidemiology and iatrogenic transmission of hepatitis C virus in egypt: A Bayesian coalescent approach Molecular Biology and Evolution. 20: 381-387. PMID 12644558 DOI: 10.1093/molbev/msg043  1
2003 Twiddy SS, Holmes EC, Rambaut A. Inferring the rate and time-scale of dengue virus evolution Molecular Biology and Evolution. 20: 122-129. PMID 12519914 DOI: 10.1093/molbev/msg010  1
2003 Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG. Measurably evolving populations Trends in Ecology and Evolution. 18: 481-488. DOI: 10.1016/S0169-5347(03)00216-7  1
2002 Pybus OG, Rambaut A, Holmes EC, Harvey PH. New inferences from tree shape: numbers of missing taxa and population growth rates. Systematic Biology. 51: 881-8. PMID 12554454  1
2002 Bromham L, Woolfit M, Lee MSY, Rambaut A. Testing the relationship between morphological and molecular rates of change along phylogenies Evolution. 56: 1921-1930. PMID 12449479  1
2002 Pybus OG, Rambaut A. GENIE: Estimating demographic history from molecular phylogenies Bioinformatics. 18: 1404-1405. PMID 12376389  1
2002 Briese T, Rambaut A, Pathmajeyan M, Bishara J, Weinberger M, Pitlik S, Ian Lipkin W. Phylogenetic analysis of a human isolate from the 2000 Israel West Nile virus epidemic Emerging Infectious Diseases. 8: 528-531. PMID 11996693 DOI: 10.3201/eid0805.010324  1
2002 Worobey M, Rambaut A, Pybus OG, Robertson DL. Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science (New York, N.Y.). 296: 211 discussion 211. PMID 11951002 DOI: 10.1126/science.296.5566.211a  1
2002 Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Bininda-Emonds OR, Lee PL, Cooper A. Flight of the dodo. Science (New York, N.Y.). 295: 1683. PMID 11872833 DOI: 10.1126/science.295.5560.1683  1
2002 Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. Journal of Molecular Evolution. 54: 156-65. PMID 11821909 DOI: 10.1007/s00239-001-0064-3  1
2002 Strimmer K, Rambaut A. Inferring confidence sets of possibly misspecified gene trees Proceedings of the Royal Society B: Biological Sciences. 269: 137-142. PMID 11798428 DOI: 10.1098/rspb.2001.1862  1
2001 Stevens J, Rambaut A. Evolutionary rate differences in trypanosomes Infection, Genetics and Evolution. 1: 143-150. PMID 12798029 DOI: 10.1016/S1567-1348(01)00018-1  1
2001 Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH. The epidemic behavior of the hepatitis C virus. Science (New York, N.Y.). 292: 2323-5. PMID 11423661 DOI: 10.1126/science.1058321  1
2001 Cooper A, Rambaut A, Macaulay V, Willerslev E, Hansen AJ, Stringer C, Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, Peacock WJ, Thorne A. Human origins and ancient human DNA [3] Science. 292: 1655-1656. PMID 11388352 DOI: 10.1126/science.292.5522.1655  1
2001 Rambaut A, Robertson DL, Pybus OG, Peeters M, Holmes EC. Phylogeny and the origin of HIV-1 Nature. 410: 1047-1048. PMID 11323659 DOI: 10.1038/35074179  1
2001 Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution Nature. 409: 704-707. PMID 11217857 DOI: 10.1038/35055536  1
2000 Harvey PH, Rambaut A. Comparative analyses for adaptive radiations. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 355: 1599-605. PMID 11127905 DOI: 10.1098/rstb.2000.0721  1
2000 Pybus OG, Rambaut A, Harvey PH. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics. 155: 1429-37. PMID 10880500  1
2000 Rambaut A. Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies Bioinformatics. 16: 395-399. PMID 10869038  1
2000 Bromham L, Penny D, Rambaut A, Hendy MD. The power of relative rates tests depends on the data Journal of Molecular Evolution. 50: 296-301. PMID 10754073  1
2000 Jenkins GM, Woelk CH, Rambaut A, Holmes EC. Testing the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta virus Journal of Molecular Evolution. 50: 98-102. PMID 10654264  1
1999 Jia XY, Briese T, Jordan I, Rambaut A, Chi HC, Mackenzie JS, Hall RA, Scherret J, Lipkin WI. Genetic analysis of West Nile New York 1999 encephalitis virus. Lancet (London, England). 354: 1971-2. PMID 10622305 DOI: 10.1016/S0140-6736(99)05384-2  1
1999 Worobey M, Rambaut A, Holmes EC. Widespread intra-serotype recombination in natural populations of dengue virus Proceedings of the National Academy of Sciences of the United States of America. 96: 7352-7357. PMID 10377418 DOI: 10.1073/pnas.96.13.7352  1
1999 Holmes EC, Worobey M, Rambaut A. Phylogenetic evidence for recombination in dengue virus Molecular Biology and Evolution. 16: 405-409. PMID 10331266  1
1998 Bromham L, Rambaut A, Fortey R, Cooper A, Penny D. Testing the Cambrian explosion hypothesis by using a molecular dating technique Proceedings of the National Academy of Sciences of the United States of America. 95: 12386-12389. PMID 9770496 DOI: 10.1073/pnas.95.21.12386  1
1998 Rambaut A, Bromham L. Estimating divergence dates from molecular sequences Molecular Biology and Evolution. 15: 442-448. PMID 9549094  1
1998 Harvey PH, Rambaut A. Phylogenetic extinction rates and comparative methodology Proceedings of the Royal Society B: Biological Sciences. 265: 1691-1696. DOI: 10.1098/rspb.1998.0490  1
1998 Stevens J, Gibson W, Noyes HA, Rambaut A. A key to understanding Trypanosoma trees [3] (multiple letters) Parasitology Today. 14: 334-335.  1
1997 Grassly NC, Adachi J, Rambaut A. PSeq-Gen: An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees Computer Applications in the Biosciences. 13: 559-560. PMID 9367131  1
1997 Rambaut A, Harvey PH, Nee S. End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences. Computer Applications in the Biosciences : Cabios. 13: 303-6. PMID 9183536  1
1997 Rambaut A, Grassly NC. Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Computer Applications in the Biosciences. 13: 235-238. PMID 9183526  1
1997 Ong CK, Nee S, Rambaut A, Bernard HU, Harvey PH. Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees. Journal of Molecular Evolution. 44: 199-206. PMID 9069180 DOI: 10.1007/PL00006136  1
1996 Rambaut A, Grassly NC, Nee S, Harvey PH. Bi-De: an application for simulating phylogenetic processes. Computer Applications in the Biosciences : Cabios. 12: 469-71. PMID 9021264  1
1996 Bromham L, Rambaut A, Harvey PH. Determinants of rate variation in mammalian DNA sequence evolution. Journal of Molecular Evolution. 43: 610-21. PMID 8995058 DOI: 10.1007/BF02202109  1
1996 Ong CK, Nee S, Rambaut A, Harvey PH. Inferring the population history of an epidemic from a phylogenetic tree. Journal of Theoretical Biology. 182: 173-8. PMID 8944148 DOI: 10.1006/jtbi.1996.0152  1
1996 Bollyky PL, Rambaut A, Harvey PH, Holmes EC. Recombination between sequences of hepatitis B virus from different genotypes. Journal of Molecular Evolution. 42: 97-102. PMID 8919861 DOI: 10.1007/BF02198834  1
1996 Bartholomew DM, Rees DJG, Rambaut A, Smith JAC. Isolation and sequence analysis of a cDNA encoding the c subunit of a vacuolar-type H+-ATPase from the CAM plant Kalanchoë daigremontiana Plant Molecular Biology. 31: 435-442. PMID 8756609  1
1996 Hart D, Nicolas Frerichs G, Rambaut A, Onions DE. Complete nucleotide sequence and transcriptional analysis of the snakehead fish retrovirus Journal of Virology. 70: 3606-3616. PMID 8648695  1
1995 Holmes EC, Nee S, Rambaut A, Garnett GP, Harvey PH. Revealing the history of infectious disease epidemics through phylogenetic trees. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 349: 33-40. PMID 8748017 DOI: 10.1098/rstb.1995.0088  1
1995 Nee S, Holmes EC, Rambaut A, Harvey PH. Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 349: 25-31. PMID 8748016 DOI: 10.1098/rstb.1995.0087  1
1995 Purvis A, Rambaut A. Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Applications in the Biosciences : Cabios. 11: 247-51. PMID 7583692  1
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