| Year |
Citation |
Score |
| 2023 |
O'Toole Á, Neher RA, Ndodo N, Borges V, Gannon B, Gomes JP, Groves N, King DJ, Maloney D, Lemey P, Lewandowski K, Loman N, Myers R, Omah IF, Suchard MA, ... ... Rambaut A, et al. APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016. Science (New York, N.Y.). 382: 595-600. PMID 37917680 DOI: 10.1126/science.adg8116 |
0.343 |
|
| 2023 |
Ndodo N, Ashcroft J, Lewandowski K, Yinka-Ogunleye A, Chukwu C, Ahmad A, King D, Akinpelu A, Maluquer de Motes C, Ribeca P, Sumner RP, Rambaut A, Chester M, Maishman T, Bamidele O, et al. Distinct monkeypox virus lineages co-circulating in humans before 2022. Nature Medicine. 29: 2317-2324. PMID 37710003 DOI: 10.1038/s41591-023-02456-8 |
0.372 |
|
| 2023 |
Robert A, Tsui Lok Hei J, Watson CH, Gsell PS, Hall Y, Rambaut A, Longini IM, Sakoba K, Kucharski AJ, Touré A, Danmadji Nadlaou S, Saidou Barry M, Fofana TO, Lansana Kaba I, Sylla L, et al. Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea. Virus Evolution. 9: vead007. PMID 36926449 DOI: 10.1093/ve/vead007 |
0.314 |
|
| 2022 |
O'Toole Á, Hill V, Jackson B, Dewar R, Sahadeo N, Colquhoun R, Rooke S, McCrone JT, Duggan K, McHugh MP, Nicholls SM, Poplawski R, Aanensen D, Holden M, Connor T, ... ... Rambaut A, et al. Genomics-informed outbreak investigations of SARS-CoV-2 using civet. Plos Global Public Health. 2: e0000704. PMID 36962792 DOI: 10.1371/journal.pgph.0000704 |
0.358 |
|
| 2022 |
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, ... Rambaut A, et al. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. Plos Biology. 20: e3001769. PMID 35998195 DOI: 10.1371/journal.pbio.3001769 |
0.303 |
|
| 2022 |
Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, ... ... Rambaut A, et al. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science (New York, N.Y.). eabp8337. PMID 35881005 DOI: 10.1126/science.abp8337 |
0.346 |
|
| 2022 |
Gutierrez B, Castelán Sánchez HG, Candido DDS, Jackson B, Fleishon S, Houzet R, Ruis C, Delaye L, Faria NR, Rambaut A, Pybus OG, Escalera-Zamudio M. Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America. Cell Host & Microbe. PMID 35853454 DOI: 10.1016/j.chom.2022.06.010 |
0.31 |
|
| 2022 |
Claro IM, Romano CM, Candido DDS, Lima EL, Lindoso JAL, Ramundo MS, Moreira FRR, Barra LAC, Borges LMS, Medeiros LA, Tomishige MYS, Moutinho T, Silva AJDD, Rodrigues CCM, Azevedo LCF, ... ... Rambaut A, et al. Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022. Revista Do Instituto De Medicina Tropical De Sao Paulo. 64: e48. PMID 35749419 DOI: 10.1590/S1678-9946202264048 |
0.356 |
|
| 2022 |
Campbell K, Gifford RJ, Singer J, Hill V, O'Toole A, Rambaut A, Hampson K, Brunker K. Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. Plos Pathogens. 18: e1010023. PMID 35500026 DOI: 10.1371/journal.ppat.1010023 |
0.416 |
|
| 2022 |
O'Toole Á, Pybus OG, Abram ME, Kelly EJ, Rambaut A. Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. Bmc Genomics. 23: 121. PMID 35148677 DOI: 10.1186/s12864-022-08358-2 |
0.315 |
|
| 2021 |
Butera Y, Mukantwari E, Artesi M, Umuringa JD, O'Toole ÁN, Hill V, Rooke S, Hong SL, Dellicour S, Majyambere O, Bontems S, Boujemla B, Quick J, Resende PC, Loman N, ... ... Rambaut A, et al. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nature Communications. 12: 5705. PMID 34588460 DOI: 10.1038/s41467-021-25985-7 |
0.327 |
|
| 2021 |
O'Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B, Yeats C, du Plessis L, Maloney D, Medd N, Attwood SW, ... ... Rambaut A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution. 7: veab064. PMID 34527285 DOI: 10.1093/ve/veab064 |
0.351 |
|
| 2021 |
Keita AK, Koundouno FR, Faye M, Düx A, Hinzmann J, Diallo H, Ayouba A, Le Marcis F, Soropogui B, Ifono K, Diagne MM, Sow MS, Bore JA, Calvignac-Spencer S, Vidal N, ... ... Rambaut A, et al. Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks. Nature. PMID 34526718 DOI: 10.1038/s41586-021-03901-9 |
0.359 |
|
| 2021 |
Jackson B, Boni MF, Bull MJ, Colleran A, Colquhoun RM, Darby AC, Haldenby S, Hill V, Lucaci A, McCrone JT, Nicholls SM, O'Toole Á, Pacchiarini N, Poplawski R, Scher E, ... ... Rambaut A, et al. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell. PMID 34499854 DOI: 10.1016/j.cell.2021.08.014 |
0.362 |
|
| 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 |
0.32 |
|
| 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 |
0.316 |
|
| 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 |
0.363 |
|
| 2020 |
Duchene S, Featherstone L, Haritopoulou-Sinanidou M, Rambaut A, Lemey P, Baele G. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evolution. 6: veaa061. PMID 33235813 DOI: 10.1093/Ve/Veaa061 |
0.437 |
|
| 2020 |
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. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Communications. 11: 5110. PMID 33037213 DOI: 10.1038/s41467-020-18877-9 |
0.35 |
|
| 2020 |
Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science (New York, N.Y.). PMID 32912998 DOI: 10.1126/Science.Abc8169 |
0.385 |
|
| 2020 |
Boni MF, Lemey P, Jiang X, Lam TT, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology. PMID 32724171 DOI: 10.1038/S41564-020-0771-4 |
0.463 |
|
| 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 |
0.377 |
|
| 2020 |
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, ... ... Rambaut A, et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nature Medicine. PMID 32678356 DOI: 10.1038/S41591-020-0997-Y |
0.407 |
|
| 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 |
0.504 |
|
| 2020 |
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, ... ... Rambaut A, et al. Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing. Journal of Clinical Microbiology. PMID 32611795 DOI: 10.1128/Jcm.00920-20 |
0.365 |
|
| 2020 |
Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O'Toole A, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. Biorxiv : the Preprint Server For Biology. PMID 32596695 DOI: 10.1101/2020.06.22.165464 |
0.354 |
|
| 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 |
0.442 |
|
| 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 |
0.467 |
|
| 2020 |
Gill MS, Lemey P, Suchard MA, Rambaut A, Baele G. Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction. Molecular Biology and Evolution. PMID 32101295 DOI: 10.1093/Molbev/Msaa047 |
0.403 |
|
| 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 |
0.463 |
|
| 2019 |
Baele G, Ayres DL, Rambaut A, Suchard MA, Lemey P. High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. Methods in Molecular Biology (Clifton, N.J.). 1910: 691-722. PMID 31278682 DOI: 10.1007/978-1-4939-9074-0_23 |
0.318 |
|
| 2019 |
Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian inference of evolutionary histories under time-dependent substitution rates. Molecular Biology and Evolution. PMID 31004175 DOI: 10.1093/Molbev/Msz094 |
0.441 |
|
| 2019 |
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, ... ... Rambaut A, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. Plos Computational Biology. 15: e1006650. PMID 30958812 DOI: 10.1371/Journal.Pcbi.1006650 |
0.324 |
|
| 2019 |
Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen Iv FA, Theys K. SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination. Virus Evolution. 5: vez003. PMID 30863552 DOI: 10.1093/Ve/Vez003 |
0.369 |
|
| 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 |
0.479 |
|
| 2019 |
Robert A, Edmunds J, Eggo R, Henao-Restrepo A-, Gsell P-, Watson CH, Longini IM, Rambaut A, Camacho A, Hué S. A39 Reconstruction of Ebola chains of transmission using sequence and epidemiological data Virus Evolution. 5. DOI: 10.1093/Ve/Vez002.038 |
0.383 |
|
| 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 |
0.353 |
|
| 2018 |
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution. 4: vey016. PMID 29942656 DOI: 10.1093/Ve/Vey016 |
0.361 |
|
| 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 |
0.712 |
|
| 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 |
0.632 |
|
| 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 |
0.724 |
|
| 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 |
0.727 |
|
| 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 |
0.724 |
|
| 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 |
0.738 |
|
| 2017 |
Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, ... ... Rambaut A, et al. Zika virus evolution and spread in the Americas. Nature. PMID 28538734 DOI: 10.1038/Nature22402 |
0.514 |
|
| 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 |
0.473 |
|
| 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 |
0.733 |
|
| 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 |
0.737 |
|
| 2017 |
Baele G, Lemey P, Rambaut A, Suchard MA. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics (Oxford, England). PMID 28200071 DOI: 10.1093/Bioinformatics/Btx088 |
0.348 |
|
| 2017 |
Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Systematic Biology. 66: e47-e65. PMID 28173504 DOI: 10.1093/Sysbio/Syw054 |
0.449 |
|
| 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 |
0.38 |
|
| 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 |
0.739 |
|
| 2016 |
Keita M, Duraffour S, Loman NJ, Rambaut A, Diallo B, Magassouba N, Carroll MW, Quick J, Sall AA, Glynn JR, Formenty P, Subissi L, Faye O. Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015. Emerging Infectious Diseases. 22: 2149-2152. PMID 27869596 DOI: 10.3201/Eid2212.160847 |
0.461 |
|
| 2016 |
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, et al. Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic. Cell. 167: 1088-1098.e6. PMID 27814506 DOI: 10.1016/J.Cell.2016.10.014 |
0.403 |
|
| 2016 |
Nickbakhsh S, Hall MD, Dorigatti I, Lycett SJ, Mulatti P, Monne I, Fusaro A, Woolhouse ME, Rambaut A, Kao RR. Modelling the impact of co-circulating low pathogenic avian influenza viruses on epidemics of highly pathogenic avian influenza in poultry. Epidemics. 17: 27-34. PMID 27788412 DOI: 10.1016/J.Epidem.2016.10.005 |
0.425 |
|
| 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 |
0.395 |
|
| 2016 |
Hall MD, Woolhouse ME, Rambaut A. The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study. Virus Evolution. 2: vew003. PMID 27774296 DOI: 10.1093/Ve/Vew003 |
0.426 |
|
| 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 |
0.704 |
|
| 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 |
0.751 |
|
| 2016 |
Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, ... ... Rambaut A, et al. Resurgence of Ebola virus disease in Guinea linked to a survivor with virus persistence in seminal fluid for more than 500 days. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 27585800 DOI: 10.1093/Cid/Ciw601 |
0.38 |
|
| 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 |
0.705 |
|
| 2016 |
Blackley DJ, Wiley MR, Ladner JT, Fallah M, Lo T, Gilbert ML, Gregory C, D'ambrozio J, Coulter S, Mate S, Balogun Z, Kugelman J, Nwachukwu W, Prieto K, Yeiah A, ... ... Rambaut A, et al. Reduced evolutionary rate in reemerged Ebola virus transmission chains. Science Advances. 2: e1600378. PMID 27386513 DOI: 10.1126/Sciadv.1600378 |
0.449 |
|
| 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 |
0.481 |
|
| 2016 |
Baele G, Suchard MA, Rambaut A, Lemey P. Emerging concepts of data integration in pathogen phylodynamics. Systematic Biology. PMID 27288481 DOI: 10.1093/sysbio/syw054 |
0.344 |
|
| 2016 |
Hall MD, Woolhouse ME, Rambaut A. Using genomics data to reconstruct transmission trees during disease outbreaks. Revue Scientifique Et Technique (International Office of Epizootics). 35: 287-96. PMID 27217184 DOI: 10.20506/Rst.35.1.2433 |
0.425 |
|
| 2016 |
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. SpreaD3: interactive visualisation of spatiotemporal history and trait evolutionary processes. Molecular Biology and Evolution. PMID 27189542 DOI: 10.1093/Molbev/Msw082 |
0.342 |
|
| 2016 |
Murray GG, 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 / British Ecological Society. 7: 80-89. PMID 27110344 DOI: 10.1111/2041-210X.12466 |
0.377 |
|
| 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 |
0.428 |
|
| 2016 |
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 JH, Becker-Ziaja B, ... ... Rambaut A, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. PMID 26840485 DOI: 10.1038/Nature16996 |
0.719 |
|
| 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 |
0.401 |
|
| 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 |
0.411 |
|
| 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, Bakel Hv, García-Sastre A. Author response: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico Elife. DOI: 10.7554/Elife.16777.035 |
0.357 |
|
| 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 |
0.382 |
|
| 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 |
0.747 |
|
| 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 |
0.386 |
|
| 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 |
0.383 |
|
| 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 |
0.413 |
|
| 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 |
0.753 |
|
| 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 |
0.758 |
|
| 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 |
0.454 |
|
| 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 |
0.435 |
|
| 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 |
0.437 |
|
| 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 : An Official Publication of the Infectious Diseases Society of America. 60: 369-77. PMID 25323704 DOI: 10.1093/Cid/Ciu812 |
0.393 |
|
| 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 |
0.674 |
|
| 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 |
0.637 |
|
| 2014 |
Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, et al. Improving pandemic influenza risk assessment. Elife. 3: e03883. PMID 25321142 DOI: 10.7554/Elife.03883 |
0.431 |
|
| 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 |
0.351 |
|
| 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 |
0.749 |
|
| 2014 |
Armitage AE, Deforche K, Welch JJ, Van Laethem K, Camacho R, Rambaut A, Iversen AK. 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: 12882-94. PMID 25165112 DOI: 10.1128/Jvi.01460-14 |
0.301 |
|
| 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 |
0.301 |
|
| 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 |
0.345 |
|
| 2014 |
Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. Plos Currents. 6. PMID 24860690 DOI: 10.1371/Currents.Outbreaks.84Eefe5Ce43Ec9Dc0Bf0670F7B8B417D |
0.716 |
|
| 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 |
0.448 |
|
| 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 |
0.4 |
|
| 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 |
0.404 |
|
| 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 |
0.468 |
|
| 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 |
0.473 |
|
| 2014 |
Worobey M, Han GZ, Rambaut A. A synchronized global sweep of the internal genes of modern avian influenza virus. Nature. 508: 254-7. PMID 24531761 DOI: 10.1038/Nature13016 |
0.493 |
|
| 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 |
0.674 |
|
| 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 |
0.356 |
|
| 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 |
0.41 |
|
| 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 |
0.425 |
|
| 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 |
0.39 |
|
| 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 |
0.319 |
|
| 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 |
0.454 |
|
| 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 |
0.338 |
|
| 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 |
0.433 |
|
| 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 |
0.331 |
|
| 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 |
0.493 |
|
| 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 |
0.408 |
|
| 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 |
0.362 |
|
| 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 |
0.325 |
|
| 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 |
0.324 |
|
| 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 |
0.386 |
|
| 2013 |
Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A. Author response: Integrating influenza antigenic dynamics with molecular evolution Elife. DOI: 10.7554/Elife.01914.025 |
0.667 |
|
| 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 |
0.404 |
|
| 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 |
0.333 |
|
| 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 |
0.366 |
|
| 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 |
0.32 |
|
| 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 |
0.434 |
|
| 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 |
0.375 |
|
| 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 |
0.423 |
|
| 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 |
0.339 |
|
| 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 |
0.395 |
|
| 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 |
0.437 |
|
| 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 |
0.456 |
|
| 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 |
0.314 |
|
| 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 |
0.491 |
|
| 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 |
0.311 |
|
| 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 |
0.393 |
|
| 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 |
0.474 |
|
| 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 |
0.416 |
|
| 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 |
0.308 |
|
| 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 |
0.484 |
|
| 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 |
0.457 |
|
| 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 |
0.364 |
|
| 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 |
0.434 |
|
| 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 |
0.434 |
|
| 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 |
0.361 |
|
| 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 |
0.399 |
|
| 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 |
0.471 |
|
| 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 |
0.391 |
|
| 2010 |
Archer J, Rambaut A, Robertson DL. Quantitative deep sequencing and HIV-1 population dynamics F1000research. 1. DOI: 10.7490/F1000Research.344.1 |
0.326 |
|
| 2009 |
Lemey P, Suchard M, Rambaut A. Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial-temporal model for the global spread of H1N1pdm. Plos Currents. 1: RRN1031. PMID 20029613 DOI: 10.1371/Currents.Rrn1031 |
0.406 |
|
| 2009 |
Rambaut A, Holmes E. The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. Plos Currents. 1: RRN1003. PMID 20025195 DOI: 10.1371/Currents.Rrn1003 |
0.521 |
|
| 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 |
0.377 |
|
| 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: e1000590. PMID 19779560 DOI: 10.1371/Journal.Ppat.1000590 |
0.363 |
|
| 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 |
0.437 |
|
| 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 |
0.444 |
|
| 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 |
0.483 |
|
| 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 |
0.43 |
|
| 2009 |
Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics Bioinformatics. 25: 1370-1376. PMID 19369496 DOI: 10.1093/Bioinformatics/Btp244 |
0.339 |
|
| 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 |
0.334 |
|
| 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 |
0.432 |
|
| 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 |
0.414 |
|
| 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 |
0.504 |
|
| 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 |
0.426 |
|
| 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 |
0.329 |
|
| 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 |
0.327 |
|
| 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 |
0.343 |
|
| 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 |
0.371 |
|
| 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 |
0.41 |
|
| 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 |
0.324 |
|
| 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 |
0.347 |
|
| 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 |
0.45 |
|
| 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 |
0.37 |
|
| 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 |
0.369 |
|
| 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 |
0.462 |
|
| 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 |
0.312 |
|
| 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 |
0.32 |
|
| 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 |
0.373 |
|
| 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 |
0.346 |
|
| 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 |
0.374 |
|
| 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 |
0.464 |
|
| 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 |
0.421 |
|
| 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 |
0.324 |
|
| 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 |
0.432 |
|
| 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 |
0.354 |
|
| 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 |
0.312 |
|
| 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 |
0.379 |
|
| 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 |
0.434 |
|
| 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 |
0.365 |
|
| 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 |
0.356 |
|
| 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 |
0.428 |
|
| 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 |
0.403 |
|
| 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 |
0.342 |
|
| 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 |
0.401 |
|
| 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 |
0.476 |
|
| 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 |
0.334 |
|
| 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 |
0.395 |
|
| 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 |
0.303 |
|
| 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 |
0.511 |
|
| 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 |
0.321 |
|
| 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 |
0.313 |
|
| 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 |
0.506 |
|
| 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 |
0.417 |
|
| 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 DOI: 10.1080/10635150290102582 |
0.549 |
|
| 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 DOI: 10.1111/J.0014-3820.2002.Tb00118.X |
0.355 |
|
| 2002 |
Pybus OG, Rambaut A. GENIE: Estimating demographic history from molecular phylogenies Bioinformatics. 18: 1404-1405. PMID 12376389 DOI: 10.1093/Bioinformatics/18.10.1404 |
0.362 |
|
| 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 |
0.418 |
|
| 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 |
0.411 |
|
| 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 |
0.656 |
|
| 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 |
0.409 |
|
| 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 |
0.334 |
|
| 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 |
0.322 |
|
| 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 |
0.543 |
|
| 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 |
0.365 |
|
| 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 |
0.42 |
|
| 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 |
0.478 |
|
| 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 |
0.45 |
|
| 2000 |
Rambaut A. Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies Bioinformatics. 16: 395-399. PMID 10869038 DOI: 10.1093/Bioinformatics/16.4.395 |
0.336 |
|
| 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 DOI: 10.1007/S002399910034 |
0.372 |
|
| 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 DOI: 10.1007/S002399910011 |
0.425 |
|
| 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 |
0.438 |
|
| 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 |
0.459 |
|
| 1999 |
Holmes EC, Worobey M, Rambaut A. Phylogenetic evidence for recombination in dengue virus Molecular Biology and Evolution. 16: 405-409. PMID 10331266 DOI: 10.1093/Oxfordjournals.Molbev.A026121 |
0.448 |
|
| 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 |
0.351 |
|
| 1998 |
Rambaut A, Bromham L. Estimating divergence dates from molecular sequences Molecular Biology and Evolution. 15: 442-448. PMID 9549094 DOI: 10.1093/Oxfordjournals.Molbev.A025940 |
0.372 |
|
| 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 |
0.477 |
|
| 1998 |
Bollyky P, Rambaut A, Grassley N, Carman W, Holmes E. Hepatitis B virus has a recent new world evolutionary origin Journal of Hepatology. 28: 96. DOI: 10.1016/S0168-8278(98)80579-5 |
0.333 |
|
| 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 DOI: 10.1093/Bioinformatics/13.3.303 |
0.677 |
|
| 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 DOI: 10.1093/Bioinformatics/13.3.235 |
0.344 |
|
| 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 |
0.677 |
|
| 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 DOI: 10.1093/Bioinformatics/12.6.469 |
0.656 |
|
| 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 |
0.522 |
|
| 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 |
0.661 |
|
| 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 |
0.595 |
|
| 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 DOI: 10.1128/Jvi.70.6.3606-3616.1996 |
0.426 |
|
| 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 |
0.714 |
|
| 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 |
0.655 |
|
| 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 DOI: 10.1093/Bioinformatics/11.3.247 |
0.527 |
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