| Year |
Citation |
Score |
| 2024 |
Holmes EC, Krammer F, Goodrum FD. Virology-The next fifty years. Cell. 187: 5128-5145. PMID 39303682 DOI: 10.1016/j.cell.2024.07.025 |
0.316 |
|
| 2024 |
Hill V, Cleemput S, Pereira JS, Gifford RJ, Fonseca V, Tegally H, Brito AF, Ribeiro G, de Souza VC, Brcko IC, Ribeiro IS, De Lima ITT, Slavov SN, Sampaio SC, Elias MC, ... ... Holmes EC, et al. A new lineage nomenclature to aid genomic surveillance of dengue virus. Plos Biology. 22: e3002834. PMID 39283942 DOI: 10.1371/journal.pbio.3002834 |
0.432 |
|
| 2024 |
Zhao J, Wan W, Yu K, Lemey P, Pettersson JH, Bi Y, Lu M, Li X, Chen Z, Zheng M, Yan G, Dai J, Li Y, Haerheng A, He N, ... ... Holmes EC, et al. Farmed fur animals harbour viruses with zoonotic spillover potential. Nature. PMID 39232170 DOI: 10.1038/s41586-024-07901-3 |
0.423 |
|
| 2024 |
Xu L, Song M, Tian X, Sun J, Wang Y, Bie M, Bi Y, Holmes EC, Guan Y, Chen J, Li J, Shi W. Five-year longitudinal surveillance reveals the continual circulation of both alpha- and beta-coronaviruses in Plateau and Gansu pikas ( spp.) at Qinghai Lake, China. Emerging Microbes & Infections. 2392693. PMID 39137298 DOI: 10.1080/22221751.2024.2392693 |
0.358 |
|
| 2024 |
Tian Z, Hu T, Holmes EC, Ji J, Shi W. Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system. Virus Evolution. 10: veae059. PMID 39119135 DOI: 10.1093/ve/veae059 |
0.367 |
|
| 2024 |
Grimwood RM, Waller SJ, Wierenga JR, Lim L, Dubrulle J, Holmes EC, Geoghegan JL. Viromes of Antarctic fish resemble the diversity found at lower latitudes. Virus Evolution. 10: veae050. PMID 39071139 DOI: 10.1093/ve/veae050 |
0.359 |
|
| 2024 |
Petrone ME, Grove J, Mélade J, Mifsud JCO, Parry RH, Marzinelli EM, Holmes EC. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proceedings of the National Academy of Sciences of the United States of America. 121: e2403805121. PMID 39018195 DOI: 10.1073/pnas.2403805121 |
0.401 |
|
| 2024 |
Waller SJ, Butcher RG, Lim L, McInnes K, Holmes EC, Geoghegan JL. The radiation of New Zealand's skinks and geckos is associated with distinct viromes. Bmc Ecology and Evolution. 24: 81. PMID 38872095 DOI: 10.1186/s12862-024-02269-4 |
0.328 |
|
| 2024 |
Mahar JE, Wille M, Harvey E, Moritz CC, Holmes EC. The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat. Virus Evolution. 10: veae044. PMID 38854849 DOI: 10.1093/ve/veae044 |
0.412 |
|
| 2024 |
Ji J, Li C, Hu T, Tian Z, Li J, Xu L, Zhou H, Holmes EC, Shi W. Diverse RNA viruses in the venom-related microenvironment of different animal phyla. Virus Evolution. 10: veae024. PMID 38827419 DOI: 10.1093/ve/veae024 |
0.373 |
|
| 2024 |
Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, ... ... Holmes EC, et al. A new lineage nomenclature to aid genomic surveillance of dengue virus. Medrxiv : the Preprint Server For Health Sciences. PMID 38798319 DOI: 10.1101/2024.05.16.24307504 |
0.431 |
|
| 2024 |
Costa VA, Holmes EC. Diversity, evolution, and emergence of fish viruses. Journal of Virology. 98: e0011824. PMID 38785422 DOI: 10.1128/jvi.00118-24 |
0.429 |
|
| 2024 |
Sadiq S, Holmes EC, Mahar JE. Genomic and phylogenetic features of the suggest microbial rather than animal hosts. Virus Evolution. 10: veae033. PMID 38756987 DOI: 10.1093/ve/veae033 |
0.395 |
|
| 2024 |
Holmes EC. The Emergence and Evolution of SARS-CoV-2. Annual Review of Virology. PMID 38631919 DOI: 10.1146/annurev-virology-093022-013037 |
0.316 |
|
| 2024 |
Waller SJ, Egan E, Crow S, Charsley A, Lokman PM, Williams EK, Holmes EC, Geoghegan JL. Host and geography impact virus diversity in New Zealand's longfin and shortfin eels. Archives of Virology. 169: 85. PMID 38546898 DOI: 10.1007/s00705-024-06019-1 |
0.37 |
|
| 2024 |
Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, ... ... Holmes EC, et al. Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity. Nature Ecology & Evolution. PMID 38519631 DOI: 10.1038/s41559-024-02365-0 |
0.417 |
|
| 2024 |
Zhou H, Tian RR, Wang XR, Yang JX, Wang YX, Zhao ML, Zhang XD, Ma YH, Lv LB, Holmes EC, Zheng YT, Shi WF. Identification of novel mammalian viruses in tree shrews ( ). Zoological Research. 45: 429-438. PMID 38485510 DOI: 10.24272/j.issn.2095-8137.2023.306 |
0.386 |
|
| 2024 |
Costa VA, Ronco F, Mifsud JCO, Harvey E, Salzburger W, Holmes EC. Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes. Current Biology : Cb. PMID 38428417 DOI: 10.1016/j.cub.2024.02.008 |
0.418 |
|
| 2024 |
Waller SJ, Tortosa P, Thurley T, O'Donnell CFJ, Jackson R, Dennis G, Grimwood RM, Holmes EC, McInnes K, Geoghegan JL. Virome analysis of New Zealand's bats reveals cross-species viral transmission among the . Virus Evolution. 10: veae008. PMID 38379777 DOI: 10.1093/ve/veae008 |
0.349 |
|
| 2024 |
Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, Mahar JE, Holmes EC. Australian terrestrial environments harbour extensive RNA virus diversity. Virology. 593: 110007. PMID 38346363 DOI: 10.1016/j.virol.2024.110007 |
0.376 |
|
| 2023 |
Harvey E, Mifsud JCO, Holmes EC, Mahar JE. Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evolution. 9: vead061. PMID 37941997 DOI: 10.1093/ve/vead061 |
0.482 |
|
| 2023 |
Dong X, Li C, Wang Y, Hu T, Zhang F, Meng F, Gao M, Han X, Wang G, Qin J, Nauwynck H, Holmes EC, Sorgeloos P, Sui L, Huang J, et al. Diversity and connectedness of brine shrimp viruses in global hypersaline ecosystems. Science China. Life Sciences. PMID 37922067 DOI: 10.1007/s11427-022-2366-8 |
0.433 |
|
| 2023 |
Petrone ME, Parry R, Mifsud JCO, Van Brussel K, Vorhees I, Richards ZT, Holmes EC. Evidence for an ancient aquatic origin of the RNA viral order . Proceedings of the National Academy of Sciences of the United States of America. 120: e2310529120. PMID 37906647 DOI: 10.1073/pnas.2310529120 |
0.482 |
|
| 2023 |
Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology. 587: 109884. PMID 37757732 DOI: 10.1016/j.virol.2023.109884 |
0.333 |
|
| 2023 |
Chen YM, Hu SJ, Lin XD, Tian JH, Lv JX, Wang MR, Luo XQ, Pei YY, Hu RX, Song ZG, Holmes EC, Zhang YZ. Host traits shape virome composition and virus transmission in wild small mammals. Cell. 186: 4662-4675.e12. PMID 37734372 DOI: 10.1016/j.cell.2023.08.029 |
0.479 |
|
| 2023 |
Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, ... ... Holmes EC, et al. Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses. Biorxiv : the Preprint Server For Biology. PMID 37732272 DOI: 10.1101/2023.08.28.555221 |
0.406 |
|
| 2023 |
He WT, Li D, Baele G, Zhao J, Jiang Z, Ji X, Veit M, Suchard MA, Holmes EC, Lemey P, Boni MF, Su S. Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evolution. 9: vead051. PMID 37711483 DOI: 10.1093/ve/vead051 |
0.431 |
|
| 2023 |
Le Lay C, Hamm JN, Williams TJ, Shi M, Cavicchioli R, Holmes EC. Viral community composition of hypersaline lakes. Virus Evolution. 9: vead057. PMID 37692898 DOI: 10.1093/ve/vead057 |
0.386 |
|
| 2023 |
Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evolution. 9: vead052. PMID 37692894 DOI: 10.1093/ve/vead052 |
0.465 |
|
| 2023 |
French RK, Anderson SH, Cain KE, Greene TC, Minor M, Miskelly CM, Montoya JM, Wille M, Muller CG, Taylor MW, Digby A, Holmes EC. Host phylogeny shapes viral transmission networks in an island ecosystem. Nature Ecology & Evolution. PMID 37679456 DOI: 10.1038/s41559-023-02192-9 |
0.389 |
|
| 2023 |
Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEML, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, ... ... Holmes EC, et al. Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil. Science Advances. 9: eadg9204. PMID 37656782 DOI: 10.1126/sciadv.adg9204 |
0.38 |
|
| 2023 |
Le Lay C, Stott MB, Shi M, Sadiq S, Holmes EC. A metatranscriptomic analysis of geothermal hot springs reveals diverse RNA viruses including the phylum Lenarviricota. Virology. 587: 109873. PMID 37647722 DOI: 10.1016/j.virol.2023.109873 |
0.315 |
|
| 2023 |
Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, Gomez de la Fuente A, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, ... ... Holmes EC, et al. Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay. Emerging Infectious Diseases. 29. PMID 37488810 DOI: 10.3201/eid2909.230523 |
0.39 |
|
| 2023 |
Van Brussel K, Mahar JE, Hall J, Bender H, Ortiz-Baez AS, Chang WS, Holmes EC, Rose K. Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions. Virology. 586: 43-55. PMID 37487325 DOI: 10.1016/j.virol.2023.07.011 |
0.309 |
|
| 2023 |
Wang J, Pan YF, Yang LF, Yang WH, Lv K, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen S, Shu YL, ... ... Holmes EC, et al. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nature Communications. 14: 4079. PMID 37429936 DOI: 10.1038/s41467-023-39835-1 |
0.454 |
|
| 2023 |
Chen P, Jin Z, Peng L, Zheng Z, Cheung YM, Guan J, Chen L, Huang Y, Fan X, Zhang Z, Shi D, Xie J, Chen R, Xiao B, Yip CH, ... ... Holmes EC, et al. Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. Journal of Virology. e0043423. PMID 37289052 DOI: 10.1128/jvi.00434-23 |
0.423 |
|
| 2023 |
Liang X, Chen X, Zhai J, Li X, Zhang X, Zhang Z, Zhang P, Wang X, Cui X, Wang H, Zhou N, Chen ZJ, Su R, Zhou F, Holmes EC, et al. Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins. Plos Pathogens. 19: e1011384. PMID 37196026 DOI: 10.1371/journal.ppat.1011384 |
0.329 |
|
| 2023 |
Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, ... ... Holmes EC, et al. Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay. Medrxiv : the Preprint Server For Health Sciences. PMID 37131602 DOI: 10.1101/2023.04.16.23288635 |
0.369 |
|
| 2023 |
Lu M, He WT, Pettersson JH, Baele G, Shi M, Holmes EC, He N, Su S. Zoonotic risk assessment among farmed mammals. Cell. 186: 2040-2040.e1. PMID 37116474 DOI: 10.1016/j.cell.2023.04.002 |
0.33 |
|
| 2023 |
Costa VA, Bellwood DR, Mifsud JCO, Van Brussel K, Geoghegan JL, Holmes EC, Harvey E. Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evolution. 9: vead011. PMID 36910859 DOI: 10.1093/ve/vead011 |
0.356 |
|
| 2023 |
Ortiz-Baez AS, Jaenson TGT, Holmes EC, Pettersson JH, Wilhelmsson P. Substantial viral and bacterial diversity at the bat-tick interface. Microbial Genomics. 9. PMID 36862584 DOI: 10.1099/mgen.0.000942 |
0.467 |
|
| 2023 |
Li C, Liu S, Zhou H, Zhu W, Cui M, Li J, Wang J, Liu J, Zhu J, Li W, Bi Y, Carr MJ, Holmes EC, Shi W. Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome. Microbiology Spectrum. e0465522. PMID 36786616 DOI: 10.1128/spectrum.04655-22 |
0.399 |
|
| 2023 |
López-Astacio RA, Adu OF, Goetschius DJ, Lee H, Weichert WS, Wasik BR, Frueh SP, Alford BK, Voorhees IEH, Flint JF, Saddoris S, Goodman LB, Holmes EC, Hafenstein SL, Parrish CR. Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus. Biorxiv : the Preprint Server For Biology. PMID 36711712 DOI: 10.1101/2023.01.18.524668 |
0.32 |
|
| 2023 |
Wille M, Lisovski S, Roshier D, Ferenczi M, Hoye BJ, Leen T, Warner S, Fouchier RAM, Hurt AC, Holmes EC, Klaassen M. Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological Sciences. 290: 20222237. PMID 36651046 DOI: 10.1098/rspb.2022.2237 |
0.321 |
|
| 2023 |
Li N, Li C, Hu T, Li J, Zhou H, Ji J, Wu J, Kang W, Holmes EC, Shi W, Xu S. Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. Microbiome. 11: 6. PMID 36631833 DOI: 10.1186/s40168-022-01446-1 |
0.316 |
|
| 2023 |
Wierenga JR, Morgan KJ, Hunter S, Taylor HS, Argilla LS, Webster T, Dubrulle J, Jorge F, Bostina M, Burga L, Holmes EC, McInnes K, Geoghegan JL. A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease. Virology. 579: 75-83. PMID 36608597 DOI: 10.1016/j.virol.2022.12.012 |
0.305 |
|
| 2022 |
Mifsud JCO, Costa VA, Petrone ME, Marzinelli EM, Holmes EC, Harvey E. Transcriptome mining extends the host range of the to non-bilaterians. Virus Evolution. 9: veac124. PMID 36694816 DOI: 10.1093/ve/veac124 |
0.423 |
|
| 2022 |
Sghaier S, Sailleau C, Marcacci M, Thabet S, Curini V, Ben Hassine T, Teodori L, Portanti O, Hammami S, Jurisic L, Spedicato M, Postic L, Gazani I, Ben Osman R, Zientara S, ... ... Holmes EC, et al. Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses. 15. PMID 36680057 DOI: 10.3390/v15010016 |
0.357 |
|
| 2022 |
Charon J, Buchmann JP, Sadiq S, Holmes EC. RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data. Virus Evolution. 8: veac082. PMID 36533143 DOI: 10.1093/ve/veac082 |
0.357 |
|
| 2022 |
Wang J, Pan YF, Yang LF, Yang WH, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen YQ, Shu YL, Guo D, ... ... Holmes EC, et al. Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses. Biorxiv : the Preprint Server For Biology. PMID 36451889 DOI: 10.1101/2022.11.23.517609 |
0.453 |
|
| 2022 |
Ortiz-Baez AS, Holmes EC, Charon J, Pettersson JH, Hesson JC. Meta-transcriptomics reveals potential virus transfer between mosquitoes and their parasitic water mites. Virus Evolution. 8: veac090. PMID 36320615 DOI: 10.1093/ve/veac090 |
0.426 |
|
| 2022 |
Costa VA, Geoghegan JL, Holmes EC, Harvey E. Genetic Reassortment between Endemic and Introduced Nodaviruses in the Murray-Darling Basin, Australia. Viruses. 14. PMID 36298741 DOI: 10.3390/v14102186 |
0.382 |
|
| 2022 |
Kerr PJ, Cattadori IM, Sim D, Liu J, Holmes EC, Read AF. Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility. Journal of Virology. 96: e0088622. PMID 36197107 DOI: 10.1128/jvi.00886-22 |
0.439 |
|
| 2022 |
Charon J, Kahlke T, Larsson ME, Abbriano R, Commault A, Burke J, Ralph P, Holmes EC. Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures. Journal of Virology. e0078322. PMID 36190242 DOI: 10.1128/jvi.00783-22 |
0.359 |
|
| 2022 |
Van Brussel K, Mahar JE, Ortiz-Baez AS, Carrai M, Spielman D, Boardman WSJ, Baker ML, Beatty JA, Geoghegan JL, Barrs VR, Holmes EC. Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology. 576: 42-51. PMID 36150229 DOI: 10.1016/j.virol.2022.09.002 |
0.426 |
|
| 2022 |
Waller SJ, Lamar S, Perry BJ, Grimwood RM, Holmes EC, Geoghegan JL. Cloacal virome of an ancient host lineage - The tuatara (Sphenodon punctatus) - Reveals abundant and diverse diet-related viruses. Virology. 575: 43-53. PMID 36058085 DOI: 10.1016/j.virol.2022.08.012 |
0.489 |
|
| 2022 |
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, ... ... Holmes EC, et al. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nature Microbiology. PMID 35982313 DOI: 10.1038/s41564-022-01191-z |
0.351 |
|
| 2022 |
Chen YM, Sadiq S, Tian JH, Chen X, Lin XD, Shen JJ, Chen H, Hao ZY, Wille M, Zhou ZC, Wu J, Li F, Wang HW, Yang WD, Xu QY, ... ... Holmes EC, et al. RNA viromes from terrestrial sites across China expand environmental viral diversity. Nature Microbiology. 7: 1312-1323. PMID 35902778 DOI: 10.1038/s41564-022-01180-2 |
0.37 |
|
| 2022 |
French RK, Filion A, Niebuhr CN, Holmes EC. Metatranscriptomic Comparison of Viromes in Endemic and Introduced Passerines in New Zealand. Viruses. 14. PMID 35891346 DOI: 10.3390/v14071364 |
0.304 |
|
| 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, ... ... Holmes EC, 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 |
0.356 |
|
| 2022 |
Sadiq S, Chen YM, Zhang YZ, Holmes EC. Resolving deep evolutionary relationships within the RNA virus phylum . Virus Evolution. 8: veac055. PMID 35795296 DOI: 10.1093/ve/veac055 |
0.397 |
|
| 2022 |
Holmes EC. The Ecology of Viral Emergence. Annual Review of Virology. PMID 35704744 DOI: 10.1146/annurev-virology-100120-015057 |
0.374 |
|
| 2022 |
Mifsud JCO, Gallagher RV, Holmes EC, Geoghegan JL. Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom. Journal of Virology. e0026022. PMID 35638822 DOI: 10.1128/jvi.00260-22 |
0.317 |
|
| 2022 |
Eden JS, Sikazwe C, Xie R, Deng YM, Sullivan SG, Michie A, Levy A, Cutmore E, Blyth CC, Britton PN, Crawford N, Dong X, Dwyer DE, Edwards KM, Horsburgh BA, ... ... Holmes EC, et al. Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nature Communications. 13: 2884. PMID 35610217 DOI: 10.1038/s41467-022-30485-3 |
0.414 |
|
| 2022 |
Wille M, Grillo V, Ban de Gouvea Pedroso S, Burgess GW, Crawley A, Dickason C, Hansbro PM, Hoque MA, Horwood PF, Kirkland PD, Kung NY, Lynch SE, Martin S, McArthur M, O'Riley K, ... ... Holmes EC, et al. Australia as a global sink for the genetic diversity of avian influenza A virus. Plos Pathogens. 18: e1010150. PMID 35536868 DOI: 10.1371/journal.ppat.1010150 |
0.47 |
|
| 2022 |
French R, Charon J, Lay CL, Muller C, Holmes EC. Human land use impacts viral diversity and abundance in a New Zealand river. Virus Evolution. 8: veac032. PMID 35494173 DOI: 10.1093/ve/veac032 |
0.332 |
|
| 2022 |
Feng KH, Brown JD, Turner GG, Holmes EC, Allison AB. Unrecognized diversity of mammalian orthoreoviruses in North American bats. Virology. 571: 1-11. PMID 35421704 DOI: 10.1016/j.virol.2022.03.012 |
0.314 |
|
| 2022 |
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Vieira Santos E, Aburjaile F, Xavier J, Fritsch H, Ribeiro Adelino TE, Pereira F, ... ... Holmes EC, et al. Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil. Medrxiv : the Preprint Server For Health Sciences. PMID 35378755 DOI: 10.1101/2021.10.07.21264644 |
0.354 |
|
| 2022 |
He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, ... ... Holmes EC, et al. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell. PMID 35298912 DOI: 10.1016/j.cell.2022.02.014 |
0.378 |
|
| 2022 |
Feng Y, Gou QY, Yang WH, Wu WC, Wang J, Holmes EC, Liang G, Shi M. A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes. Virus Evolution. 8: veac006. PMID 35242359 DOI: 10.1093/ve/veac006 |
0.453 |
|
| 2022 |
Perry BJ, Darestani MM, Ara MG, Hoste A, Jandt JM, Dutoit L, Holmes EC, Ingram T, Geoghegan JL. Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition. Viruses. 14. PMID 35215850 DOI: 10.3390/v14020257 |
0.406 |
|
| 2022 |
Shi M, Zhao S, Yu B, Wu WC, Hu Y, Tian JH, Yin W, Ni F, Hu HL, Geng S, Tan L, Peng Y, Song ZG, Wang W, Chen YM, ... Holmes EC, et al. Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. Plos Pathogens. 18: e1010259. PMID 35176118 DOI: 10.1371/journal.ppat.1010259 |
0.387 |
|
| 2022 |
Harvey E, Holmes EC. Diversity and evolution of the animal virome. Nature Reviews. Microbiology. PMID 34983966 DOI: 10.1038/s41579-021-00665-x |
0.427 |
|
| 2021 |
Charon J, Murray S, Holmes EC. Revealing RNA virus diversity and evolution in unicellular algae transcriptomes. Virus Evolution. 7: veab070. PMID 36819971 DOI: 10.1093/ve/veab070 |
0.342 |
|
| 2021 |
Charon J, Murray S, Holmes EC. Revealing RNA virus diversity and evolution in unicellular algae transcriptomes. Virus Evolution. 7: veab070. PMID 36819971 DOI: 10.1093/ve/veab070 |
0.342 |
|
| 2021 |
Van Brussel K, Holmes EC. Zoonotic disease and virome diversity in bats. Current Opinion in Virology. 52: 192-202. PMID 34954661 DOI: 10.1016/j.coviro.2021.12.008 |
0.37 |
|
| 2021 |
Porter AF, Cobbin J, Li CX, Eden JS, Holmes EC. Metagenomic Identification of Viral Sequences in Laboratory Reagents. Viruses. 13. PMID 34834931 DOI: 10.3390/v13112122 |
0.38 |
|
| 2021 |
Mahar JE, Jenckel M, Huang N, Smertina E, Holmes EC, Strive T, Hall RN. Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus Evolution. 7: veab080. PMID 34754513 DOI: 10.1093/ve/veab080 |
0.334 |
|
| 2021 |
Duchene S, Featherstone L, Freiesleben de Blasio B, Holmes EC, Bohlin J, Pettersson JH. The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution. Euro Surveillance : Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin. 26. PMID 34738512 DOI: 10.2807/1560-7917.ES.2021.26.44.2001996 |
0.342 |
|
| 2021 |
Ortiz-Baez AS, Shi M, Hoffmann AA, Holmes EC. RNA virome diversity and infection in individual flies. The Journal of General Virology. 102. PMID 34704919 DOI: 10.1099/jgv.0.001639 |
0.466 |
|
| 2021 |
Bordicchia M, Fumian TM, Van Brussel K, Russo AG, Carrai M, Le SJ, Pesavento PA, Holmes EC, Martella V, White P, Beatty JA, Shi M, Barrs VR. Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks. Viruses. 13. PMID 34696470 DOI: 10.3390/v13102040 |
0.374 |
|
| 2021 |
Cobbin JC, Charon J, Harvey E, Holmes EC, Mahar JE. Current challenges to virus discovery by meta-transcriptomics. Current Opinion in Virology. 51: 48-55. PMID 34592710 DOI: 10.1016/j.coviro.2021.09.007 |
0.429 |
|
| 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, ... ... Holmes EC, 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 |
0.363 |
|
| 2021 |
Miller AK, Mifsud JCO, Costa VA, Grimwood RM, Kitson J, Baker C, Brosnahan CL, Pande A, Holmes EC, Gemmell NJ, Geoghegan JL. Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the . Virus Evolution. 7: veab050. PMID 34527280 DOI: 10.1093/ve/veab050 |
0.418 |
|
| 2021 |
Telenti A, Arvin A, Corey L, Corti D, Diamond MS, García-Sastre A, Garry RF, Holmes EC, Pang P, Virgin HW. After the pandemic: perspectives on the future trajectory of COVID-19. Nature. PMID 34237771 DOI: 10.1038/s41586-021-03792-w |
0.352 |
|
| 2021 |
Wille M, Shi M, Hurt AC, Klaassen M, Holmes EC. RNA virome abundance and diversity is associated with host age in a bird species. Virology. 561: 98-106. PMID 34182259 DOI: 10.1016/j.virol.2021.06.007 |
0.416 |
|
| 2021 |
Zhou H, Ji J, Chen X, Bi Y, Li J, Wang Q, Hu T, Song H, Zhao R, Chen Y, Cui M, Zhang Y, Hughes AC, Holmes EC, Shi W. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell. PMID 34147139 DOI: 10.1016/j.cell.2021.06.008 |
0.422 |
|
| 2021 |
Chappell JG, Tsoleridis T, Clark G, Berry L, Holmes N, Moore C, Carlile M, Sang F, Debebe BJ, Wright V, Irving WL, Thomson BJ, Boswell TCJ, Willingham I, Joseph A, ... ... Holmes EC, et al. Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. The Journal of General Virology. 102. PMID 34130773 DOI: 10.1099/jgv.0.001595 |
0.377 |
|
| 2021 |
Barnard KN, Wasik BR, Alford-Lawrence BK, Hayward JJ, Weichert WS, Voorhees IEH, Holmes EC, Parrish CR. Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. Journal of Evolutionary Biology. PMID 34114711 DOI: 10.1111/jeb.13890 |
0.338 |
|
| 2021 |
Chandra S, Harvey E, Emery D, Holmes EC, Šlapeta J. Unbiased Characterization of the Microbiome and Virome of Questing Ticks. Frontiers in Microbiology. 12: 627327. PMID 34054743 DOI: 10.3389/fmicb.2021.627327 |
0.35 |
|
| 2021 |
Costa VA, Mifsud JCO, Gilligan D, Williamson JE, Holmes EC, Geoghegan JL. Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia. Virus Evolution. 7: veab034. PMID 34017611 DOI: 10.1093/ve/veab034 |
0.388 |
|
| 2021 |
Di Giallonardo F, Puglia I, Curini V, Cammà C, Mangone I, Calistri P, Cobbin JCA, Holmes EC, Lorusso A. Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy. Viruses. 13. PMID 33946747 DOI: 10.3390/v13050794 |
0.306 |
|
| 2021 |
Geoghegan JL, Douglas J, Ren X, Storey M, Hadfield J, Silander OK, Freed NE, Jelley L, Jefferies S, Sherwood J, Paine S, Huang S, Sporle A, Baker MG, Murdoch DR, ... ... Holmes EC, et al. Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand. Emerging Infectious Diseases. 27: 1317-1322. PMID 33900175 DOI: 10.3201/eid2705.204579 |
0.369 |
|
| 2021 |
Gräf T, Vazquez C, Giovanetti M, de Bruycker-Nogueira F, Fonseca V, Claro IM, de Jesus JG, Gómez A, Xavier J, de Mendonça MCL, Villalba S, Torales J, Gamarra ML, Thézé J, de Filippis AMB, ... ... Holmes EC, et al. Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay. Emerging Infectious Diseases. 27: 1393-1404. PMID 33900172 DOI: 10.3201/eid2705.204244 |
0.492 |
|
| 2021 |
Wille M, Geoghegan JL, Holmes EC. How accurately can we assess zoonotic risk? Plos Biology. 19: e3001135. PMID 33878111 DOI: 10.1371/journal.pbio.3001135 |
0.317 |
|
| 2021 |
Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, ... ... Holmes EC, et al. Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil. Nature Communications. 12: 2296. PMID 33863880 DOI: 10.1038/s41467-021-22607-0 |
0.375 |
|
| 2021 |
Yang R, Peng J, Zhai J, Xiao K, Zhang X, Li X, Chen X, Chen ZJ, Holmes EC, Irwin DM, Shan F, Shen X, Chen W, Shen Y. Pathogenicity and transmissibility of a novel respirovirus isolated from a Malayan pangolin. The Journal of General Virology. 102. PMID 33843572 DOI: 10.1099/jgv.0.001586 |
0.429 |
|
| 2021 |
Grimwood RM, Holmes EC, Geoghegan JL. A Novel Rubi-Like Virus in the Pacific Electric Ray () Reveals the Complex Evolutionary History of the . Viruses. 13. PMID 33807136 DOI: 10.3390/v13040585 |
0.463 |
|
| 2021 |
Geoghegan JL, Di Giallonardo F, Wille M, Ortiz-Baez AS, Costa VA, Ghaly T, Mifsud JCO, Turnbull OMH, Bellwood DR, Williamson JE, Holmes EC. Virome composition in marine fish revealed by meta-transcriptomics. Virus Evolution. 7: veab005. PMID 33623709 DOI: 10.1093/ve/veab005 |
0.409 |
|
| 2021 |
Alfsnes K, Lagerqvist N, Vene S, Bohlin J, Verner-Carlsson J, Ekqvist D, Bråve A, Holmes EC, Shi W, Pettersson JH. Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990. One Health (Amsterdam, Netherlands). 12: 100217. PMID 33553563 DOI: 10.1016/j.onehlt.2021.100217 |
0.33 |
|
| 2021 |
Hu T, Li J, Zhou H, Li C, Holmes EC, Shi W. Bioinformatics resources for SARS-CoV-2 discovery and surveillance. Briefings in Bioinformatics. PMID 33416890 DOI: 10.1093/bib/bbaa386 |
0.309 |
|
| 2020 |
Guo JJ, Lin XD, Chen YM, Hao ZY, Wang ZX, Yu ZM, Lu M, Li K, Qin XC, Wang W, Holmes EC, Hou W, Zhang YZ. Diversity and circulation of Jingmen tick virus in ticks and mammals. Virus Evolution. 6: veaa051. PMID 33976906 DOI: 10.1093/ve/veaa051 |
0.444 |
|
| 2020 |
Campbell SJ, Ashley W, Gil-Fernandez M, Newsome TM, Di Giallonardo F, Ortiz-Baez AS, Mahar JE, Towerton AL, Gillings M, Holmes EC, Carthey AJR, Geoghegan JL. Red fox viromes in urban and rural landscapes. Virus Evolution. 6: veaa065. PMID 33365150 DOI: 10.1093/Ve/Veaa065 |
0.357 |
|
| 2020 |
Di Giallonardo F, Duchene S, Puglia I, Curini V, Profeta F, Cammà C, Marcacci M, Calistri P, Holmes EC, Lorusso A. Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses. 12. PMID 33327566 DOI: 10.3390/v12121438 |
0.319 |
|
| 2020 |
Wang W, Lin XD, Zhang HL, Wang MR, Guan XQ, Holmes EC, Zhang YZ. Extensive genetic diversity and host range of rodent-borne coronaviruses. Virus Evolution. 6: veaa078. PMID 33318860 DOI: 10.1093/ve/veaa078 |
0.419 |
|
| 2020 |
Geoghegan JL, Ren X, Storey M, Hadfield J, Jelley L, Jefferies S, Sherwood J, Paine S, Huang S, Douglas J, Mendes FK, Sporle A, Baker MG, Murdoch DR, French N, ... ... Holmes EC, et al. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nature Communications. 11: 6351. PMID 33311501 DOI: 10.1038/s41467-020-20235-8 |
0.359 |
|
| 2020 |
Di Teodoro G, Valleriani F, Puglia I, Monaco F, Di Pancrazio C, Luciani M, Krasteva I, Petrini A, Marcacci M, D'Alterio N, Curini V, Iorio M, Migliorati G, Di Domenico M, Morelli D, ... ... Holmes EC, et al. SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Veterinary Microbiology. 252: 108933. PMID 33278734 DOI: 10.1016/j.vetmic.2020.108933 |
0.331 |
|
| 2020 |
Porter AF, Pettersson JH, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC. Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evolution. 6: veaa064. PMID 33240526 DOI: 10.1093/Ve/Veaa064 |
0.569 |
|
| 2020 |
Brussel KV, Wang X, Shi M, Carrai M, Li J, Martella V, Beatty JA, Holmes EC, Barrs VR. Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats. Viruses. 12. PMID 33198334 DOI: 10.3390/v12111301 |
0.444 |
|
| 2020 |
Turnbull OMH, Ortiz-Baez AS, Eden JS, Shi M, Williamson JE, Gaston TF, Zhang YZ, Holmes EC, Geoghegan JL. Meta-Transcriptomic Identification of Divergent in Fish. Viruses. 12. PMID 33158212 DOI: 10.3390/v12111254 |
0.438 |
|
| 2020 |
Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses. 12. PMID 33086653 DOI: 10.3390/v12101180 |
0.369 |
|
| 2020 |
Lay CL, Shi M, Buček A, Bourguignon T, Lo N, Holmes EC. Unmapped RNA Virus Diversity in Termites and their Symbionts. Viruses. 12. PMID 33050289 DOI: 10.3390/v12101145 |
0.421 |
|
| 2020 |
Parry R, Wille M, Turnbull OMH, Geoghegan JL, Holmes EC. Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association. Viruses. 12. PMID 32962015 DOI: 10.3390/V12091042 |
0.52 |
|
| 2020 |
Ortiz-Baez AS, Cousins K, Eden JS, Chang WS, Harvey E, Pettersson JH, Carver S, Polkinghorne A, Šlapeta J, Rose K, Holmes EC. Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia. Parasites & Vectors. 13: 447. PMID 32891158 DOI: 10.1186/S13071-020-04325-6 |
0.363 |
|
| 2020 |
Pettersson JH, Ellström P, Ling J, Nilsson I, Bergström S, González-Acuña D, Olsen B, Holmes EC. Circumpolar diversification of the Ixodes uriae tick virome. Plos Pathogens. 16: e1008759. PMID 32745135 DOI: 10.1371/Journal.Ppat.1008759 |
0.569 |
|
| 2020 |
Xavier J, Giovanetti M, Adelino T, Fonseca V, Barbosa da Costa AV, Ribeiro AA, Felicio KN, Duarte CG, Ferreira Silva MV, Salgado Á, Lima MT, de Jesus R, Fabri A, Soares Zoboli CF, Souza Santos TG, ... ... Holmes EC, et al. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerging Microbes & Infections. 9: 1824-1834. PMID 32726185 DOI: 10.1080/22221751.2020.1803146 |
0.43 |
|
| 2020 |
Duggan AT, Klunk J, Porter AF, Dhody AN, Hicks R, Smith GL, Humphreys M, McCollum AM, Davidson WB, Wilkins K, Li Y, Burke A, Polasky H, Flanders L, Poinar D, ... ... Holmes EC, et al. The origins and genomic diversity of American Civil War Era smallpox vaccine strains. Genome Biology. 21: 175. PMID 32684155 DOI: 10.1186/S13059-020-02079-Z |
0.324 |
|
| 2020 |
Wille M, Holmes EC. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. Fems Microbiology Reviews. PMID 32672814 DOI: 10.1093/Femsre/Fuaa026 |
0.491 |
|
| 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 |
0.544 |
|
| 2020 |
Pollock DD, Castoe TA, Perry BW, Lytras S, Wade KJ, Robertson DL, Holmes EC, Boni MF, Kosakovsky Pond SL, Parry R, Carlton EJ, Wood JLN, Pennings PS, Goldstein RA. Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Molecular Biology and Evolution. PMID 32658964 DOI: 10.1093/Molbev/Msaa178 |
0.492 |
|
| 2020 |
Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, Eden JS, Chang S, Gall M, Draper J, Sim EM, Bachmann NL, Carter I, Basile K, Byun R, ... ... Holmes EC, et al. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature Medicine. PMID 32647358 DOI: 10.1038/S41591-020-1000-7 |
0.413 |
|
| 2020 |
Chang WS, Eden JS, Hall J, Shi M, Rose K, Holmes EC. Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease. Journal of Virology. PMID 32581107 DOI: 10.1128/Jvi.00606-20 |
0.485 |
|
| 2020 |
Ling J, Vinnersten TP, Hesson JC, Bohlin J, Roligheten E, Holmes EC, Pettersson JH. Identification of hepatitis C virus in the common bed bug - a potential, but uncommon route for HCV infection? Emerging Microbes & Infections. 1-10. PMID 32525459 DOI: 10.1080/22221751.2020.1780950 |
0.39 |
|
| 2020 |
Ortiz-Baez AS, Eden JS, Moritz C, Holmes EC. A Divergent in an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons. Viruses. 12. PMID 32512909 DOI: 10.3390/V12060613 |
0.462 |
|
| 2020 |
Faye O, de Lourdes Monteiro M, Vrancken B, Prot M, Lequime S, Diarra M, Ndiaye O, Valdez T, Tavarez S, Ramos J, da Veiga Leal S, Pires C, Moreira A, Tavares MF, Fernandes L, ... ... Holmes EC, et al. Genomic Epidemiology of 2015-2016 Zika Virus Outbreak in Cape Verde. Emerging Infectious Diseases. 26: 1084-1090. PMID 32441631 DOI: 10.3201/Eid2606.190928 |
0.517 |
|
| 2020 |
Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Current Biology : Cb. PMID 32416074 DOI: 10.1016/J.Cub.2020.05.023 |
0.45 |
|
| 2020 |
Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O'Sullivan MV, Sintchenko V, ... ... Holmes EC, et al. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evolution. 6: veaa027. PMID 32296544 DOI: 10.1093/Ve/Veaa027 |
0.463 |
|
| 2020 |
Gao WH, Lin XD, Chen YM, Xie CG, Tan ZZ, Zhou JJ, Chen S, Holmes EC, Zhang YZ. Newly identified viral genomes in pangolins with fatal disease. Virus Evolution. 6: veaa020. PMID 32296543 DOI: 10.1093/Ve/Veaa020 |
0.558 |
|
| 2020 |
Wille M, Harvey E, Shi M, Gonzalez-Acuña D, Holmes EC, Hurt AC. Sustained RNA virome diversity in Antarctic penguins and their ticks. The Isme Journal. PMID 32286545 DOI: 10.1038/S41396-020-0643-1 |
0.516 |
|
| 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 |
0.319 |
|
| 2020 |
Hayward JA, Tachedjian M, Kohl C, Johnson A, Dearnley M, Jesaveluk B, Langer C, Solymosi PD, Hille G, Nitsche A, Sánchez CA, Werner A, Kontos D, Crameri G, Marsh GA, ... ... Holmes EC, et al. Infectious KoRV-related retroviruses circulating in Australian bats. Proceedings of the National Academy of Sciences of the United States of America. PMID 32284399 DOI: 10.1073/Pnas.1915400117 |
0.509 |
|
| 2020 |
Zhang YZ, Holmes EC. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell. PMID 32220310 DOI: 10.1016/J.Cell.2020.03.035 |
0.462 |
|
| 2020 |
Lam TT, Shum MH, Zhu HC, Tong YG, Ni XB, Liao YS, Wei W, Cheung WY, Li WJ, Li LF, Leung GM, Holmes EC, Hu YL, Guan Y. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. PMID 32218527 DOI: 10.1038/S41586-020-2169-0 |
0.417 |
|
| 2020 |
Mahar JE, Shi M, Hall RN, Strive T, Holmes EC. Comparative analysis of RNA virome composition in rabbits and associated ectoparasites. Journal of Virology. PMID 32188733 DOI: 10.1128/Jvi.02119-19 |
0.566 |
|
| 2020 |
Li CX, Li W, Zhou J, Zhang B, Feng Y, Xu CP, Lu YY, Holmes EC, Shi M. High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection. Scientific Reports. 10: 3963. PMID 32127629 DOI: 10.1038/S41598-020-60992-6 |
0.46 |
|
| 2020 |
R Marcelino V, Holmes EC, Sorrell TC. The use of taxon-specific reference databases compromises metagenomic classification. Bmc Genomics. 21: 184. PMID 32106809 DOI: 10.1186/S12864-020-6592-2 |
0.385 |
|
| 2020 |
Schlub TE, Holmes EC. Properties and abundance of overlapping genes in viruses. Virus Evolution. 6: veaa009. PMID 32071766 DOI: 10.1093/Ve/Veaa009 |
0.494 |
|
| 2020 |
Grubaugh ND, Petrone ME, Holmes EC. We shouldn't worry when a virus mutates during disease outbreaks. Nature Microbiology. PMID 32071422 DOI: 10.1038/S41564-020-0690-4 |
0.4 |
|
| 2020 |
Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, ... ... Holmes EC, et al. A new coronavirus associated with human respiratory disease in China. Nature. PMID 32015508 DOI: 10.1038/S41586-020-2008-3 |
0.454 |
|
| 2020 |
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, ... ... Holmes EC, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet (London, England). PMID 32007145 DOI: 10.1016/S0140-6736(20)30251-8 |
0.473 |
|
| 2020 |
Carrai M, Van Brussel K, Shi M, Li CX, Chang WS, Munday JS, Voss K, McLuckie A, Taylor D, Laws A, Holmes EC, Barrs VR, Beatty JA. Identification of A Novel Papillomavirus Associated with Squamous Cell Carcinoma in A Domestic Cat. Viruses. 12. PMID 31968684 DOI: 10.3390/V12010124 |
0.37 |
|
| 2020 |
Batovska J, Buchmann JP, Holmes EC, Lynch SE. Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes. Microbiology Resource Announcements. 9. PMID 31919150 DOI: 10.1128/MRA.01476-19 |
0.388 |
|
| 2020 |
Guo J, Lin X, Chen Y, Hao Z, Wang Z, Yu Z, Lu M, Li K, Qin X, Wang W, Holmes EC, Hou W, Zhang Y. Diversity and circulation of Jingmen tick virus in ticks and mammals Virus Evolution. DOI: 10.1093/Ve/Veaa051 |
0.544 |
|
| 2019 |
Tsoleridis T, Chappell JG, Monchatre-Leroy E, Umhang G, Shi M, Bennett M, Tarlinton RE, McClure CP, Holmes EC, Ball JK. Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits. Viruses. 12. PMID 31906044 DOI: 10.3390/V12010047 |
0.551 |
|
| 2019 |
Cunha MDP, Duarte-Neto AN, Pour SZ, Ortiz-Baez AS, Černý J, Pereira BBS, Braconi CT, Ho YL, Perondi B, Sztajnbok J, Alves VAF, Dolhnikoff M, Holmes EC, Saldiva PHN, Zanotto PMA. Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases. Scientific Reports. 9: 20418. PMID 31892699 DOI: 10.1038/S41598-019-56650-1 |
0.525 |
|
| 2019 |
Charon J, Grigg MJ, Eden JS, Piera KA, Rana H, William T, Rose K, Davenport MP, Anstey NM, Holmes EC. Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease. Plos Pathogens. 15: e1008216. PMID 31887217 DOI: 10.1371/Journal.Ppat.1008216 |
0.459 |
|
| 2019 |
Wille M, Holmes EC. The Ecology and Evolution of Influenza Viruses. Cold Spring Harbor Perspectives in Medicine. PMID 31871237 DOI: 10.1101/Cshperspect.A038489 |
0.554 |
|
| 2019 |
Van Brussel K, Carrai M, Lin C, Kelman M, Setyo L, Aberdein D, Brailey J, Lawler M, Maher S, Plaganyi I, Lewis E, Hawkswell A, Allison AB, Meers J, Martella V, ... ... Holmes EC, et al. Distinct Lineages of Feline Parvovirus Associated with Epizootic Outbreaks in Australia, New Zealand and the United Arab Emirates. Viruses. 11. PMID 31847268 DOI: 10.3390/V11121155 |
0.412 |
|
| 2019 |
Novelo M, Hall MD, Pak D, Young PR, Holmes EC, McGraw EA. Intra-host growth kinetics of dengue virus in the mosquito Aedes aegypti. Plos Pathogens. 15: e1008218. PMID 31790509 DOI: 10.1371/Journal.Ppat.1008218 |
0.479 |
|
| 2019 |
Chen Y, Wei X, Zhang G, Holmes EC, Cui J. Identification and evolution of avian endogenous foamy viruses. Virus Evolution. 5: vez049. PMID 31777663 DOI: 10.1093/Ve/Vez049 |
0.561 |
|
| 2019 |
Porter AF, Shi M, Eden JS, Zhang YZ, Holmes EC. Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics. Viruses. 11. PMID 31775324 DOI: 10.3390/V11121092 |
0.448 |
|
| 2019 |
French RK, Holmes EC. An Ecosystems Perspective on Virus Evolution and Emergence. Trends in Microbiology. PMID 31744665 DOI: 10.1016/J.Tim.2019.10.010 |
0.526 |
|
| 2019 |
Pettersson JH, Shi M, Eden JS, Holmes EC, Hesson JC. Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors and in Northern Europe. Viruses. 11. PMID 31698792 DOI: 10.3390/V11111033 |
0.481 |
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| 2019 |
Bucek A, Šobotník J, He S, Shi M, McMahon DP, Holmes EC, Roisin Y, Lo N, Bourguignon T. Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies. Current Biology : Cb. PMID 31630948 DOI: 10.1016/J.Cub.2019.08.076 |
0.369 |
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| 2019 |
Voorhees IEH, Lee H, Allison AB, Lopez-Astacio R, Goodman LB, Oyesola OO, Omobowale O, Fagbohun O, Dubovi EJ, Hafenstein SL, Holmes EC, Parrish CR. Limited intra-host diversity and background evolution accompany 40 years of canine parvovirus host adaptation and spread. Journal of Virology. PMID 31619551 DOI: 10.1128/Jvi.01162-19 |
0.525 |
|
| 2019 |
Lu M, Li F, Liao Y, Shen JJ, Xu JM, Chen YZ, Li JH, Holmes EC, Zhang YZ. Epidemiology and Diversity of Rickettsiales Bacteria in Humans and Animals in Jiangsu and Jiangxi provinces, China. Scientific Reports. 9: 13176. PMID 31511528 DOI: 10.1038/S41598-019-49059-3 |
0.373 |
|
| 2019 |
Wasik BR, Voorhees IEH, Barnard KN, Alford-Lawrence BK, Weichert WS, Hood G, Nogales A, Martínez-Sobrido L, Holmes EC, Parrish CR. Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. Journal of Virology. PMID 31511393 DOI: 10.1128/Jvi.01039-19 |
0.525 |
|
| 2019 |
Pettersson JH, Piorkowski G, Mayxay M, Rattanavong S, Vongsouvath M, Davong V, Alfsnes K, Eldholm V, de Lamballerie X, Holmes EC, Newton PN, Dubot-Pérès A. Meta-transcriptomic identification of hepatitis B virus in cerebrospinal fluid in patients with central nervous system disease. Diagnostic Microbiology and Infectious Disease. 114878. PMID 31451314 DOI: 10.1016/J.Diagmicrobio.2019.114878 |
0.432 |
|
| 2019 |
Poon LLM, Song T, Wentworth DE, Holmes EC, Greenbaum BD, Peiris JSM, Cowling BJ, Ghedin E. Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'. Nature Genetics. PMID 31406345 DOI: 10.1038/S41588-019-0486-8 |
0.451 |
|
| 2019 |
Li CX, Chang WS, Mitsakos K, Rodger J, Holmes EC, Hudson BJ. Identification of a Novel Equine Papillomavirus in Semen from a Thoroughbred Stallion with a Penile Lesion. Viruses. 11. PMID 31382657 DOI: 10.3390/V11080713 |
0.43 |
|
| 2019 |
Shi W, Ke C, Fang S, Li J, Song H, Li X, Hu T, Wu J, Chen T, Yi L, Song Y, Wang X, Xing W, Huang W, Xiao H, ... ... Holmes EC, et al. Co-circulation and persistence of multiple A/H3N2 influenza variants in China. Emerging Microbes & Infections. 8: 1157-1167. PMID 31373538 DOI: 10.1080/22221751.2019.1648183 |
0.42 |
|
| 2019 |
Chang WS, Pettersson JH, Le Lay C, Shi M, Lo N, Wille M, Eden JS, Holmes EC. Novel hepatitis D-like agents in vertebrates and invertebrates. Virus Evolution. 5: vez021. PMID 31321078 DOI: 10.1093/Ve/Vez021 |
0.56 |
|
| 2019 |
Harvey E, Rose K, Eden JS, Lawrence A, Doggett SL, Holmes EC. Identification of diverse arthropod associated viruses in native Australian fleas. Virology. 535: 189-199. PMID 31319276 DOI: 10.1016/J.Virol.2019.07.010 |
0.551 |
|
| 2019 |
Wang J, Firth C, Amos-Ritchie R, Davis SS, Yin H, Holmes EC, Blasdell KR, Walker PJ. Evolutionary history of Simbu serogroup orthobunyaviruses in the Australian episystem. Virology. 535: 32-44. PMID 31261025 DOI: 10.1016/J.Virol.2019.06.013 |
0.777 |
|
| 2019 |
Wille M, Shi M, Klaassen M, Hurt AC, Holmes EC. Virome heterogeneity and connectivity in waterfowl and shorebird communities. The Isme Journal. PMID 31239538 DOI: 10.1038/S41396-019-0458-0 |
0.492 |
|
| 2019 |
Bonnaud EM, Troupin C, Dacheux L, Holmes EC, Monchatre-Leroy E, Tanguy M, Bouchier C, Cliquet F, Barrat J, Bourhy H. Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission. Plos Pathogens. 15: e1007799. PMID 31220188 DOI: 10.1371/Journal.Ppat.1007799 |
0.519 |
|
| 2019 |
Koh C, Audsley MD, Di Giallonardo F, Kerton EJ, Young PR, Holmes EC, McGraw EA. Sustained -mediated blocking of dengue virus isolates following serial passage in cell culture. Virus Evolution. 5: vez012. PMID 31191980 DOI: 10.1093/Ve/Vez012 |
0.509 |
|
| 2019 |
Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Telfer B, Cooper C, Price K, Selvey C, Holden J, Bachmann N, Lee FJ, Dwyer DE, Duchêne S, ... Holmes EC, et al. Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia. Viruses. 11. PMID 31137836 DOI: 10.3390/V11050482 |
0.374 |
|
| 2019 |
Zhang YZ, Chen YM, Wang W, Qin XC, Holmes EC. Expanding the RNA Virosphere by Unbiased Metagenomics. Annual Review of Virology. PMID 31100994 DOI: 10.1146/Annurev-Virology-092818-015851 |
0.532 |
|
| 2019 |
Mahar JE, Hall RN, Shi M, Mourant R, Huang N, Strive T, Holmes EC. The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus. Virus Evolution. 5: vez005. PMID 30997155 DOI: 10.1093/Ve/Vez005 |
0.569 |
|
| 2019 |
Holmes EC, Duchêne S. Can Sequence Phylogenies Safely Infer the Origin of the Global Virome? Mbio. 10. PMID 30992348 DOI: 10.1128/Mbio.00289-19 |
0.427 |
|
| 2019 |
Nie FY, Tian JH, Lin XD, Yu B, Xing JG, Cao JH, Holmes EC, Ma RZ, Zhang YZ. Discovery of a highly divergent hepadnavirus in shrews from China. Virology. 531: 162-170. PMID 30884426 DOI: 10.1016/J.Virol.2019.03.007 |
0.544 |
|
| 2019 |
Chong R, Shi M, Grueber CE, Holmes EC, Hogg CJ, Belov K, Barrs VR. Fecal viral diversity of captive and wild Tasmanian devils characterized using virion-enriched metagenomics and meta-transcriptomics. Journal of Virology. PMID 30867308 DOI: 10.1128/Jvi.00205-19 |
0.537 |
|
| 2019 |
Wei X, Chen Y, Duan G, Holmes EC, Cui J. A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evolution. 5: vez001. PMID 30838130 DOI: 10.1093/Ve/Vez001 |
0.568 |
|
| 2019 |
Harvey E, Madden D, Polkinghorne A, Holmes EC. Identification of A Novel Picorna-Like Virus, Burpengary Virus, that is Negatively Associated with Chlamydial Disease in the Koala. Viruses. 11. PMID 30832350 DOI: 10.3390/V11030211 |
0.565 |
|
| 2019 |
Holmes EC, Duchêne S. Evolutionary stasis of viruses? Nature Reviews. Microbiology. PMID 30814682 DOI: 10.1038/S41579-019-0168-7 |
0.544 |
|
| 2019 |
Dehhaghi M, Kazemi Shariat Panahi H, Holmes EC, Hudson BJ, Schloeffel R, Guillemin GJ. Human Tick-Borne Diseases in Australia. Frontiers in Cellular and Infection Microbiology. 9: 3. PMID 30746341 DOI: 10.3389/Fcimb.2019.00003 |
0.485 |
|
| 2019 |
Kerr PJ, Eden JS, Giallonardo FD, Peacock D, Liu J, Strive T, Read AF, Holmes EC. Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia. Journal of Virology. PMID 30728252 DOI: 10.1128/Jvi.01994-18 |
0.589 |
|
| 2019 |
Tsoleridis T, Chappell JG, Onianwa O, Marston DA, Fooks AR, Monchatre-Leroy E, Umhang G, Müller MA, Drexler JF, Drosten C, Tarlinton RE, McClure CP, Holmes EC, Ball JK. Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally. Viruses. 11. PMID 30704076 DOI: 10.3390/V11020125 |
0.409 |
|
| 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 |
0.488 |
|
| 2018 |
Wille M, Netter HJ, Littlejohn M, Yuen L, Shi M, Eden JS, Klaassen M, Holmes EC, Hurt AC. A Divergent Hepatitis D-Like Agent in Birds. Viruses. 10. PMID 30562970 DOI: 10.3390/V10120720 |
0.488 |
|
| 2018 |
Geoghegan JL, Holmes EC. Evolutionary Virology at 40. Genetics. 210: 1151-1162. PMID 30523166 DOI: 10.1534/Genetics.118.301556 |
0.559 |
|
| 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 |
0.351 |
|
| 2018 |
Harvey E, Rose K, Eden JS, Lo N, Abeyasuriya T, Shi M, Doggett SL, Holmes EC. Extensive Diversity of RNA Viruses in Australian Ticks. Journal of Virology. PMID 30404810 DOI: 10.1128/Jvi.01358-18 |
0.541 |
|
| 2018 |
Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC. Hidden diversity and evolution of viruses in market fish. Virus Evolution. 4: vey031. PMID 30397510 DOI: 10.1093/Ve/Vey031 |
0.485 |
|
| 2018 |
Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds. Molecular Ecology. PMID 30375075 DOI: 10.1111/Mec.14918 |
0.561 |
|
| 2018 |
Geoghegan JL, Holmes EC. The phylogenomics of evolving virus virulence. Nature Reviews. Genetics. PMID 30305704 DOI: 10.1038/S41576-018-0055-5 |
0.513 |
|
| 2018 |
Roediger B, Lee Q, Tikoo S, Cobbin JCA, Henderson JM, Jormakka M, O'Rourke MB, Padula MP, Pinello N, Henry M, Wynne M, Santagostino SF, Brayton CF, Rasmussen L, Lisowski L, ... ... Holmes EC, et al. An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis. Cell. PMID 30220458 DOI: 10.1016/J.Cell.2018.08.013 |
0.322 |
|
| 2018 |
Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DE, Holmes EC, Eden JS. Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia. Viruses. 10. PMID 30200580 DOI: 10.3390/V10090476 |
0.525 |
|
| 2018 |
Aghazadeh M, Shi M, Pesavento PA, Durham AC, Polley T, Donahoe SL, Troyer RM, Barrs VR, Holmes EC, Beatty JA. Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma. Viruses. 10. PMID 30200210 DOI: 10.3390/V10090464 |
0.374 |
|
| 2018 |
Zhang YZ, Wu WC, Shi M, Holmes EC. The diversity, evolution and origins of vertebrate RNA viruses. Current Opinion in Virology. 31: 9-16. PMID 30114593 DOI: 10.1016/J.Coviro.2018.07.017 |
0.467 |
|
| 2018 |
Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience. PMID 30101298 DOI: 10.1093/Gigascience/Giy095 |
0.363 |
|
| 2018 |
Schlub TE, Buchmann JP, Holmes EC. A simple method to detect candidate overlapping genes in viruses using single genome sequences. Molecular Biology and Evolution. PMID 30099499 DOI: 10.1093/Molbev/Msy155 |
0.469 |
|
| 2018 |
Shi M, White VL, Schlub T, Eden JS, Hoffmann AA, Holmes EC. No detectable effect of Mel on the prevalence and abundance of the RNA virome of . Proceedings. Biological Sciences. 285. PMID 30051873 DOI: 10.1098/Rspb.2018.1165 |
0.495 |
|
| 2018 |
Panzarin V, Holmes EC, Abbadi M, Zamperin G, Quartesan R, Milani A, Schivo A, Bille L, Dalla Pozza M, Monne I, Toffan A. Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout. Virus Evolution. 4: vey019. PMID 30046454 DOI: 10.1093/Ve/Vey019 |
0.544 |
|
| 2018 |
Cobbin JCA, Britton PN, Burrell R, Thosar D, Selvakumar K, Eden JS, Jones CA, Holmes EC. A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital. Virus Evolution. 4: vey020. PMID 30026965 DOI: 10.1093/Ve/Vey020 |
0.349 |
|
| 2018 |
Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ. Author Correction: The evolutionary history of vertebrate RNA viruses. Nature. PMID 29946168 DOI: 10.1038/S41586-018-0310-0 |
0.34 |
|
| 2018 |
Russo AG, Eden JS, Enosi Tuipulotu D, Shi M, Selechnik D, Shine R, Rollins LA, Holmes EC, White PA. Viral discovery in the invasive Australian cane toad () using metatranscriptomic and genomic approaches. Journal of Virology. PMID 29899109 DOI: 10.1128/Jvi.00768-18 |
0.52 |
|
| 2018 |
Voorhees IEH, Dalziel BD, Glaser A, Dubovi EJ, Murcia PR, Newbury S, Toohey-Kurth K, Su S, Kriti D, Van Bakel H, Goodman LB, Leutenegger C, Holmes EC, Parrish CR. Multiple incursions and recurrent epidemic fade-out of H3N2 canine influenza A virus in the United States. Journal of Virology. PMID 29875234 DOI: 10.1128/Jvi.00323-18 |
0.587 |
|
| 2018 |
Geoghegan JL, Pirotta V, Harvey E, Smith A, Buchmann JP, Ostrowski M, Eden JS, Harcourt R, Holmes EC. Virological Sampling of Inaccessible Wildlife with Drones. Viruses. 10. PMID 29865228 DOI: 10.3390/V10060300 |
0.47 |
|
| 2018 |
Aghazadeh M, Shi M, Barrs VR, McLuckie AJ, Lindsay SA, Jameson B, Hampson B, Holmes EC, Beatty JA. A Novel Hepadnavirus Identified in an Immunocompromised Domestic Cat in Australia. Viruses. 10. PMID 29772771 DOI: 10.3390/V10050269 |
0.494 |
|
| 2018 |
Liu J, Xu J, Liu L, Wei X, Song Y, Fang B, Yu X, Li X, Ye G, Du Y, Chen M, Shi W, Liu D, Holmes EC, Cui J. Publisher Correction: Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China. Scientific Reports. 8: 7588. PMID 29748572 DOI: 10.1038/S41598-018-25257-3 |
0.441 |
|
| 2018 |
Di Giallonardo F, Audsley MD, Shi M, Young PR, McGraw EA, Holmes EC. Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line. The Journal of General Virology. PMID 29741476 DOI: 10.1099/Jgv.0.001079 |
0.539 |
|
| 2018 |
Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ. The evolutionary history of vertebrate RNA viruses. Nature. PMID 29618816 DOI: 10.1038/S41586-018-0012-7 |
0.532 |
|
| 2018 |
Zhang YZ, Shi M, Holmes EC. Using Metagenomics to Characterize an Expanding Virosphere. Cell. 172: 1168-1172. PMID 29522738 DOI: 10.1016/J.Cell.2018.02.043 |
0.507 |
|
| 2018 |
Duchêne S, Holmes EC. Estimating evolutionary rates in giant viruses using ancient genomes. Virus Evolution. 4: vey006. PMID 29511572 DOI: 10.1093/Ve/Vey006 |
0.456 |
|
| 2018 |
Fukuto HS, Vadyvaloo V, McPhee JB, Poinar HN, Holmes EC, Bliska JB. A single amino acid change in the response regulator PhoP acquired duringevolution affects PhoP target gene transcription and polymyxin B susceptibility. Journal of Bacteriology. PMID 29440252 DOI: 10.1128/Jb.00050-18 |
0.311 |
|
| 2018 |
Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC. Correction: Continental synchronicity of human influenza virus epidemics despite climactic variation. Plos Pathogens. 14: e1006903. PMID 29414984 DOI: 10.1371/Journal.Ppat.1006903 |
0.444 |
|
| 2018 |
Liu J, Xu J, Liu L, Wei X, Song Y, Fang B, Yu X, Li X, Ye G, Du Y, Chen M, Shi W, Liu D, Holmes EC, Cui J. Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China. Scientific Reports. 8: 2486. PMID 29410505 DOI: 10.1038/S41598-018-20988-9 |
0.494 |
|
| 2018 |
Leopardi S, Holmes EC, Gastaldelli M, Tassoni L, Priori P, Scaravelli D, Zamperin G, De Benedictis P. Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 29355607 DOI: 10.1016/J.Meegid.2018.01.012 |
0.407 |
|
| 2018 |
Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC. Continental synchronicity of human influenza virus epidemics despite climactic variation. Plos Pathogens. 14: e1006780. PMID 29324895 DOI: 10.1371/Journal.Ppat.1006780 |
0.519 |
|
| 2018 |
Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN. The paradox of HBV evolution as revealed from a 16th century mummy. Plos Pathogens. 14: e1006750. PMID 29300782 DOI: 10.1371/Journal.Ppat.1006750 |
0.489 |
|
| 2017 |
Mahar JE, Read AJ, Gu X, Urakova N, Mourant R, Piper M, Haboury S, Holmes EC, Strive T, Hall RN. Detection and Circulation of a Novel Rabbit Hemorrhagic Disease Virus in Australia. Emerging Infectious Diseases. 24: 22-31. PMID 29260677 DOI: 10.3201/Eid2401.170412 |
0.454 |
|
| 2017 |
Rodríguez-Nevado C, Lam TT, Holmes EC, Pagán I. The impact of host genetic diversity on virus evolution and emergence. Ecology Letters. PMID 29207441 DOI: 10.1111/Ele.12890 |
0.4 |
|
| 2017 |
Nie FY, Lin XD, Hao ZY, Chen XN, Wang ZX, Wang MR, Wu J, Wang HW, Zhao G, Ma RZ, Holmes EC, Zhang YZ. Extensive diversity and evolution of hepadnaviruses in bats in China. Virology. 514: 88-97. PMID 29153861 DOI: 10.1016/J.Virol.2017.11.005 |
0.431 |
|
| 2017 |
Shi M, Zhang YZ, Holmes EC. Meta-transcriptomics and The Evolutionary Biology of RNA Viruses. Virus Research. PMID 29111455 DOI: 10.1016/J.Virusres.2017.10.016 |
0.563 |
|
| 2017 |
Mahar JE, Hall RN, Peacock D, Kovaliski J, Piper M, Mourant R, Huang N, Campbell S, Gu X, Read A, Urakova N, Cox T, Holmes EC, Strive T. Rabbit haemorrhagic disease virus 2 (GI.2) is replacing endemic strains of RHDV in the Australian landscape within 18 months of its arrival. Journal of Virology. PMID 29093089 DOI: 10.1128/Jvi.01374-17 |
0.472 |
|
| 2017 |
Qi W, Jia W, Liu D, Li J, Bi Y, Xie S, Li B, Hu T, Du Y, Xing L, Zhang J, Zhang F, Wei X, Eden JS, Li H, ... ... Holmes EC, et al. Emergence and adaptation of a novel highly pathogenic H7N9 influenza virus in birds and humans from a 2013-human-infecting low pathogenic ancestor. Journal of Virology. PMID 29070694 DOI: 10.1128/Jvi.00921-17 |
0.519 |
|
| 2017 |
Geoghegan JL, Holmes EC. Predicting virus emergence amid evolutionary noise. Open Biology. 7. PMID 29070612 DOI: 10.1098/Rsob.170189 |
0.493 |
|
| 2017 |
Porter AF, Duggan AT, Poinar HN, Holmes EC. Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses. 9. PMID 28956829 DOI: 10.3390/V9100276 |
0.371 |
|
| 2017 |
Pettersson JH, Shi M, Bohlin J, Eldholm V, Brynildsrud OB, Paulsen KM, Andreassen Å, Holmes EC. Characterizing the virome of Ixodes ricinus ticks from northern Europe. Scientific Reports. 7: 10870. PMID 28883464 DOI: 10.1038/S41598-017-11439-Y |
0.578 |
|
| 2017 |
Voorhees IEH, Glaser AL, Toohey-Kurth K, Newbury S, Dalziel BD, Dubovi EJ, Poulsen K, Leutenegger C, Willgert KJE, Brisbane-Cohen L, Richardson-Lopez J, Holmes EC, Parrish CR. Spread of Canine Influenza A(H3N2) Virus, United States. Emerging Infectious Diseases. 23. PMID 28858604 DOI: 10.3201/Eid2312.170246 |
0.527 |
|
| 2017 |
Kerr PJ, Cattadori IM, Liu J, Sim DG, Dodds JW, Brooks JW, Kennett MJ, Holmes EC, Read AF. Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype. Proceedings of the National Academy of Sciences of the United States of America. PMID 28808019 DOI: 10.1073/Pnas.1710336114 |
0.476 |
|
| 2017 |
Eden JS, Chisholm RH, Bull RA, White PA, Holmes EC, Tanaka MM. Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution. 3: vex018. PMID 28775894 DOI: 10.1093/Ve/Vex018 |
0.442 |
|
| 2017 |
Liu J, Cattadori IM, Sim DG, Eden JS, Holmes EC, Read AF, Kerr PJ. Reverse engineering field isolates of myxoma virus demonstrates that some gene disruptions or loss of function do not explain virulence changes observed in the field. Journal of Virology. PMID 28768866 DOI: 10.1128/Jvi.01289-17 |
0.423 |
|
| 2017 |
Wang W, Lin XD, Liao Y, Guan XQ, Guo WP, Xing JG, Holmes EC, Zhang YZ. Discovery of a highly divergent coronavirus in the Asian house shrew from China illuminates the origin of the alphacoronaviruses. Journal of Virology. PMID 28637760 DOI: 10.1128/Jvi.00764-17 |
0.574 |
|
| 2017 |
Shi M, Neville P, Nicholson J, Eden JS, Imrie A, Holmes EC. High Resolution Meta-Transcriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. Journal of Virology. PMID 28637756 DOI: 10.1128/Jvi.00680-17 |
0.562 |
|
| 2017 |
Fourment M, Darling AE, Holmes EC. The impact of migratory flyways on the spread of avian influenza virus in North America. Bmc Evolutionary Biology. 17: 118. PMID 28545432 DOI: 10.1186/S12862-017-0965-4 |
0.503 |
|
| 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, ... ... Holmes EC, et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. PMID 28538727 DOI: 10.1038/Nature22401 |
0.5 |
|
| 2017 |
Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. Journal of Virology. PMID 28515299 DOI: 10.1128/Jvi.00158-17 |
0.541 |
|
| 2017 |
Lu M, Tian JH, Yu B, Guo WP, Holmes EC, Zhang YZ. Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China. Ticks and Tick-Borne Diseases. PMID 28411028 DOI: 10.1016/J.Ttbdis.2017.03.006 |
0.337 |
|
| 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, ... ... Holmes EC, et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. PMID 28405027 DOI: 10.1038/Nature22040 |
0.517 |
|
| 2017 |
Du Y, Chen M, Yang J, Jia Y, Han S, Holmes EC, Cui J. Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China. Journal of Virology. PMID 28404845 DOI: 10.1128/Jvi.00143-17 |
0.526 |
|
| 2017 |
Simon-Loriere E, Faye O, Prot M, Casademont I, Fall G, Fernandez-Garcia MD, Diagne MM, Kipela JM, Fall IS, Holmes EC, Sakuntabhai A, Sall AA. Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa. The New England Journal of Medicine. 376: 1483-1485. PMID 28402771 DOI: 10.1056/Nejmc1701600 |
0.504 |
|
| 2017 |
Lin XD, Wang W, Hao ZY, Wang ZX, Guo WP, Guan XQ, Wang MR, Wang HW, Zhou RH, Li MH, Tang GP, Wu J, Holmes EC, Zhang YZ. Extensive diversity of coronaviruses in bats from China. Virology. 507: 1-10. PMID 28384506 DOI: 10.1016/J.Virol.2017.03.019 |
0.416 |
|
| 2017 |
Nicholson LJ, Mahar JE, Strive T, Zheng T, Holmes EC, Ward VK, Duckworth JA. Discovery and characterization of a benign rabbit calicivirus in New Zealand. Applied and Environmental Microbiology. PMID 28363968 DOI: 10.1128/Aem.00090-17 |
0.347 |
|
| 2017 |
Cobbin JC, Alfelali M, Barasheed O, Taylor J, Dwyer DE, Kok J, Booy R, Holmes EC, Rashid H. Multiple sources of genetic diversity of influenza A viruses during the Hajj. Journal of Virology. PMID 28331081 DOI: 10.1128/Jvi.00096-17 |
0.548 |
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| 2017 |
Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Dresely V, Farrell M, Farrer AG, Francken M, Gully N, Haak W, ... ... Holmes EC, et al. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. PMID 28273061 DOI: 10.1038/Nature21674 |
0.335 |
|
| 2017 |
Kerr PJ, Cattadori IM, Rogers MB, Fitch A, Geber A, Liu J, Sim DG, Boag B, Eden JS, Ghedin E, Read AF, Holmes EC. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia. Plos Pathogens. 13: e1006252. PMID 28253375 DOI: 10.1371/Journal.Ppat.1006252 |
0.48 |
|
| 2017 |
Chen LJ, Lin XD, Tian JH, Liao Y, Ying XH, Shao JW, Yu B, Guo JJ, Wang MR, Peng Y, Shi M, Holmes EC, Yang ZQ, Zhang YZ. Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China. Virology. 505: 33-41. PMID 28222327 DOI: 10.1016/J.Virol.2017.02.009 |
0.513 |
|
| 2017 |
Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. Plos Pathogens. 13: e1006215. PMID 28178344 DOI: 10.1371/Journal.Ppat.1006215 |
0.527 |
|
| 2017 |
Di Giallonardo F, Schlub TE, Shi M, Holmes EC. Dinucleotide composition in animal RNA viruses is shaped more by virus family than host species. Journal of Virology. PMID 28148785 DOI: 10.1128/Jvi.02381-16 |
0.496 |
|
| 2017 |
Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, Kuzmin IV, Holmes EC, Tong S. Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. Journal of Virology. PMID 28077633 DOI: 10.1128/Jvi.01953-16 |
0.518 |
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| 2017 |
Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, ... ... Holmes EC, et al. A molecular portrait of maternal sepsis from Byzantine Troy. Elife. 6. PMID 28072390 DOI: 10.7554/Elife.20983 |
0.329 |
|
| 2016 |
Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes EC, Bourhy H. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. Plos Pathogens. 12: e1006041. PMID 27977811 DOI: 10.1371/Journal.Ppat.1006041 |
0.51 |
|
| 2016 |
Duggan AT, Perdomo MF, Piombino-Mascali D, Marciniak S, Poinar D, Emery MV, Buchmann JP, Duchêne S, Jankauskas R, Humphreys M, Golding GB, Southon J, Devault A, Rouillard JM, Sahl JW, ... ... Holmes EC, et al. 17(th) Century Variola Virus Reveals the Recent History of Smallpox. Current Biology : Cb. PMID 27939314 DOI: 10.1016/J.Cub.2016.10.061 |
0.464 |
|
| 2016 |
Guo WP, Tian JH, Lin XD, Ni XB, Chen XP, Liao Y, Yang SY, Dumler JS, Holmes EC, Zhang YZ. Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species. Scientific Reports. 6: 38770. PMID 27934910 DOI: 10.1038/Srep38770 |
0.397 |
|
| 2016 |
McColl KA, Sunarto A, Holmes EC. Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia. Virology Journal. 13: 206. PMID 27931224 DOI: 10.1186/S12985-016-0666-4 |
0.487 |
|
| 2016 |
Marciniak S, Prowse TL, Herring DA, Klunk J, Kuch M, Duggan AT, Bondioli L, Holmes EC, Poinar HN. Plasmodium falciparum malaria in 1(st)-2(nd) century CE southern Italy. Current Biology : Cb. 26: R1220-R1222. PMID 27923126 DOI: 10.1016/J.Cub.2016.10.016 |
0.322 |
|
| 2016 |
Chappell KJ, Brealey JC, Amarilla AA, Watterson D, Hulse L, Palmieri C, Johnston SD, Holmes EC, Meers J, Young PR. Phylogenetic diversity of Koala Retrovirus within a Wild Koala Population. Journal of Virology. PMID 27881645 DOI: 10.1128/Jvi.01820-16 |
0.394 |
|
| 2016 |
Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ. Redefining the invertebrate RNA virosphere. Nature. PMID 27880757 DOI: 10.1038/Nature20167 |
0.502 |
|
| 2016 |
Liu W, Pickering P, Duchêne S, Holmes EC, Aaskov JG. Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia. Emerging Infectious Diseases. 22: 2146-2148. PMID 27869598 DOI: 10.3201/Eid2212.160813 |
0.525 |
|
| 2016 |
Urbanowicz RA, McClure CP, Sakuntabhai A, Sall AA, Kobinger G, Müller MA, Holmes EC, Rey FA, Simon-Loriere E, Ball JK. Human Adaptation of Ebola Virus during the West African Outbreak. Cell. 167: 1079-1087.e5. PMID 27814505 DOI: 10.1016/J.Cell.2016.10.013 |
0.498 |
|
| 2016 |
Hackenbrack N, Rogers MB, Ashley RE, Keel MK, Kubiski SV, Bryan JA, Ghedin E, Holmes EC, Hafenstein SL, Allison AB. Evolution and cryo-EM capsid structure of a North American bat adenovirus and its relationship to other mastadenoviruses. Journal of Virology. PMID 27807242 DOI: 10.1128/Jvi.01504-16 |
0.424 |
|
| 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 |
0.564 |
|
| 2016 |
Huang C, Liu WJ, Xu W, Jin T, Zhao Y, Song J, Shi Y, Ji W, Jia H, Zhou Y, Wen H, Zhao H, Liu H, Li H, Wang Q, ... ... Holmes EC, et al. A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene. Plos Pathogens. 12: e1005883. PMID 27676249 DOI: 10.1371/Journal.Ppat.1005883 |
0.517 |
|
| 2016 |
Holmes EC. The Expanding Virosphere. Cell Host & Microbe. 20: 279-280. PMID 27631697 DOI: 10.1016/J.Chom.2016.08.007 |
0.438 |
|
| 2016 |
Abbadi M, Fusaro A, Ceolin C, Casarotto C, Quartesan R, Dalla Pozza M, Cattoli G, Toffan A, Holmes EC, Panzarin V. Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy. Frontiers in Microbiology. 7: 1306. PMID 27602026 DOI: 10.3389/Fmicb.2016.01306 |
0.549 |
|
| 2016 |
Geoghegan JL, Senior AM, Holmes EC. Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proceedings. Biological Sciences / the Royal Society. 283. PMID 27581875 DOI: 10.1098/Rspb.2016.0727 |
0.464 |
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| 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 |
0.436 |
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| 2016 |
Mahar JE, Nicholson L, Eden JS, Duchêne S, Kerr PJ, Duckworth J, Ward VK, Holmes EC, Strive T. Benign Rabbit Caliciviruses Exhibit Similar Evolutionary Dynamics to their Virulent Relatives. Journal of Virology. PMID 27512059 DOI: 10.1128/Jvi.01212-16 |
0.449 |
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| 2016 |
Duchêne S, Geoghegan JL, Holmes EC, Ho SY. Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. Bioinformatics (Oxford, England). PMID 27412094 DOI: 10.1093/Bioinformatics/Btw421 |
0.372 |
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| 2016 |
Dill JA, Camus AC, Leary JH, Di Giallonardo F, Holmes EC, Ng TF. Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses. Journal of Virology. PMID 27334580 DOI: 10.1128/Jvi.00832-16 |
0.507 |
|
| 2016 |
Feng KH, Sun M, Iketani S, Holmes EC, Parrish CR. Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression. Virology. 496: 138-146. PMID 27314620 DOI: 10.1016/J.Virol.2016.06.001 |
0.358 |
|
| 2016 |
Lam TT, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annual Review of Genomics and Human Genetics. PMID 27216777 DOI: 10.1146/Annurev-Genom-083115-022628 |
0.506 |
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| 2016 |
Li K, Lin XD, Huang KY, Zhang B, Shi M, Guo WP, Wang MR, Wang W, Xing JG, Li MH, Hong WS, Holmes EC, Zhang YZ. Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology. 494: 168-177. PMID 27115729 DOI: 10.1016/J.Virol.2016.04.017 |
0.345 |
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| 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 |
0.417 |
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| 2016 |
Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC. Virological factors that increase the transmissibility of emerging human viruses. Proceedings of the National Academy of Sciences of the United States of America. PMID 27001840 DOI: 10.1073/Pnas.1521582113 |
0.483 |
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| 2016 |
Valastro V, Holmes EC, Britton P, Fusaro A, Jackwood MW, Cattoli G, Monne I. S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 39: 349-64. PMID 26883378 DOI: 10.1016/J.Meegid.2016.02.015 |
0.522 |
|
| 2016 |
Holmes EC. Complexities of Estimating Evolutionary Rates in Viruses. Journal of Virology. 90: 2155. PMID 26822594 DOI: 10.1128/Jvi.02570-15 |
0.345 |
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| 2016 |
Bos KI, Herbig A, Sahl J, Waglechner N, Fourment M, Forrest SA, Klunk J, Schuenemann VJ, Poinar D, Kuch M, Golding GB, Dutour O, Keim P, Wagner DM, Holmes EC, et al. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. Elife. 5. PMID 26795402 DOI: 10.7554/Elife.12994 |
0.341 |
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| 2016 |
Chen LJ, Lin XD, Guo WP, Tian JH, Wang W, Ying XH, Wang MR, Yu B, Yang ZQ, Shi M, Holmes EC, Zhang YZ. Diversity and evolution of avian influenza viruses in live poultry markets, free range poultry and wild wetland birds in China. The Journal of General Virology. PMID 26758561 DOI: 10.1099/Jgv.0.000399 |
0.504 |
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| 2016 |
Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, et al. Quantifying influenza virus diversity and transmission in humans. Nature Genetics. PMID 26727660 DOI: 10.1038/Ng.3479 |
0.558 |
|
| 2016 |
Duchêne S, Di Giallonardo F, Holmes EC. Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales. Molecular Biology and Evolution. 33: 255-67. PMID 26416981 DOI: 10.1093/Molbev/Msv207 |
0.39 |
|
| 2015 |
Sabir JS, Lam TT, Ahmed MM, Li L, Shen Y, Abo-Aba SE, Qureshi MI, Abu-Zeid M, Zhang Y, Khiyami MA, Alharbi NS, Hajrah NH, Sabir MJ, Mutwakil MH, Kabli SA, ... ... Holmes EC, et al. Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia. Science (New York, N.Y.). PMID 26678874 DOI: 10.1126/Science.Aac8608 |
0.46 |
|
| 2015 |
Tan Y, Hassan F, Schuster JE, Simenauer A, Selvarangan R, Halpin RA, Lin X, Fedorova N, Stockwell TB, Tsan-Yuk Lam T, Chappell JD, Hartert TV, Holmes EC, Das SR. Molecular evolution and intra-clade recombination of Enterovirus D68 during the 2014 outbreak in the United States. Journal of Virology. PMID 26656685 DOI: 10.1128/Jvi.02418-15 |
0.454 |
|
| 2015 |
Hall RN, Mahar JE, Haboury S, Stevens V, Holmes EC, Strive T. Emerging Rabbit Hemorrhagic Disease Virus 2 (RHDVb), Australia. Emerging Infectious Diseases. 21: 2276-8. PMID 26583277 DOI: 10.3201/Eid2112.151210 |
0.427 |
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| 2015 |
Di Giallonardo F, Geoghegan JL, Docherty DE, McLean RG, Zody MC, Qu J, Yang X, Birren BW, Malboeuf CM, Newman RM, Ip HS, Holmes EC. Fluid Spatial Dynamics of West Nile Virus in the USA: Rapid Spread in a Permissive Host Environment. Journal of Virology. PMID 26512086 DOI: 10.1128/Jvi.02305-15 |
0.577 |
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| 2015 |
Allison AB, Organtini LJ, Zhang S, Hafenstein SL, Holmes EC, Parrish CR. Single mutations in the VP2 300 loop region of the three-fold spike of the carnivore parvovirus capsid can determine host range. Journal of Virology. PMID 26512077 DOI: 10.1128/Jvi.02636-15 |
0.406 |
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| 2015 |
Shi M, Lin XD, Vasilakis N, Tian JH, Li CX, Chen LJ, Eastwood G, Diao XN, Chen MH, Chen X, Qin XC, Widen SG, Wood TG, Tesh RB, Xu J, ... Holmes EC, et al. Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. Journal of Virology. PMID 26491167 DOI: 10.1128/Jvi.02036-15 |
0.559 |
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| 2015 |
Katzelnick LC, Fonville JM, Gromowski GD, Bustos Arriaga J, Green A, James SL, Lau L, Montoya M, Wang C, VanBlargan LA, Russell CA, Thu HM, Pierson TC, Buchy P, Aaskov JG, ... ... Holmes EC, et al. Dengue viruses cluster antigenically but not as discrete serotypes. Science (New York, N.Y.). 349: 1338-43. PMID 26383952 DOI: 10.1126/Science.Aac5017 |
0.404 |
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| 2015 |
Buchmann JP, Holmes EC. Cell Walls and the Convergent Evolution of the Viral Envelope. Microbiology and Molecular Biology Reviews : Mmbr. 79: 403-18. PMID 26378223 DOI: 10.1128/Mmbr.00017-15 |
0.509 |
|
| 2015 |
Eden JS, Read AJ, Duckworth JA, Strive T, Holmes EC. Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia. Journal of Virology. 89: 12217-20. PMID 26378178 DOI: 10.1128/Jvi.01937-15 |
0.524 |
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| 2015 |
Wang W, Yu B, Lin XD, Kong DG, Wang J, Tian JH, Li MH, Holmes EC, Zhang YZ. Reemergence and Autochthonous Transmission of Dengue Virus, Eastern China, 2014. Emerging Infectious Diseases. 21: 1670-3. PMID 26292098 DOI: 10.3201/Eid2109.150622 |
0.402 |
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| 2015 |
Lam TT, Zhu H, Chong YL, Holmes EC, Guan Y. Puzzling origins of the Ebola outbreak in the Democratic Republic of the Congo, 2014. Journal of Virology. PMID 26202242 DOI: 10.1128/Jvi.01226-15 |
0.351 |
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| 2015 |
Pollett S, Nelson MI, Kasper M, Tinoco Y, Simons M, Romero C, Silva M, Lin X, Halpin RA, Fedorova N, Stockwell TB, Wentworth D, Holmes EC, Bausch DG. Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012. Emerging Infectious Diseases. 21: 1330-8. PMID 26196599 DOI: 10.3201/Eid2108.150084 |
0.54 |
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| 2015 |
Eden JS, Kovaliski J, Duckworth JA, Swain G, Mahar JE, Strive T, Holmes EC. Comparative Phylodynamics of Rabbit Hemorrhagic Disease Virus in Australia and New Zealand. Journal of Virology. 89: 9548-58. PMID 26157125 DOI: 10.1128/Jvi.01100-15 |
0.554 |
|
| 2015 |
Fourment M, Holmes EC. Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry. Bmc Evolutionary Biology. 15: 120. PMID 26111936 DOI: 10.1186/S12862-015-0410-5 |
0.538 |
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| 2015 |
Di Giallonardo F, Holmes EC. Exploring Host-Pathogen Interactions through Biological Control. Plos Pathogens. 11: e1004865. PMID 26110272 DOI: 10.1371/Journal.Ppat.1004865 |
0.336 |
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| 2015 |
Patterson Ross Z, Komadina N, Deng YM, Spirason N, Kelly HA, Sullivan SG, Barr IG, Holmes EC. Inter-Seasonal Influenza is Characterized by Extended Virus Transmission and Persistence. Plos Pathogens. 11: e1004991. PMID 26107631 DOI: 10.1371/Journal.Ppat.1004991 |
0.477 |
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| 2015 |
Simon-Loriere E, Faye O, Faye O, Koivogui L, Magassouba N, Keita S, Thiberge JM, Diancourt L, Bouchier C, Vandenbogaert M, Caro V, Fall G, Buchmann JP, Matranga CB, Sabeti PC, ... ... Holmes EC, et al. Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic. Nature. 524: 102-4. PMID 26106863 DOI: 10.1038/Nature14612 |
0.574 |
|
| 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, ... ... Holmes EC, 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 |
0.558 |
|
| 2015 |
Geoghegan JL, Tan LV, Kühnert D, Halpin RA, Lin X, Simenauer A, Akopov A, Das SR, Stockwell TB, Shrivastava S, Ngoc NM, Uyen LT, Tuyen NT, Thanh TT, Hang VT, ... ... Holmes EC, et al. Phylodynamics of Enterovirus A71-Associated Hand, Foot and Mouth Disease in Viet Nam. Journal of Virology. PMID 26085170 DOI: 10.1128/Jvi.00706-15 |
0.358 |
|
| 2015 |
Lambrechts L, Ferguson NM, Harris E, Holmes EC, McGraw EA, O'Neill SL, Ooi EE, Ritchie SA, Ryan PA, Scott TW, Simmons CP, Weaver SC. Assessing the epidemiological effect of wolbachia for dengue control. The Lancet. Infectious Diseases. PMID 26051887 DOI: 10.1016/S1473-3099(15)00091-2 |
0.429 |
|
| 2015 |
Sintchenko V, Holmes EC. The role of pathogen genomics in assessing disease transmission. Bmj (Clinical Research Ed.). 350: h1314. PMID 25964672 DOI: 10.1136/Bmj.H1314 |
0.415 |
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| 2015 |
Wang M, Barasheed O, Rashid H, Booy R, El Bashir H, Haworth E, Ridda I, Holmes EC, Dwyer DE, Nguyen-Van-Tam J, Memish ZA, Heron L. A cluster-randomised controlled trial to test the efficacy of facemasks in preventing respiratory viral infection among Hajj pilgrims. Journal of Epidemiology and Global Health. 5: 181-9. PMID 25922328 DOI: 10.1016/J.Jegh.2014.08.002 |
0.332 |
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| 2015 |
Feng KH, Gonzalez G, Deng L, Yu H, Tse VL, Huang L, Huang K, Wasik BR, Zhou B, Wentworth DE, Holmes EC, Chen X, Varki A, Murcia PR, Parrish CR. Equine and Canine Influenza H3N8 Viruses Show Minimal Biological Differences Despite Phylogenetic Divergence. Journal of Virology. 89: 6860-73. PMID 25903329 DOI: 10.1128/Jvi.00521-15 |
0.526 |
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| 2015 |
Thomas JM, Allison AB, Holmes EC, Phillips JE, Bunting EM, Yabsley MJ, Brown JD. Molecular Surveillance for Lymphoproliferative Disease Virus in Wild Turkeys (Meleagris gallopavo) from the Eastern United States. Plos One. 10: e0122644. PMID 25897755 DOI: 10.1371/Journal.Pone.0122644 |
0.371 |
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| 2015 |
Duchêne S, Ho SY, Holmes EC. Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models. Bmc Evolutionary Biology. 15: 36. PMID 25886870 DOI: 10.1186/S12862-015-0312-6 |
0.327 |
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| 2015 |
Rogers MB, Song T, Sebra R, Greenbaum BD, Hamelin ME, Fitch A, Twaddle A, Cui L, Holmes EC, Boivin G, Ghedin E. Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection. Mbio. 6. PMID 25852163 DOI: 10.1128/Mbio.02464-14 |
0.526 |
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| 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 |
0.452 |
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| 2015 |
Duchêne S, Duchêne D, Holmes EC, Ho SY. The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data. Molecular Biology and Evolution. 32: 1895-906. PMID 25771196 DOI: 10.1093/Molbev/Msv056 |
0.383 |
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| 2015 |
Lam TT, Zhou B, Wang J, Chai Y, Shen Y, Chen X, Ma C, Hong W, Chen Y, Zhang Y, Duan L, Chen P, Jiang J, Zhang Y, Li L, ... ... Holmes EC, et al. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature. 522: 102-5. PMID 25762140 DOI: 10.1038/Nature14348 |
0.516 |
|
| 2015 |
Kerr PJ, Liu J, Cattadori I, Ghedin E, Read AF, Holmes EC. Myxoma virus and the Leporipoxviruses: an evolutionary paradigm. Viruses. 7: 1020-61. PMID 25757062 DOI: 10.3390/V7031020 |
0.566 |
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| 2015 |
Tan le V, Tuyen NT, Thanh TT, Ngan TT, Van HM, Sabanathan S, Van TT, Thanh le TM, Nguyet LA, Geoghegan JL, Ong KC, Perera D, Hang VT, Ny NT, Anh NT, ... ... Holmes EC, et al. A generic assay for whole-genome amplification and deep sequencing of enterovirus A71. Journal of Virological Methods. 215: 30-6. PMID 25704598 DOI: 10.1016/J.Jviromet.2015.02.011 |
0.368 |
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| 2015 |
Walker PJ, Firth C, Widen SG, Blasdell KR, Guzman H, Wood TG, Paradkar PN, Holmes EC, Tesh RB, Vasilakis N. Evolution of genome size and complexity in the rhabdoviridae. Plos Pathogens. 11: e1004664. PMID 25679389 DOI: 10.1371/Journal.Ppat.1004664 |
0.73 |
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| 2015 |
Ernst T, McCarthy S, Chidlow G, Luang-Suarkia D, Holmes EC, Smith DW, Imrie A. Emergence of a new lineage of dengue virus type 2 identified in travelers entering Western Australia from Indonesia, 2010-2012. Plos Neglected Tropical Diseases. 9: e0003442. PMID 25635775 DOI: 10.1371/Journal.Pntd.0003442 |
0.471 |
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| 2015 |
Li CX, Shi M, Tian JH, Lin XD, Kang YJ, Chen LJ, Qin XC, Xu J, Holmes EC, Zhang YZ. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife. 4. PMID 25633976 DOI: 10.7554/Elife.05378 |
0.549 |
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| 2015 |
Lopes AM, Dalton KP, Magalhães MJ, Parra F, Esteves PJ, Holmes EC, Abrantes J. Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events. The Journal of General Virology. 96: 1309-19. PMID 25626685 DOI: 10.1099/Vir.0.000070 |
0.469 |
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| 2015 |
Vijaykrishna D, Holmes EC, Joseph U, Fourment M, Su YC, Halpin R, Lee RT, Deng YM, Gunalan V, Lin X, Stockwell TB, Fedorova NB, Zhou B, Spirason N, Kühnert D, et al. The contrasting phylodynamics of human influenza B viruses. Elife. 4: e05055. PMID 25594904 DOI: 10.7554/Elife.05055 |
0.42 |
|
| 2015 |
Holmes EC, Zhang YZ. The evolution and emergence of hantaviruses. Current Opinion in Virology. 10: 27-33. PMID 25562117 DOI: 10.1016/j.coviro.2014.12.007 |
0.365 |
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| 2015 |
Parrish CR, Murcia PR, Holmes EC. Influenza virus reservoirs and intermediate hosts: dogs, horses, and new possibilities for influenza virus exposure of humans. Journal of Virology. 89: 2990-4. PMID 25540375 DOI: 10.1128/Jvi.03146-14 |
0.528 |
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| 2015 |
Li K, Lin XD, Wang W, Shi M, Guo WP, Zhang XH, Xing JG, He JR, Wang K, Li MH, Cao JH, Jiang ML, Holmes EC, Zhang YZ. Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China. Virology. 476: 37-42. PMID 25506671 DOI: 10.1016/J.Virol.2014.11.026 |
0.421 |
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| 2015 |
Blasdell KR, Guzman H, Widen SG, Firth C, Wood TG, Holmes EC, Tesh RB, Vasilakis N, Walker PJ. Ledantevirus: a proposed new genus in the Rhabdoviridae has a strong ecological association with bats. The American Journal of Tropical Medicine and Hygiene. 92: 405-10. PMID 25487727 DOI: 10.4269/Ajtmh.14-0606 |
0.797 |
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| 2015 |
Allison AB, Stallknecht DE, Holmes EC. Evolutionary genetics and vector adaptation of recombinant viruses of the western equine encephalitis antigenic complex provides new insights into alphavirus diversity and host switching. Virology. 474: 154-62. PMID 25463613 DOI: 10.1016/J.Virol.2014.10.024 |
0.546 |
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| 2015 |
Wang W, Lin XD, Guo WP, Zhou RH, Wang MR, Wang CQ, Ge S, Mei SH, Li MH, Shi M, Holmes EC, Zhang YZ. Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology. 474: 19-27. PMID 25463600 DOI: 10.1016/J.Virol.2014.10.017 |
0.419 |
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| 2015 |
Di Giallonardo F, Holmes EC. Viral biocontrol: grand experiments in disease emergence and evolution. Trends in Microbiology. 23: 83-90. PMID 25455418 DOI: 10.1016/J.Tim.2014.10.004 |
0.528 |
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| 2015 |
Allison AB, Ballard JR, Tesh RB, Brown JD, Ruder MG, Keel MK, Munk BA, Mickley RM, Gibbs SE, Travassos da Rosa AP, Ellis JC, Ip HS, Shearn-Bochsler VI, Rogers MB, Ghedin E, ... Holmes EC, et al. Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus. Journal of Virology. 89: 1389-403. PMID 25392223 DOI: 10.1128/Jvi.02019-14 |
0.538 |
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| 2015 |
Li C, Shi M, Tian J, Lin X, Kang Y, Chen L, Qin X, Xu J, Holmes EC, Zhang Y. Author response: Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses Elife. DOI: 10.7554/Elife.05378.024 |
0.395 |
|
| 2015 |
Vijaykrishna D, Holmes EC, Joseph U, Fourment M, Su YC, Halpin R, Lee RT, Deng Y, Gunalan V, Lin X, Stockwell TB, Fedorova NB, Zhou B, Spirason N, Kühnert D, et al. Author response: The contrasting phylodynamics of human influenza B viruses Elife. DOI: 10.7554/Elife.05055.023 |
0.403 |
|
| 2015 |
Fourment M, Holmes E. Avian influenza virus data sets Bmc Evolutionary Biology. DOI: 10.5281/Zenodo.18622 |
0.468 |
|
| 2015 |
Pollett S, Nelson MI, Kasper M, Tinoco Y, Simons M, Romero C, Silva M, Lin X, Halpin RA, Fedorova N, Stockwell TB, Wentworth D, Holmes EC, Bausch DG. Phylogeography of influenza A(H3N2) virus in Peru, 2010–2012 Emerging Infectious Diseases. 21: 1330-1338. DOI: 10.3201/eid2108.150084 |
0.368 |
|
| 2015 |
Simmons HE, Prendeville HR, Dunham JP, Ferrari MJ, Earnest JD, Pilson D, Munkvold GP, Holmes EC, Stephenson AG. Transgenic virus resistance in crop-wild cucurbita pepo does not prevent vertical transmission of zucchini yellow mosaic virus Plant Disease. 99: 1616-1621. DOI: 10.1094/Pdis-10-14-1062-Re |
0.367 |
|
| 2014 |
Cui J, Zhao W, Huang Z, Jarvis ED, Gilbert MT, Walker PJ, Holmes EC, Zhang G. Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biology. 15: 539. PMID 25496498 DOI: 10.1186/S13059-014-0539-3 |
0.467 |
|
| 2014 |
Blasdell KR, Widen SG, Diviney SM, Firth C, Wood TG, Guzman H, Holmes EC, Tesh RB, Vasilakis N, Walker PJ. Koolpinyah and Yata viruses: two newly recognised ephemeroviruses from tropical regions of Australia and Africa. Veterinary Microbiology. 174: 547-53. PMID 25457369 DOI: 10.1016/J.Vetmic.2014.09.031 |
0.787 |
|
| 2014 |
Barasheed O, Rashid H, Alfelali M, Tashani M, Azeem M, Bokhary H, Kalantan N, Samkari J, Heron L, Kok J, Taylor J, El Bashir H, Memish ZA, Haworth E, Holmes EC, et al. Viral respiratory infections among Hajj pilgrims in 2013. Virologica Sinica. 29: 364-71. PMID 25413828 DOI: 10.1007/S12250-014-3507-X |
0.476 |
|
| 2014 |
Geoghegan JL, Walker PJ, Duchemin JB, Jeanne I, Holmes EC. Seasonal drivers of the epidemiology of arthropod-borne viruses in Australia. Plos Neglected Tropical Diseases. 8: e3325. PMID 25412443 DOI: 10.1371/Journal.Pntd.0003325 |
0.484 |
|
| 2014 |
Holmes EC. Freezing viruses in time. Proceedings of the National Academy of Sciences of the United States of America. 111: 16643-4. PMID 25404311 DOI: 10.1073/Pnas.1419827111 |
0.397 |
|
| 2014 |
Allison AB, Kohler DJ, Ortega A, Hoover EA, Grove DM, Holmes EC, Parrish CR. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species. Plos Pathogens. 10: e1004475. PMID 25375184 DOI: 10.1371/Journal.Ppat.1004475 |
0.496 |
|
| 2014 |
Dalziel BD, Huang K, Geoghegan JL, Arinaminpathy N, Dubovi EJ, Grenfell BT, Ellner SP, Holmes EC, Parrish CR. Contact heterogeneity, rather than transmission efficiency, limits the emergence and spread of canine influenza virus. Plos Pathogens. 10: e1004455. PMID 25340642 DOI: 10.1371/Journal.Ppat.1004455 |
0.532 |
|
| 2014 |
Lopes AM, Capucci L, Gavier-Widén D, Le Gall-Reculé G, Brocchi E, Barbieri I, Quéméner A, Le Pendu J, Geoghegan JL, Holmes EC, Esteves PJ, Abrantes J. Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV). Virology. 468: 104-12. PMID 25155199 DOI: 10.1016/J.Virol.2014.08.002 |
0.424 |
|
| 2014 |
Elsworth P, Cooke BD, Kovaliski J, Sinclair R, Holmes EC, Strive T. Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits (Oryctolagus cuniculus). Virology. 464: 415-23. PMID 25146599 DOI: 10.1016/J.Virol.2014.06.037 |
0.471 |
|
| 2014 |
Dunham JP, Simmons HE, Holmes EC, Stephenson AG. Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Research. 191: 172-9. PMID 25107623 DOI: 10.1016/J.Virusres.2014.07.030 |
0.446 |
|
| 2014 |
Wang CQ, Gao JH, Li M, Guo WP, Lu MQ, Wang W, Hu MX, Li MH, Yang J, Liang HJ, Tian XF, Holmes EC, Zhang YZ. Co-circulation of Hantaan, Kenkeme, and Khabarovsk Hantaviruses in Bolshoy Ussuriysky Island, China. Virus Research. 191: 51-8. PMID 25087879 DOI: 10.1016/J.Virusres.2014.07.021 |
0.529 |
|
| 2014 |
Kang YJ, Diao XN, Zhao GY, Chen MH, Xiong Y, Shi M, Fu WM, Guo YJ, Pan B, Chen XP, Holmes EC, Gillespie JJ, Dumler SJ, Zhang YZ. Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales. Bmc Evolutionary Biology. 14: 167. PMID 25073875 DOI: 10.1186/S12862-014-0167-2 |
0.357 |
|
| 2014 |
Fourment M, Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. Bmc Evolutionary Biology. 14: 163. PMID 25055743 DOI: 10.1186/S12862-014-0163-6 |
0.316 |
|
| 2014 |
Nelson MI, Wentworth DE, Culhane MR, Vincent AL, Viboud C, LaPointe MP, Lin X, Holmes EC, Detmer SE. Introductions and evolution of human-origin seasonal influenza a viruses in multinational swine populations. Journal of Virology. 88: 10110-9. PMID 24965467 DOI: 10.1128/Jvi.01080-14 |
0.55 |
|
| 2014 |
Lin XD, Zhou RH, Fan FN, Ying XH, Sun XY, Wang W, Holmes EC, Zhang YZ. Biodiversity and evolution of Imjin virus and Thottapalayam virus in Crocidurinae shrews in Zhejiang Province, China. Virus Research. 189: 114-20. PMID 24874196 DOI: 10.1016/J.Virusres.2014.05.014 |
0.56 |
|
| 2014 |
Duchêne S, Holmes EC, Ho SY. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings. Biological Sciences / the Royal Society. 281. PMID 24850916 DOI: 10.1098/Rspb.2014.0732 |
0.471 |
|
| 2014 |
Qin XC, Shi M, Tian JH, Lin XD, Gao DY, He JR, Wang JB, Li CX, Kang YJ, Yu B, Zhou DJ, Xu J, Plyusnin A, Holmes EC, Zhang YZ. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proceedings of the National Academy of Sciences of the United States of America. 111: 6744-9. PMID 24753611 DOI: 10.1073/Pnas.1324194111 |
0.506 |
|
| 2014 |
Cui J, Schlub TE, Holmes EC. An allometric relationship between the genome length and virion volume of viruses. Journal of Virology. 88: 6403-10. PMID 24672040 DOI: 10.1128/Jvi.00362-14 |
0.4 |
|
| 2014 |
Chen ZH, Qin XC, Song R, Shen Y, Chen XP, Wang W, Zhao YX, Zhang JS, He JR, Li MH, Zhao XH, Liu DW, Fu XK, Tian D, Li XW, ... ... Holmes EC, et al. Co-circulation of multiple hemorrhagic fever diseases with distinct clinical characteristics in Dandong, China. Plos One. 9: e89896. PMID 24587107 DOI: 10.1371/Journal.Pone.0089896 |
0.301 |
|
| 2014 |
Eden JS, Hewitt J, Lim KL, Boni MF, Merif J, Greening G, Ratcliff RM, Holmes EC, Tanaka MM, Rawlinson WD, White PA. The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012. Virology. 450: 106-13. PMID 24503072 DOI: 10.1016/J.Virol.2013.12.005 |
0.478 |
|
| 2014 |
Allison AB, Kevin Keel M, Philips JE, Cartoceti AN, Munk BA, Nemeth NM, Welsh TI, Thomas JM, Crum JM, Lichtenwalner AB, Fadly AM, Zavala G, Holmes EC, Brown JD. Avian oncogenesis induced by lymphoproliferative disease virus: a neglected or emerging retroviral pathogen? Virology. 450: 2-12. PMID 24503062 DOI: 10.1016/J.Virol.2013.11.037 |
0.545 |
|
| 2014 |
Monne I, Fusaro A, Nelson MI, Bonfanti L, Mulatti P, Hughes J, Murcia PR, Schivo A, Valastro V, Moreno A, Holmes EC, Cattoli G. Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. Journal of Virology. 88: 4375-88. PMID 24501401 DOI: 10.1128/Jvi.03181-13 |
0.559 |
|
| 2014 |
Wagner DM, Klunk J, Harbeck M, Devault A, Waglechner N, Sahl JW, Enk J, Birdsell DN, Kuch M, Lumibao C, Poinar D, Pearson T, Fourment M, Golding B, Riehm JM, ... ... Holmes EC, et al. Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis. The Lancet. Infectious Diseases. 14: 319-26. PMID 24480148 DOI: 10.1016/S1473-3099(13)70323-2 |
0.386 |
|
| 2014 |
Nelson MI, Njouom R, Viboud C, Niang MN, Kadjo H, Ampofo W, Adebayo A, Tarnagda Z, Miller MA, Holmes EC, Diop OM. Multiyear persistence of 2 pandemic A/H1N1 influenza virus lineages in West Africa. The Journal of Infectious Diseases. 210: 121-5. PMID 24446525 DOI: 10.1093/Infdis/Jiu047 |
0.506 |
|
| 2014 |
Vasilakis N, Castro-Llanos F, Widen SG, Aguilar PV, Guzman H, Guevara C, Fernandez R, Auguste AJ, Wood TG, Popov V, Mundal K, Ghedin E, Kochel TJ, Holmes EC, Walker PJ, et al. Arboretum and Puerto Almendras viruses: two novel rhabdoviruses isolated from mosquitoes in Peru. The Journal of General Virology. 95: 787-92. PMID 24421116 DOI: 10.1099/Vir.0.058685-0 |
0.51 |
|
| 2014 |
Devault AM, Golding GB, Waglechner N, Enk JM, Kuch M, Tien JH, Shi M, Fisman DN, Dhody AN, Forrest S, Bos KI, Earn DJ, Holmes EC, Poinar HN. Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. The New England Journal of Medicine. 370: 334-40. PMID 24401020 DOI: 10.1056/Nejmoa1308663 |
0.367 |
|
| 2014 |
Allison AB, Mead DG, Palacios GF, Tesh RB, Holmes EC. Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses. Virology. 448: 284-92. PMID 24314659 DOI: 10.1016/J.Virol.2013.10.024 |
0.372 |
|
| 2014 |
Kovaliski J, Sinclair R, Mutze G, Peacock D, Strive T, Abrantes J, Esteves PJ, Holmes EC. Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many. Molecular Ecology. 23: 408-20. PMID 24251353 DOI: 10.1111/Mec.12596 |
0.538 |
|
| 2014 |
Trinidad L, Blasdell KR, Joubert DA, Davis SS, Melville L, Kirkland PD, Coulibaly F, Holmes EC, Walker PJ. Evolution of bovine ephemeral fever virus in the Australian episystem. Journal of Virology. 88: 1525-35. PMID 24227855 DOI: 10.1128/Jvi.02797-13 |
0.473 |
|
| 2014 |
Holmes EC. Pandemics-Keep Calm and Carry On Plos Biology. 12. DOI: 10.1371/Journal.Pbio.1001780 |
0.363 |
|
| 2014 |
Vasilakis N, Widen S, Travassos Da Rosa APA, Wood TG, Walker PJ, Holmes EC, Tesh RB. Malpais spring virus is a new species in the genus vesiculovirus Virology Journal. 10. DOI: 10.1186/1743-422X-10-69 |
0.421 |
|
| 2013 |
Rabaa MA, Simmons CP, Fox A, Le MQ, Nguyen TT, Le HY, Gibbons RV, Nguyen XT, Holmes EC, Aaskov JG. Dengue virus in sub-tropical northern and central Viet Nam: population immunity and climate shape patterns of viral invasion and maintenance. Plos Neglected Tropical Diseases. 7: e2581. PMID 24340118 DOI: 10.1371/Journal.Pntd.0002581 |
0.476 |
|
| 2013 |
Shi M, Lemey P, Singh Brar M, Suchard MA, Murtaugh MP, Carman S, D'Allaire S, Delisle B, Lambert MÈ, Gagnon CA, Ge L, Qu Y, Yoo D, Holmes EC, Chi-Ching Leung F. The spread of type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: a phylogeographic approach. Virology. 447: 146-54. PMID 24210109 DOI: 10.1016/J.Virol.2013.08.028 |
0.488 |
|
| 2013 |
Wang W, Wang MR, Lin XD, Guo WP, Li MH, Mei SH, Li ZM, Cong ML, Jiang RL, Zhou RH, Holmes EC, Plyusnin A, Zhang YZ. Ongoing spillover of Hantaan and Gou hantaviruses from rodents is associated with hemorrhagic fever with renal syndrome (HFRS) in China. Plos Neglected Tropical Diseases. 7: e2484. PMID 24147168 DOI: 10.1371/Journal.Pntd.0002484 |
0.458 |
|
| 2013 |
Tong S, Zhu X, Li Y, Shi M, Zhang J, Bourgeois M, Yang H, Chen X, Recuenco S, Gomez J, Chen LM, Johnson A, Tao Y, Dreyfus C, Yu W, ... ... Holmes EC, et al. New world bats harbor diverse influenza A viruses. Plos Pathogens. 9: e1003657. PMID 24130481 DOI: 10.1371/Journal.Ppat.1003657 |
0.542 |
|
| 2013 |
Cui J, Eden JS, Holmes EC, Wang LF. Adaptive evolution of bat dipeptidyl peptidase 4 (dpp4): implications for the origin and emergence of Middle East respiratory syndrome coronavirus. Virology Journal. 10: 304. PMID 24107353 DOI: 10.1186/1743-422X-10-304 |
0.416 |
|
| 2013 |
Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Twaddle AC, Hudson PJ, Tscharke DC, Read AF, Holmes EC, Ghedin E. Genome scale evolution of myxoma virus reveals host-pathogen adaptation and rapid geographic spread. Journal of Virology. 87: 12900-15. PMID 24067966 DOI: 10.1128/Jvi.02060-13 |
0.536 |
|
| 2013 |
Ghedin E, Rogers MB, Widen SG, Guzman H, Travassos da Rosa AP, Wood TG, Fitch A, Popov V, Holmes EC, Walker PJ, Vasilakis N, Tesh RB. Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea. The Journal of General Virology. 94: 2609-15. PMID 24062532 DOI: 10.1099/Vir.0.055939-0 |
0.503 |
|
| 2013 |
Tan Y, Guan W, Lam TT, Pan S, Wu S, Zhan Y, Viboud C, Holmes EC, Yang Z. Differing epidemiological dynamics of influenza B virus lineages in Guangzhou, southern China, 2009-2010. Journal of Virology. 87: 12447-56. PMID 24027322 DOI: 10.1128/Jvi.01039-13 |
0.492 |
|
| 2013 |
Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Hudson PJ, Tscharke DC, Holmes EC, Ghedin E. Comparative analysis of the complete genome sequence of the California MSW strain of myxoma virus reveals potential host adaptations. Journal of Virology. 87: 12080-9. PMID 23986601 DOI: 10.1128/Jvi.01923-13 |
0.413 |
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| 2013 |
Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Holmes EC, Birren B, Galagan J, Feldman MW. The role of selection in shaping diversity of natural M. tuberculosis populations. Plos Pathogens. 9: e1003543. PMID 23966858 DOI: 10.1371/Journal.Ppat.1003543 |
0.321 |
|
| 2013 |
Shi M, Holmes EC, Brar MS, Leung FC. Recombination is associated with an outbreak of novel highly pathogenic porcine reproductive and respiratory syndrome viruses in China. Journal of Virology. 87: 10904-7. PMID 23885071 DOI: 10.1128/Jvi.01270-13 |
0.481 |
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| 2013 |
Levitt AL, Singh R, Cox-Foster DL, Rajotte E, Hoover K, Ostiguy N, Holmes EC. Cross-species transmission of honey bee viruses in associated arthropods. Virus Research. 176: 232-40. PMID 23845302 DOI: 10.1016/J.Virusres.2013.06.013 |
0.539 |
|
| 2013 |
Simmons HE, Dunham JP, Zinn KE, Munkvold GP, Holmes EC, Stephenson AG. Zucchini yellow mosaic virus (ZYMV, Potyvirus): vertical transmission, seed infection and cryptic infections. Virus Research. 176: 259-64. PMID 23845301 DOI: 10.1016/J.Virusres.2013.06.016 |
0.379 |
|
| 2013 |
Vasilakis N, Widen S, Mayer SV, Seymour R, Wood TG, Popov V, Guzman H, Travassos da Rosa AP, Ghedin E, Holmes EC, Walker PJ, Tesh RB. Niakha virus: a novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal. Virology. 444: 80-9. PMID 23773405 DOI: 10.1016/J.Virol.2013.05.035 |
0.46 |
|
| 2013 |
Simon-Loriere E, Holmes EC, Pagán I. The effect of gene overlapping on the rate of RNA virus evolution. Molecular Biology and Evolution. 30: 1916-28. PMID 23686658 DOI: 10.1093/Molbev/Mst094 |
0.445 |
|
| 2013 |
Saira K, Lin X, DePasse JV, Halpin R, Twaddle A, Stockwell T, Angus B, Cozzi-Lepri A, Delfino M, Dugan V, Dwyer DE, Freiberg M, Horban A, Losso M, Lynfield R, ... ... Holmes EC, et al. Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus. Journal of Virology. 87: 8064-74. PMID 23678180 DOI: 10.1128/Jvi.00240-13 |
0.498 |
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| 2013 |
Nguyet MN, Duong TH, Trung VT, Nguyen TH, Tran CN, Long VT, Dui le T, Nguyen HL, Farrar JJ, Holmes EC, Rabaa MA, Bryant JE, Nguyen TT, Nguyen HT, Nguyen LT, et al. Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proceedings of the National Academy of Sciences of the United States of America. 110: 9072-7. PMID 23674683 DOI: 10.1073/Pnas.1303395110 |
0.442 |
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| 2013 |
Quan PL, Firth C, Conte JM, Williams SH, Zambrana-Torrelio CM, Anthony SJ, Ellison JA, Gilbert AT, Kuzmin IV, Niezgoda M, Osinubi MO, Recuenco S, Markotter W, Breiman RF, Kalemba L, ... ... Holmes EC, et al. Bats are a major natural reservoir for hepaciviruses and pegiviruses. Proceedings of the National Academy of Sciences of the United States of America. 110: 8194-9. PMID 23610427 DOI: 10.1073/Pnas.1303037110 |
0.804 |
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| 2013 |
Fusaro A, Monne I, Salomoni A, Angot A, Trolese M, Ferrè N, Mutinelli F, Holmes EC, Capua I, Lemey P, Cattoli G, De Benedictis P. The introduction of fox rabies into Italy (2008-2011) was due to two viral genetic groups with distinct phylogeographic patterns Infection, Genetics and Evolution. 17: 202-209. PMID 23603764 DOI: 10.1016/J.Meegid.2013.03.051 |
0.43 |
|
| 2013 |
Lam TT, Chong YL, Shi M, Hon CC, Li J, Martin DP, Tang JW, Mok CK, Shih SR, Yip CW, Jiang J, Hui RK, Pybus OG, Holmes EC, Leung FC. Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 18: 367-78. PMID 23548803 DOI: 10.1016/J.Meegid.2013.03.015 |
0.523 |
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| 2013 |
Wang L, Yin Q, He G, Rossiter SJ, Holmes EC, Cui J. Ancient invasion of an extinct gammaretrovirus in cetaceans. Virology. 441: 66-9. PMID 23545142 DOI: 10.1016/J.Virol.2013.03.006 |
0.407 |
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| 2013 |
Hayward JA, Tachedjian M, Cui J, Field H, Holmes EC, Wang LF, Tachedjian G. Identification of diverse full-length endogenous betaretroviruses in megabats and microbats. Retrovirology. 10: 35. PMID 23537098 DOI: 10.1186/1742-4690-10-35 |
0.367 |
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| 2013 |
Vasilakis N, Widen S, Travassos da Rosa AP, Wood TG, Walker PJ, Holmes EC, Tesh RB. Malpais spring virus is a new species in the genus vesiculovirus. Virology Journal. 10: 69. PMID 23497016 DOI: 10.1186/1743-422X-10-69 |
0.511 |
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| 2013 |
Simon-Loriere E, Holmes EC. Gene duplication is infrequent in the recent evolutionary history of RNA viruses Molecular Biology and Evolution. 30: 1263-1269. PMID 23486612 DOI: 10.1093/Molbev/Mst044 |
0.481 |
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| 2013 |
Ke R, Aaskov J, Holmes EC, Lloyd-Smith JO. Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses. Plos Pathogens. 9: e1003193. PMID 23468631 DOI: 10.1371/Journal.Ppat.1003193 |
0.52 |
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| 2013 |
Nougairede A, De Fabritus L, Aubry F, Gould EA, Holmes EC, de Lamballerie X. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. Plos Pathogens. 9: e1003172. PMID 23436995 DOI: 10.1371/Journal.Ppat.1003172 |
0.507 |
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| 2013 |
Guo WP, Lin XD, Wang W, Tian JH, Cong ML, Zhang HL, Wang MR, Zhou RH, Wang JB, Li MH, Xu J, Holmes EC, Zhang YZ. Phylogeny and origins of hantaviruses harbored by bats, insectivores, and rodents. Plos Pathogens. 9: e1003159. PMID 23408889 DOI: 10.1371/Journal.Ppat.1003159 |
0.566 |
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| 2013 |
Murcia PR, Baillie GJ, Stack JC, Jervis C, Elton D, Mumford JA, Daly J, Kellam P, Grenfell BT, Holmes EC, Wood JL. Evolution of equine influenza virus in vaccinated horses. Journal of Virology. 87: 4768-71. PMID 23388708 DOI: 10.1128/Jvi.03379-12 |
0.417 |
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| 2013 |
Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Guan Y, Wood JL, Brown IH, Kellam P, Pybus OG. The evolutionary dynamics of influenza A virus adaptation to mammalian hosts. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120382. PMID 23382435 DOI: 10.1098/Rstb.2012.0382 |
0.556 |
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| 2013 |
Viboud C, Nelson MI, Tan Y, Holmes EC. Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120199. PMID 23382422 DOI: 10.1098/Rstb.2012.0199 |
0.485 |
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| 2013 |
Rabaa MA, Klungthong C, Yoon IK, Holmes EC, Chinnawirotpisan P, Thaisomboonsuk B, Srikiatkhachorn A, Rothman AL, Tannitisupawong D, Aldstadt J, Nisalak A, Mammen MP, Gibbons RV, Endy TP, Fansiri T, et al. Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand. Plos Neglected Tropical Diseases. 7: e1990. PMID 23350000 DOI: 10.1371/Journal.Pntd.0001990 |
0.429 |
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| 2013 |
Holmes EC. What can we predict about viral evolution and emergence? Current Opinion in Virology. 3: 180-184. PMID 23273851 DOI: 10.1016/J.Coviro.2012.12.003 |
0.318 |
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| 2013 |
Tao Y, Shi M, Conrardy C, Kuzmin IV, Recuenco S, Agwanda B, Alvarez DA, Ellison JA, Gilbert AT, Moran D, Niezgoda M, Lindblade KA, Holmes EC, Breiman RF, Rupprecht CE, et al. Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. The Journal of General Virology. 94: 738-48. PMID 23239573 DOI: 10.1099/Vir.0.047928-0 |
0.495 |
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| 2013 |
Allison AB, Kohler DJ, Fox KA, Brown JD, Gerhold RW, Shearn-Bochsler VI, Dubovi EJ, Parrish CR, Holmes EC. Frequent cross-species transmission of parvoviruses among diverse carnivore hosts. Journal of Virology. 87: 2342-7. PMID 23221559 DOI: 10.1128/Jvi.02428-12 |
0.404 |
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| 2013 |
Stack JC, Murcia PR, Grenfell BT, Wood JL, Holmes EC. Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation. Proceedings. Biological Sciences / the Royal Society. 280: 20122173. PMID 23135678 DOI: 10.1098/Rspb.2012.2173 |
0.499 |
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| 2013 |
Cheng X, Tan Y, He M, Lam TT, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, ... ... Holmes EC, et al. Epidemiological dynamics and phylogeography of influenza virus in southern China. The Journal of Infectious Diseases. 207: 106-14. PMID 22930808 DOI: 10.1093/Infdis/Jis526 |
0.502 |
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| 2013 |
Holmes EC. Virus evolution Fields Virology: Sixth Edition. 1. |
0.435 |
|
| 2012 |
Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JL, Holmes EC, Murcia PR. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. Plos Pathogens. 8: e1003081. PMID 23308065 DOI: 10.1371/Journal.Ppat.1003081 |
0.536 |
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| 2012 |
Kerr PJ, Ghedin E, DePasse JV, Fitch A, Cattadori IM, Hudson PJ, Tscharke DC, Read AF, Holmes EC. Evolutionary history and attenuation of myxoma virus on two continents. Plos Pathogens. 8: e1002950. PMID 23055928 DOI: 10.1371/Journal.Ppat.1002950 |
0.508 |
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| 2012 |
Nielsen AC, Gyhrs ML, Holmes EC, Cui J. Co-circulation and persistence of genetically distinct saffold viruses, Denmark. Emerging Infectious Diseases. 18: 1694-6. PMID 23017727 DOI: 10.3201/Eid1810.120793 |
0.459 |
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| 2012 |
Nelson MI, Detmer SE, Wentworth DE, Tan Y, Schwartzbard A, Halpin RA, Stockwell TB, Lin X, Vincent AL, Gramer MR, Holmes EC. Genomic reassortment of influenza A virus in North American swine, 1998-2011. The Journal of General Virology. 93: 2584-9. PMID 22993190 DOI: 10.1099/Vir.0.045930-0 |
0.523 |
|
| 2012 |
Ghedin E, Holmes EC, DePasse JV, Pinilla LT, Fitch A, Hamelin ME, Papenburg J, Boivin G. Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. The Journal of Infectious Diseases. 206: 1504-11. PMID 22966122 DOI: 10.1093/Infdis/Jis571 |
0.46 |
|
| 2012 |
Shi M, Jagger BW, Wise HM, Digard P, Holmes EC, Taubenberger JK. Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus. Journal of Virology. 86: 12411-3. PMID 22951836 DOI: 10.1128/Jvi.01677-12 |
0.424 |
|
| 2012 |
Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A, Yu J, Sangal V, Brown DJ, Coia JE, Kim DW, Choi SY, Kim SH, da Silveira WD, Pickard DJ, Farrar JJ, et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genetics. 44: 1056-9. PMID 22863732 DOI: 10.1038/Ng.2369 |
0.42 |
|
| 2012 |
Nelson MI, Gramer MR, Vincent AL, Holmes EC. Global transmission of influenza viruses from humans to swine. The Journal of General Virology. 93: 2195-203. PMID 22791604 DOI: 10.1099/Vir.0.044974-0 |
0.498 |
|
| 2012 |
Nelson MI, Vincent AL, Kitikoon P, Holmes EC, Gramer MR. Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011. Journal of Virology. 86: 8872-8. PMID 22696653 DOI: 10.1128/Jvi.00259-12 |
0.496 |
|
| 2012 |
Cui J, Tachedjian G, Tachedjian M, Holmes EC, Zhang S, Wang LF. Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats. The Journal of General Virology. 93: 2037-45. PMID 22694899 DOI: 10.1099/Vir.0.043760-0 |
0.497 |
|
| 2012 |
Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, Ormond D, Oliver K, Elton D, Mumford JA, Caccamo M, Kellam P, Grenfell BT, Holmes EC, Wood JL. Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. Plos Pathogens. 8: e1002730. PMID 22693449 DOI: 10.1371/Journal.Ppat.1002730 |
0.53 |
|
| 2012 |
Simmons HE, Dunham JP, Stack JC, Dickins BJ, Pagán I, Holmes EC, Stephenson AG. Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus. The Journal of General Virology. 93: 1831-40. PMID 22592263 DOI: 10.1099/Vir.0.042622-0 |
0.47 |
|
| 2012 |
Lam TT, Hon CC, Lemey P, Pybus OG, Shi M, Tun HM, Li J, Jiang J, Holmes EC, Leung FC. Phylodynamics of H5N1 avian influenza virus in Indonesia. Molecular Ecology. 21: 3062-77. PMID 22574738 DOI: 10.1111/J.1365-294X.2012.05577.X |
0.575 |
|
| 2012 |
Cui J, Holmes EC. Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses. Journal of Virology. 86: 7688-91. PMID 22553337 DOI: 10.1128/Jvi.00769-12 |
0.424 |
|
| 2012 |
Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB. PHYRN: a robust method for phylogenetic analysis of highly divergent sequences. Plos One. 7: e34261. PMID 22514627 DOI: 10.1371/Journal.Pone.0034261 |
0.344 |
|
| 2012 |
Cui J, Holmes EC. Evidence for an endogenous papillomavirus-like element in the platypus genome Journal of General Virology. 93: 1362-1366. PMID 22422067 DOI: 10.1099/Vir.0.041483-0 |
0.393 |
|
| 2012 |
Cui J, Holmes EC. Endogenous RNA viruses of plants in insect genomes Virology. 427: 77-79. PMID 22410578 DOI: 10.1016/J.Virol.2012.02.014 |
0.459 |
|
| 2012 |
Pagán I, Holmes EC, Simon-Loriere E. Level of gene expression is a major determinant of protein evolution in the viral order Mononegavirales Journal of Virology. 86: 5253-5263. PMID 22345453 DOI: 10.1128/Jvi.06050-11 |
0.464 |
|
| 2012 |
Cui J, Holmes EC. Endogenous lentiviruses in the ferret genome Journal of Virology. 86: 3383-3385. PMID 22238305 DOI: 10.1128/Jvi.06652-11 |
0.364 |
|
| 2012 |
Lam TT, Zhu H, Smith DK, Guan Y, Holmes EC, Pybus OG. The recombinant origin of emerging human norovirus GII.4/2008: intra-genotypic exchange of the capsid P2 domain. The Journal of General Virology. 93: 817-22. PMID 22238233 DOI: 10.1099/Vir.0.039057-0 |
0.425 |
|
| 2012 |
Allison AB, Holmes EC, Potgieter AC, Wright IM, Sailleau C, Breard E, Ruder MG, Stallknecht DE. Segmental configuration and putative origin of the reassortant orbivirus, epizootic hemorrhagic disease virus serotype 6, strain Indiana. Virology. 424: 67-75. PMID 22230700 DOI: 10.1016/J.Virol.2011.12.004 |
0.501 |
|
| 2012 |
Boni MF, Smith GJ, Holmes EC, Vijaykrishna D. No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Gene. 494: 242-5. PMID 22226809 DOI: 10.1016/J.Gene.2011.10.041 |
0.488 |
|
| 2012 |
Stucker KM, Pagan I, Cifuente JO, Kaelber JT, Lillie TD, Hafenstein S, Holmes EC, Parrish CR. The role of evolutionary intermediates in the host adaptation of canine parvovirus. Journal of Virology. 86: 1514-21. PMID 22114336 DOI: 10.1128/Jvi.06222-11 |
0.488 |
|
| 2012 |
Thai KT, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT, Farrar J, van Doorn HR, de Jong MD, Birren BW, Holmes EC, et al. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. Journal of Virology. 86: 835-43. PMID 22090119 DOI: 10.1128/Jvi.05985-11 |
0.492 |
|
| 2012 |
Allison AB, Harbison CE, Pagan I, Stucker KM, Kaelber JT, Brown JD, Ruder MG, Keel MK, Dubovi EJ, Holmes EC, Parrish CR. Role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus. Journal of Virology. 86: 865-72. PMID 22072763 DOI: 10.1128/Jvi.06187-11 |
0.494 |
|
| 2012 |
Panzarin V, Fusaro A, Monne I, Cappellozza E, Patarnello P, Bovo G, Capua I, Holmes EC, Cattoli G. Molecular epidemiology and evolutionary dynamics of betanodavirus in southern Europe Infection, Genetics and Evolution. 12: 63-70. PMID 22036789 DOI: 10.1016/J.Meegid.2011.10.007 |
0.515 |
|
| 2012 |
Cook S, Moureau G, Kitchen A, Gould EA, de Lamballerie X, Holmes EC, Harbach RE. Molecular evolution of the insect-specific flaviviruses. The Journal of General Virology. 93: 223-34. PMID 22012464 DOI: 10.1099/Vir.0.036525-0 |
0.479 |
|
| 2012 |
Lam TT, Ip HS, Ghedin E, Wentworth DE, Halpin RA, Stockwell TB, Spiro DJ, Dusek RJ, Bortner JB, Hoskins J, Bales BD, Yparraguirre DR, Holmes EC. Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecology Letters. 15: 24-33. PMID 22008513 DOI: 10.1111/J.1461-0248.2011.01703.X |
0.495 |
|
| 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 |
0.522 |
|
| 2011 |
Holmes EC. Genomics: Plague's progress Nature. 478: 465-466. PMID 22031436 DOI: 10.1038/478465A |
0.367 |
|
| 2011 |
Holmes EC. The evolution of endogenous viral elements Cell Host and Microbe. 10: 368-377. PMID 22018237 DOI: 10.1016/J.Chom.2011.09.002 |
0.489 |
|
| 2011 |
Cattoli G, Fusaro A, Monne I, Coven F, Joannis T, El-Hamid HSA, Hussein AA, Cornelius C, Amarin NM, Mancin M, Holmes EC, Capua I. Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry Vaccine. 29: 9368-9375. PMID 22001877 DOI: 10.1016/J.Vaccine.2011.09.127 |
0.46 |
|
| 2011 |
My PVT, Rabaa MA, Vinh H, Holmes EC, Hoang NVM, Vinh NT, Phuong LT, Tham NT, Bay PVB, Campbell JI, Farrar J, Baker S. The emergence of rotavirus G12 and the prevalence of enteric viruses in hospitalized pediatric diarrheal patients in Southern Vietnam American Journal of Tropical Medicine and Hygiene. 85: 768-775. PMID 21976585 DOI: 10.4269/Ajtmh.2011.11-0364 |
0.409 |
|
| 2011 |
Torres-Pérez F, Palma RE, Hjelle B, Holmes EC, Cook JA. Spatial but not temporal co-divergence of a virus and its mammalian host. Molecular Ecology. 20: 4109-22. PMID 21880089 DOI: 10.1111/J.1365-294X.2011.05241.X |
0.444 |
|
| 2011 |
Lam TT, Zhu H, Wang J, Smith DK, Holmes EC, Webster RG, Webby R, Peiris JM, Guan Y. Reassortment events among swine influenza A viruses in China: implications for the origin of the 2009 influenza pandemic. Journal of Virology. 85: 10279-85. PMID 21795347 DOI: 10.1128/Jvi.05262-11 |
0.527 |
|
| 2011 |
Simon-Loriere E, Holmes EC. Why do RNA viruses recombine? Nature Reviews Microbiology. 9: 617-626. PMID 21725337 DOI: 10.1038/Nrmicro2614 |
0.455 |
|
| 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 |
0.534 |
|
| 2011 |
Fusaro A, Monne I, Salviato A, Valastro V, Schivo A, Amarin NM, Gonzalez C, Ismail MM, Al-Ankari AR, Al-Blowi MH, Khan OA, Ali ASM, Hedayati A, Garcia JG, Ziay GM, ... ... Holmes EC, et al. Phylogeography and evolutionary history of reassortant H9N2 viruses with potential human health implications Journal of Virology. 85: 8413-8421. PMID 21680519 DOI: 10.1128/Jvi.00219-11 |
0.539 |
|
| 2011 |
Vasilakis N, Cardosa J, Hanley KA, Holmes EC, Weaver SC. Fever from the forest: prospects for the continued emergence of sylvatic dengue virus and its impact on public health. Nature Reviews. Microbiology. 9: 532-41. PMID 21666708 DOI: 10.1038/Nrmicro2595 |
0.426 |
|
| 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 |
0.471 |
|
| 2011 |
Morens DM, Holmes EC, Davis AS, Taubenberger JK. Global rinderpest eradication: lessons learned and why humans should celebrate too. The Journal of Infectious Diseases. 204: 502-5. PMID 21653230 DOI: 10.1093/Infdis/Jir327 |
0.356 |
|
| 2011 |
Holmes EC, Ghedin E, Halpin RA, Stockwell TB, Zhang XQ, Fleming R, Davey R, Benson CA, Mehta S, Taplitz R, Liu YT, Brouwer KC, Wentworth DE, Lin X, Schooley RT, et al. Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community. Journal of Virology. 85: 6923-9. PMID 21593168 DOI: 10.1128/Jvi.00438-11 |
0.512 |
|
| 2011 |
Holmes EC. What does virus evolution tell us about virus origins? Journal of Virology. 85: 5247-51. PMID 21450811 DOI: 10.1128/JVI.02203-10 |
0.464 |
|
| 2011 |
Liu WJ, Rourke MF, Holmes EC, Aaskov JG. Persistence of multiple genetic lineages within intrahost populations of Ross River virus. Journal of Virology. 85: 5674-8. PMID 21430052 DOI: 10.1128/Jvi.02622-10 |
0.5 |
|
| 2011 |
Murcia PR, Wood JL, Holmes EC. Genome-scale evolution and phylodynamics of equine H3N8 influenza A virus. Journal of Virology. 85: 5312-22. PMID 21430049 DOI: 10.1128/Jvi.02619-10 |
0.527 |
|
| 2011 |
Bhatt S, Holmes EC, Pybus OG. The genomic rate of molecular adaptation of the human influenza A virus Molecular Biology and Evolution. 28: 2443-2451. PMID 21415025 DOI: 10.1093/Molbev/Msr044 |
0.529 |
|
| 2011 |
Ghedin E, Laplante J, DePasse J, Wentworth DE, Santos RP, Lepow ML, Porter J, Stellrecht K, Lin X, Operario D, Griesemer S, Fitch A, Halpin RA, Stockwell TB, Spiro DJ, ... Holmes EC, et al. Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance. The Journal of Infectious Diseases. 203: 168-74. PMID 21288815 DOI: 10.1093/Infdis/Jiq040 |
0.53 |
|
| 2011 |
Kitchen A, Shackelton LA, Holmes EC. Family level phylogenies reveal modes of macroevolution in RNA viruses. Proceedings of the National Academy of Sciences of the United States of America. 108: 238-43. PMID 21173251 DOI: 10.1073/Pnas.1011090108 |
0.476 |
|
| 2011 |
Simmons HE, Holmes EC, Stephenson AG. Rapid turnover of intra-host genetic diversity in Zucchini yellow mosaic virus. Virus Research. 155: 389-96. PMID 21138748 DOI: 10.1016/J.Virusres.2010.11.007 |
0.495 |
|
| 2011 |
Nelson MI, Tan Y, Ghedin E, Wentworth DE, St George K, Edelman L, Beck ET, Fan J, Lam TT, Kumar S, Spiro DJ, Simonsen L, Viboud C, Holmes EC, Henrickson KJ, et al. Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. Journal of Virology. 85: 828-34. PMID 21068250 DOI: 10.1128/Jvi.01762-10 |
0.471 |
|
| 2011 |
Holmes EC. What does virus evolution tell us about virus origins? Journal of Virology. 85: 9655-9655. DOI: 10.1128/Jvi.02203-10 |
0.552 |
|
| 2011 |
Volk SM, Chen R, Tsetsarkin KA, Adams AP, Garcia TI, Sall AA, Nasar F, Schuh AJ, Holmes EC, Higgs S, Maharaj PD, Brault AC, Weaver SC. Author's correction: Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates Journal of Virology. 85: 5706. DOI: 10.1128/Jvi.00628-11 |
0.472 |
|
| 2011 |
Simmons HE, Holmes EC, Gildow FE, Bothe-Goralczyk MA, Stephenson AG. Experimental verification of seed transmission of Zucchini yellow mosaic virus Plant Disease. 95: 751-754. DOI: 10.1094/Pdis-11-10-0843 |
0.367 |
|
| 2011 |
Holmes EC. Virology: Pathogenic passengers Nature. 478: 319-320. DOI: 10.1038/478319A |
0.407 |
|
| 2010 |
Singh R, Levitt AL, Rajotte EG, Holmes EC, Ostiguy N, Vanengelsdorp D, Lipkin WI, Depamphilis CW, Toth AL, Cox-Foster DL. RNA viruses in hymenopteran pollinators: evidence of inter-Taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species. Plos One. 5: e14357. PMID 21203504 DOI: 10.1371/Journal.Pone.0014357 |
0.562 |
|
| 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 |
0.449 |
|
| 2010 |
Hayward JJ, Dubovi EJ, Scarlett JM, Janeczko S, Holmes EC, Parrish CR. Microevolution of canine influenza virus in shelters and its molecular epidemiology in the United States. Journal of Virology. 84: 12636-45. PMID 20943966 DOI: 10.1128/Jvi.01350-10 |
0.565 |
|
| 2010 |
Holmes EC. Malaria: The gorilla connection Nature. 467: 404-405. PMID 20864986 DOI: 10.1038/467404A |
0.314 |
|
| 2010 |
Jahnke M, Holmes EC, Kerr PJ, Wright JD, Strive T. Evolution and phylogeography of the nonpathogenic calicivirus RCV-A1 in wild rabbits in Australia Journal of Virology. 84: 12397-12404. PMID 20861266 DOI: 10.1128/Jvi.00777-10 |
0.372 |
|
| 2010 |
Pagán I, Firth C, Holmes EC. Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus tobamovirus Journal of Molecular Evolution. 71: 298-307. PMID 20838783 DOI: 10.1007/S00239-010-9385-4 |
0.77 |
|
| 2010 |
Rabaa MA, Hang VTT, Wills B, Farrar J, Simmons CP, Holmes EC. Phylogeography of recently emerged DENV-2 in southern Viet Nam. Plos Neglected Tropical Diseases. 4. PMID 20668540 DOI: 10.1371/Journal.Pntd.0000766 |
0.444 |
|
| 2010 |
Vu TT, Holmes EC, Duong V, Nguyen TQ, Tran TH, Quail M, Churcher C, Parkhill J, Cardosa J, Farrar J, Wills B, Lennon NJ, Birren BW, Buchy P, Henn MR, et al. Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia. Plos Neglected Tropical Diseases. 4: e757. PMID 20651932 DOI: 10.1371/Journal.Pntd.0000757 |
0.548 |
|
| 2010 |
Dacheux L, Berthet N, Dissard G, Holmes EC, Delmas O, Larrous F, Guigon G, Dickinson P, Faye O, Sall AA, Old IG, Kong K, Kennedy GC, Manuguerra JC, Cole ST, et al. Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses. Journal of Virology. 84: 9557-74. PMID 20610710 DOI: 10.1128/Jvi.00771-10 |
0.446 |
|
| 2010 |
Romano CM, de Carvalho-Mello IMVG, Jamal LF, de Melo FL, Iamarino A, Motoki M, Pinho JRR, Holmes EC, Zanotto PMdA. Social networks shape the transmission dynamics of hepatitis C virus Plos One. 5. PMID 20585651 DOI: 10.1371/Journal.Pone.0011170 |
0.348 |
|
| 2010 |
Carrillo-Valenzo E, Danis-Lozano R, Velasco-Hernández JX, Sánchez-Burgos G, Alpuche C, López I, Rosales C, Baronti C, de Lamballerie X, Holmes EC, Ramos-Castañeda J. Evolution of dengue virus in Mexico is characterized by frequent lineage replacement. Archives of Virology. 155: 1401-12. PMID 20549264 DOI: 10.1007/S00705-010-0721-1 |
0.574 |
|
| 2010 |
Carpi G, Holmes EC, Kitchen A. The evolutionary dynamics of bluetongue virus. Journal of Molecular Evolution. 70: 583-92. PMID 20526713 DOI: 10.1007/S00239-010-9354-Y |
0.515 |
|
| 2010 |
Holmes EC. Helping the Resistance Science. 328: 1243-1244. PMID 20522766 DOI: 10.1126/Science.1190994 |
0.374 |
|
| 2010 |
Holmes EC. The RNA virus quasispecies: fact or fiction? Journal of Molecular Biology. 400: 271-273. PMID 20493194 DOI: 10.1016/J.Jmb.2010.05.032 |
0.427 |
|
| 2010 |
Boni MF, de Jong MD, van Doorn HR, Holmes EC. Guidelines for identifying homologous recombination events in influenza A virus. Plos One. 5: e10434. PMID 20454662 DOI: 10.1371/Journal.Pone.0010434 |
0.523 |
|
| 2010 |
Murcia PR, Baillie GJ, Daly J, Elton D, Jervis C, Mumford JA, Newton R, Parrish CR, Hoelzer K, Dougan G, Parkhill J, Lennard N, Ormond D, Moule S, Whitwham A, ... ... Holmes EC, et al. Intra- and interhost evolutionary dynamics of equine influenza virus. Journal of Virology. 84: 6943-54. PMID 20444896 DOI: 10.1128/Jvi.00112-10 |
0.571 |
|
| 2010 |
Volk SM, Chen R, Tsetsarkin KA, Adams AP, Garcia TI, Sall AA, Nasar F, Schuh AJ, Holmes EC, Higgs S, Maharaj PD, Brault AC, Weaver SC. Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. Journal of Virology. 84: 6497-504. PMID 20410280 DOI: 10.1128/Jvi.01603-09 |
0.508 |
|
| 2010 |
Pagán I, Holmes EC. Long-Term Evolution of the Luteoviridae: Time Scale and Mode of Virus Speciation Journal of Virology. 84: 6177-6187. PMID 20375155 DOI: 10.1128/Jvi.02160-09 |
0.476 |
|
| 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 |
0.786 |
|
| 2010 |
Holmes EC. Does hepatitis C virus really form quasispecies Infection, Genetics and Evolution. 10: 431-432. PMID 20304103 DOI: 10.1016/J.Meegid.2010.03.006 |
0.396 |
|
| 2010 |
Ghedin E, Wentworth DE, Halpin RA, Lin X, Bera J, DePasse J, Fitch A, Griesemer S, Hine E, Katzel DA, Overton L, Proudfoot K, Sitz J, Szczypinski B, StGeorge K, ... ... Holmes EC, et al. Unseasonal transmission of H3N2 influenza A virus during the swine-origin H1N1 pandemic. Journal of Virology. 84: 5715-8. PMID 20237080 DOI: 10.1128/Jvi.00018-10 |
0.49 |
|
| 2010 |
Hoelzer K, Murcia PR, Baillie GJ, Wood JL, Metzger SM, Osterrieder N, Dubovi EJ, Holmes EC, Parrish CR. Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs. Journal of Virology. 84: 5329-35. PMID 20219907 DOI: 10.1128/Jvi.02469-09 |
0.481 |
|
| 2010 |
Vasilakis N, Cardosa J, Diallo M, Sall AA, Holmes EC, Hanley KA, Weaver SC, Mota J, Rico-Hesse R. Sylvatic dengue viruses share the pathogenic potential of urban/endemic dengue viruses. Journal of Virology. 84: 3726-7; author reply. PMID 20212326 DOI: 10.1128/Jvi.02640-09 |
0.468 |
|
| 2010 |
Fusaro A, Nelson MI, Joannis T, Bertolotti L, Monne I, Salviato A, Olaleye O, Shittu I, Sulaiman L, Lombin LH, Capua I, Holmes EC, Cattoli G. Evolutionary dynamics of multiple sublineages of H5N1 influenza viruses in Nigeria from 2006 to 2008. Journal of Virology. 84: 3239-3247. PMID 20071565 DOI: 10.1128/Jvi.02385-09 |
0.545 |
|
| 2010 |
Chen R, Holmes EC. Hitchhiking and the Population Genetic Structure of Avian Influenza Virus Journal of Molecular Evolution. 70: 98-105. PMID 20041240 DOI: 10.1007/S00239-009-9312-8 |
0.449 |
|
| 2010 |
Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Muñoz-Jordán JL, Pybus OG, Holmes EC, Gubler DJ. Epidemic dynamics revealed in dengue evolution. Molecular Biology and Evolution. 27: 811-8. PMID 19965886 DOI: 10.1093/Molbev/Msp285 |
0.5 |
|
| 2010 |
Balmaseda A, Standish K, Mercado JC, Matute JC, Tellez Y, SaborÃo S, Hammond SN, Nuñez A, Avilés W, Henn MR, Holmes EC, Gordon A, Coloma J, Kuan G, Harris E. Trends in patterns of dengue transmission over 4 years in a pediatric cohort study in Nicaragua. The Journal of Infectious Diseases. 201: 5-14. PMID 19929380 DOI: 10.1086/648592 |
0.39 |
|
| 2010 |
Sall AA, Faye O, Diallo M, Firth C, Kitchen A, Holmes EC. Yellow fever virus exhibits slower evolutionary dynamics than dengue virus. Journal of Virology. 84: 765-72. PMID 19889759 DOI: 10.1128/Jvi.01738-09 |
0.809 |
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| 2010 |
Holmes EC. Evolution in health and medicine Sackler colloquium: The comparative genomics of viral emergence. Proceedings of the National Academy of Sciences of the United States of America. 107: 1742-1746. PMID 19858482 DOI: 10.1073/Pnas.0906193106 |
0.565 |
|
| 2010 |
Jones A, Lowry K, Aaskov J, Holmes EC, Kitchen A. Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy. The Journal of General Virology. 91: 182-8. PMID 19759236 DOI: 10.1099/Vir.0.014209-0 |
0.421 |
|
| 2010 |
Grard G, Moureau G, Charrel RN, Holmes EC, Gould EA, de Lamballerie X. Genomics and evolution of Aedes-borne flaviviruses. The Journal of General Virology. 91: 87-94. PMID 19741066 DOI: 10.1099/Vir.0.014506-0 |
0.574 |
|
| 2009 |
Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, Stockwell T, Lin X, Griesemer S, Kumar S, Bose M, ... ... Holmes E, et al. The early diversification of influenza A/H1N1pdm. Plos Currents. 1: RRN1126. PMID 20029664 DOI: 10.1371/Currents.Rrn1126 |
0.536 |
|
| 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 |
0.556 |
|
| 2009 |
Halloran ME, Holmes EC. Invited commentary: Evaluating vaccination programs using genetic sequence data. American Journal of Epidemiology. 170: 1464-6; discussion 1. PMID 19910381 DOI: 10.1093/Aje/Kwp366 |
0.355 |
|
| 2009 |
Dorji T, Yoon IK, Holmes EC, Wangchuk S, Tobgay T, Nisalak A, Chinnawirotpisan P, Sangkachantaranon K, Gibbons RV, Jarman RG. Diversity and origin of dengue virus serotypes 1, 2, and 3, Bhutan. Emerging Infectious Diseases. 15: 1630-2. PMID 19861059 DOI: 10.3201/Eid1510.090123 |
0.522 |
|
| 2009 |
Firth C, Charleston MA, Duffy S, Shapiro B, Holmes EC. Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. Journal of Virology. 83: 12813-21. PMID 19812157 DOI: 10.1128/Jvi.01719-09 |
0.763 |
|
| 2009 |
Kerr PJ, Kitchen A, Holmes EC. Origin and phylodynamics of rabbit hemorrhagic disease virus. Journal of Virology. 83: 12129-38. PMID 19759153 DOI: 10.1128/Jvi.01523-09 |
0.488 |
|
| 2009 |
Holmes EC. RNA virus genomics: a world of possibilities Journal of Clinical Investigation. 119: 2488-2495. PMID 19729846 DOI: 10.1172/Jci38050 |
0.497 |
|
| 2009 |
Cook S, Moureau G, Harbach RE, Mukwaya L, Goodger K, Ssenfuka F, Gould E, Holmes EC, de Lamballerie X. Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda. The Journal of General Virology. 90: 2669-78. PMID 19656970 DOI: 10.1099/Vir.0.014183-0 |
0.466 |
|
| 2009 |
Ghedin E, Fitch A, Boyne A, Griesemer S, DePasse J, Bera J, Zhang X, Halpin RA, Smit M, Jennings L, St George K, Holmes EC, Spiro DJ. Mixed infection and the genesis of influenza virus diversity. Journal of Virology. 83: 8832-41. PMID 19553313 DOI: 10.1128/Jvi.00773-09 |
0.545 |
|
| 2009 |
Bahl J, Vijaykrishna D, Holmes EC, Smith GJ, Guan Y. Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts. Virology. 390: 289-97. PMID 19501380 DOI: 10.1016/J.Virol.2009.05.002 |
0.517 |
|
| 2009 |
Holmes EC, Tio P, Perera D, Muhi J, Cardosa J. Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia Virus Research. 143: 1-5. PMID 19463715 DOI: 10.1016/J.Virusres.2009.02.020 |
0.51 |
|
| 2009 |
Cardosa J, Ooi MH, Tio PH, Perera D, Holmes EC, Bibi K, Manap ZA. Dengue virus serotype 2 from a sylvatic lineage isolated from a patient with dengue hemorrhagic fever. Plos Neglected Tropical Diseases. 3. PMID 19399166 DOI: 10.1371/Journal.Pntd.0000423 |
0.556 |
|
| 2009 |
Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. The origin and global emergence of adamantane resistant A/H3N2 influenza viruses Virology. 388: 270-278. PMID 19394063 DOI: 10.1016/J.Virol.2009.03.026 |
0.475 |
|
| 2009 |
Dunham EJ, Dugan VG, Kaser EK, Perkins SE, Brown IH, Holmes EC, Taubenberger JK. Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses. Journal of Virology. 83: 5485-94. PMID 19297491 DOI: 10.1128/Jvi.02565-08 |
0.55 |
|
| 2009 |
Talbi C, Holmes EC, Benedictis Pd, Faye O, Nakouné E, Gamatié D, Diarra A, Elmamy BO, Sow A, Adjogoua EV, Sangare O, Dundon WG, Capua I, Sall AA, Bourhy H. Evolutionary history and dynamics of dog rabies virus in western and central Africa. Journal of General Virology. 90: 783-791. PMID 19264663 DOI: 10.1099/Vir.0.007765-0 |
0.484 |
|
| 2009 |
Duffy S, Holmes EC. Validation of high rates of nucleotide substitution in geminiviruses: Phylogenetic evidence from East African cassava mosaic viruses Journal of General Virology. 90: 1539-1547. PMID 19264617 DOI: 10.1099/Vir.0.009266-0 |
0.477 |
|
| 2009 |
Schreiber MJ, Holmes EC, Ong SH, Soh HS, Liu W, Tanner L, Aw PP, Tan HC, Ng LC, Leo YS, Low JG, Ong A, Ooi EE, Vasudevan SG, Hibberd ML. Genomic epidemiology of a dengue virus epidemic in urban Singapore. Journal of Virology. 83: 4163-73. PMID 19211734 DOI: 10.1128/Jvi.02445-08 |
0.5 |
|
| 2009 |
Botosso VF, Zanotto PM, Ueda M, Arruda E, Gilio AE, Vieira SE, Stewien KE, Peret TC, Jamal LF, Pardini MI, Pinho JR, Massad E, Sant'anna OA, Holmes EC, Durigon EL, et al. Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus. Plos Pathogens. 5: e1000254. PMID 19119418 DOI: 10.1371/Journal.Ppat.1000254 |
0.41 |
|
| 2009 |
Chen R, Holmes EC. Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds. Virology. 383: 156-161. PMID 19000628 DOI: 10.1016/J.Virol.2008.10.015 |
0.522 |
|
| 2009 |
Bourhy H, Reynes JM, Dunham EJ, Dacheux L, Larrous F, Huong VTQ, Xu G, Yan J, Miranda MEG, Holmes EC. The origin and phylogeography of dog rabies virus. The Journal of General Virology. 89: 2673-2681. PMID 18931062 DOI: 10.1099/Vir.0.2008/003913-0 |
0.5 |
|
| 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 |
0.309 |
|
| 2009 |
Holmes EC. The Evolutionary Genetics of Emerging Viruses Annual Review of Ecology, Evolution, and Systematics. 40: 353-372. DOI: 10.1146/Annurev.Ecolsys.110308.120248 |
0.469 |
|
| 2008 |
Graaf Md, Osterhaus ADME, Fouchier RAM, Holmes EC. Evolutionary dynamics of human and avian metapneumoviruses Journal of General Virology. 89: 2933-2942. PMID 19008378 DOI: 10.1099/Vir.0.2008/006957-0 |
0.417 |
|
| 2008 |
Ramsden C, Holmes EC, Charleston MA. Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence Molecular Biology and Evolution. 26: 143-153. PMID 18922760 DOI: 10.1093/Molbev/Msn234 |
0.459 |
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