PSU Profiles
Last Name

Edward Holmes

InstitutionEberly College of Science
AddressW230A Millennium Science Cmplx
University Park, PA 16802
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    Other Positions
    InstitutionHuck Institutes of the Life Sciences

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    Professor in Biology


    B.Sc., University of London (University College), UK. (1986).
    Ph.D., University of Cambridge, UK. (1990).


    Dr. Holmes' research integrates ideas from a number of different fields, most notably evolutionary genetics, virology, infectious disease epidemiology, and bioinformatics. His current concentration is on three main areas (virus evolutionary genetics, virus comparative genomics, and virus molecular epidemiology) using primarily RNA virus study systems.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC. Continental synchronicity of human influenza virus epidemics despite climactic variation. PLoS Pathog. 2018 Jan; 14(1):e1006780. PMID: 29324895.
      View in: PubMed
    2. 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 Pathog. 2018 Jan; 14(1):e1006750. PMID: 29300782.
      View in: PubMed
    3. 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, Tian H, Li W, Su G, Lao G, Xu C, Xu B, Liu W, Zhang G, Ren T, Holmes EC, Cui J, Shi W, Gao GF, Liao M. Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor. J Virol. 2018 Jan 15; 92(2). PMID: 29070694.
      View in: PubMed
    4. 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. Emerg Infect Dis. 2018 01; 24(1):22-31. PMID: 29260677.
      View in: PubMed
    5. 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. Emerg Infect Dis. 2017 Dec; 23(12):1950-1957. PMID: 28858604.
      View in: PubMed
    6. Rodríguez-Nevado C, Lam TT, Holmes EC, Pagán I. The impact of host genetic diversity on virus evolution and emergence. Ecol Lett. 2017 Dec 05. PMID: 29207441.
      View in: PubMed
    7. 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. 2018 Jan 15; 514:88-97. PMID: 29153861.
      View in: PubMed
    8. 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. J Virol. 2017 Nov 01. PMID: 29093089.
      View in: PubMed
    9. Geoghegan JL, Holmes EC. Predicting virus emergence amid evolutionary noise. Open Biol. 2017 Oct; 7(10). PMID: 29070612.
      View in: PubMed
    10. Porter AF, Duggan AT, Poinar HN, Holmes EC. Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses. 2017 Sep 28; 9(10). PMID: 28956829.
      View in: PubMed
    11. 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 Losses of Function Do Not Explain Virulence Changes Observed in the Field. J Virol. 2017 Oct 15; 91(20). PMID: 28768866.
      View in: PubMed
    12. 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. Sci Rep. 2017 Sep 07; 7(1):10870. PMID: 28883464.
      View in: PubMed
    13. 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. Proc Natl Acad Sci U S A. 2017 Aug 29; 114(35):9397-9402. PMID: 28808019.
      View in: PubMed
    14. Shi M, Neville P, Nicholson J, Eden JS, Imrie A, Holmes EC. High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. J Virol. 2017 Sep 01; 91(17). PMID: 28637756.
      View in: PubMed
    15. 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 Evol. 2017 Jul; 3(2):vex018. PMID: 28775894.
      View in: PubMed
    16. 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. J Virol. 2017 Aug 15; 91(16). PMID: 28515299.
      View in: PubMed
    17. Eden JS, Rose K, Ng J, Shi M, Wang Q, Sintchenko V, Holmes EC. Francisella tularensis ssp. holarctica in Ringtail Possums, Australia. Emerg Infect Dis. 2017 07; 23(7):1198-1201. PMID: 28628459.
      View in: PubMed
    18. 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. J Virol. 2017 Jun 21. PMID: 28637760.
      View in: PubMed
    19. 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. J Virol. 2017 Jun 15; 91(12). PMID: 28404845.
      View in: PubMed
    20. Fourment M, Darling AE, Holmes EC. The impact of migratory flyways on the spread of avian influenza virus in North America. BMC Evol Biol. 2017 May 25; 17(1):118. PMID: 28545432.
      View in: PubMed
    21. Nicholson LJ, Mahar JE, Strive T, Zheng T, Holmes EC, Ward VK, Duckworth JA. Benign Rabbit Calicivirus in New Zealand. Appl Environ Microbiol. 2017 Jun 01; 83(11). PMID: 28363968.
      View in: PubMed
    22. 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, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017 04 20; 544(7650):309-315. PMID: 28405027.
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    23. 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. 2017 07; 507:1-10. PMID: 28384506.
      View in: PubMed
    24. Di Giallonardo F, Schlub TE, Shi M, Holmes EC. Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species. J Virol. 2017 Apr 15; 91(8). PMID: 28148785.
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    25. Lu M, Tian JH, Yu B, Guo WP, Holmes EC, Zhang YZ. Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China. Ticks Tick Borne Dis. 2017 Jun; 8(4):574-580. PMID: 28411028.
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    26. 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, Hardy K, Harvati K, Held P, Holmes EC, Kaidonis J, Lalueza-Fox C, de la Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K, Cooper A. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. 2017 04 20; 544(7650):357-361. PMID: 28273061.
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    27. 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 Pathog. 2017 Mar; 13(3):e1006252. PMID: 28253375.
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    28. 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. 2017 05; 505:33-41. PMID: 28222327.
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    29. 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. J Virol. 2017 Mar 01; 91(5). PMID: 28077633.
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    30. Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog. 2017 Feb; 13(2):e1006215. PMID: 28178344.
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    31. 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, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS. A molecular portrait of maternal sepsis from Byzantine Troy. Elife. 2017 Jan 10; 6. PMID: 28072390.
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    32. Hackenbrack N, Rogers MB, Ashley RE, Keel MK, Kubiski SV, Bryan JA, Ghedin E, Holmes EC, Hafenstein SL, Allison AB. Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses. J Virol. 2017 Jan 15; 91(2). PMID: 27807242.
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    33. 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 Pathog. 2016 Dec; 12(12):e1006041. PMID: 27977811.
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    34. 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. Sci Rep. 2016 Dec 09; 6:38770. PMID: 27934910.
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    35. McColl KA, Sunarto A, Holmes EC. Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia. Virol J. 2016 12 08; 13(1):206. PMID: 27931224.
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    36. 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, Dutour O, Hedman K, Sajantila A, Smith GL, Holmes EC, Poinar HN. 17th Century Variola Virus Reveals the Recent History of Smallpox. Curr Biol. 2016 Dec 19; 26(24):3407-3412. PMID: 27939314.
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    37. Marciniak S, Prowse TL, Herring DA, Klunk J, Kuch M, Duggan AT, Bondioli L, Holmes EC, Poinar HN. Plasmodium falciparum malaria in 1st-2nd century CE southern Italy. Curr Biol. 2016 Dec 05; 26(23):R1220-R1222. PMID: 27923126.
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    38. Liu W, Pickering P, Duchêne S, Holmes EC, Aaskov JG. Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia. Emerg Infect Dis. 2016 12; 22(12):2146-2148. PMID: 27869598.
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    39. Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC. Genome-scale rates of evolutionary change in bacteria. Microb Genom. 2016 Nov; 2(11):e000094. PMID: 28348834.
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    40. 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. 2016 Nov 23. PMID: 27880757.
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    41. 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. 2016 11 03; 167(4):1079-1087.e5. PMID: 27814505.
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    42. Holmes EC, Dudas G, Rambaut A, Andersen KG. The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature. 2016 10 13; 538(7624):193-200. PMID: 27734858.
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    43. Mahar JE, Nicholson L, Eden JS, Duchêne S, Kerr PJ, Duckworth J, Ward VK, Holmes EC, Strive T. Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives. J Virol. 2016 10 15; 90(20):9317-29. PMID: 27512059.
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    44. 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, Wu Y, Wang L, Liu D, Liu G, Yu H, Holmes EC, Lu L, Gao GF. A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene. PLoS Pathog. 2016 Sep; 12(9):e1005883. PMID: 27676249.
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    45. Holmes EC. The Expanding Virosphere. Cell Host Microbe. 2016 09 14; 20(3):279-280. PMID: 27631697.
      View in: PubMed
    46. Geoghegan JL, Senior AM, Holmes EC. Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proc Biol Sci. 2016 Aug 31; 283(1837). PMID: 27581875; PMCID: PMC5013787 [Available on 08/31/17].
    47. 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. Front Microbiol. 2016; 7:1306. PMID: 27602026; PMCID: PMC4994472.
    48. 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. J Virol. 2016 09 01; 90(17):7920-33. PMID: 27334580; PMCID: PMC4988138 [Available on 02/12/17].
    49. 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. 2016 Aug 12; 353(6300):658. PMID: 27516592.
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    50. Duchêne S, Geoghegan JL, Holmes EC, Ho SY. Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. Bioinformatics. 2016 11 15; 32(22):3375-3379. PMID: 27412094.
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    51. 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. 2016 09; 496:138-146. PMID: 27314620; PMCID: PMC4969160 [Available on 09/01/17].
    52. Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SY, Holmes EC. Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evol Biol. 2016 May 26; 16(1):115. PMID: 27230264; PMCID: PMC4880944.
    53. Lam TT, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet. 2016 Aug 31; 17:193-218. PMID: 27216777.
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    54. 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. 2016 07; 494:168-77. PMID: 27115729.
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    55. 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 Pathog. 2016 Apr; 12(4):e1005525. PMID: 27058957; PMCID: PMC4825935.
    56. Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC. Virological factors that increase the transmissibility of emerging human viruses. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):4170-5. PMID: 27001840; PMCID: PMC4839412 [Available on 10/12/16].
    57. Fourment M, Holmes EC. Seqotron: a user-friendly sequence editor for Mac OS X. BMC Res Notes. 2016 Feb 17; 9:106. PMID: 26887850; PMCID: PMC4756450.
    58. 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. Infect Genet Evol. 2016 Apr; 39:349-364. PMID: 26883378.
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    59. Holmes EC. Complexities of Estimating Evolutionary Rates in Viruses. J Virol. 2016 Feb; 90(4):2155. PMID: 26822594; PMCID: PMC4734009.
    60. 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, Krause J, Poinar HN. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. Elife. 2016 Jan 21; 5:e12994. PMID: 26795402; PMCID: PMC4798955.
    61. 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. J Gen Virol. 2016 Apr; 97(4):844-54. PMID: 26758561.
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    62. 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, Peiris JS, Cowling BJ, Ghedin E. Quantifying influenza virus diversity and transmission in humans. Nat Genet. 2016 Feb; 48(2):195-200. PMID: 26727660; PMCID: PMC4731279.
    63. 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, Alsulaimany FA, Obaid AY, Zhou B, Smith DK, Holmes EC, Zhu H, Guan Y. Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia. Science. 2016 Jan 01; 351(6268):81-4. PMID: 26678874.
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    64. Tan Y, Hassan F, Schuster JE, Simenauer A, Selvarangan R, Halpin RA, Lin X, Fedorova N, Stockwell TB, Lam TT, Chappell JD, Hartert TV, Holmes EC, Das SR. Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States. J Virol. 2015 Dec 09; 90(4):1997-2007. PMID: 26656685; PMCID: PMC4733988.
    65. Hall RN, Mahar JE, Haboury S, Stevens V, Holmes EC, Strive T. Emerging Rabbit Hemorrhagic Disease Virus 2 (RHDVb), Australia. Emerg Infect Dis. 2015 Dec; 21(12):2276-8. PMID: 26583277; PMCID: PMC4672455.
    66. Buchmann JP, Holmes EC. Cell Walls and the Convergent Evolution of the Viral Envelope. Microbiol Mol Biol Rev. 2015 Dec; 79(4):403-18. PMID: 26378223; PMCID: PMC4651029 [Available on 12/01/16].
    67. 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. J Virol. 2015 Oct 28; 90(2):753-67. PMID: 26512077; PMCID: PMC4702700.
    68. 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 United States: Rapid Spread in a Permissive Host Environment. J Virol. 2015 Oct 28; 90(2):862-72. PMID: 26512086; PMCID: PMC4702690.
    69. 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, Zhang YZ. Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses. J Virol. 2015 Oct 21; 90(2):659-69. PMID: 26491167; PMCID: PMC4702705.
    70. Duchêne S, Di Giallonardo F, Holmes EC. Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales. Mol Biol Evol. 2016 Jan; 33(1):255-67. PMID: 26416981.
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    71. 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, Muñoz-Jordán JL, Vasilakis N, Gibbons RV, Tesh RB, Osterhaus AD, Fouchier RA, Durbin A, Simmons CP, Holmes EC, Harris E, Whitehead SS, Smith DJ. Dengue viruses cluster antigenically but not as discrete serotypes. Science. 2015 Sep 18; 349(6254):1338-43. PMID: 26383952; PMCID: PMC4876809.
    72. 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. J Virol. 2015 Dec; 89(23):12217-20. PMID: 26378178; PMCID: PMC4645337.
    73. 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. Emerg Infect Dis. 2015 Sep; 21(9):1670-3. PMID: 26292098; PMCID: PMC4550164.
    74. 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. Emerg Infect Dis. 2015 Aug; 21(8):1330-8. PMID: 26196599; PMCID: PMC4517729.
    75. Lam TT, Zhu H, Chong YL, Holmes EC, Guan Y. Puzzling Origins of the Ebola Outbreak in the Democratic Republic of the Congo, 2014. J Virol. 2015 Oct; 89(19):10130-2. PMID: 26202242; PMCID: PMC4577917.
    76. Duchêne DA, Duchêne S, Holmes EC, Ho SY. Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations. Mol Biol Evol. 2015 Nov; 32(11):2986-95. PMID: 26163668.
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    77. 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. J Virol. 2015 Sep; 89(18):9548-58. PMID: 26157125; PMCID: PMC4542356.
    78. Guo WP, Lin XD, Chen YP, Liu Q, Wang W, Wang CQ, Li MH, Sun XY, Shi M, Holmes EC, Zhang YZ. Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China. J Clin Virol. 2015 Sep; 70:29-38. PMID: 26305816.
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    79. Fourment M, Holmes EC. Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry. BMC Evol Biol. 2015 Jun 26; 15:120. PMID: 26111936; PMCID: PMC4481119.
    80. Di Giallonardo F, Holmes EC. Exploring Host-Pathogen Interactions through Biological Control. PLoS Pathog. 2015 Jun; 11(6):e1004865. PMID: 26110272; PMCID: PMC4482387.
    81. 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 Pathog. 2015 Jun; 11(6):e1004991. PMID: 26107631; PMCID: PMC4479464.
    82. 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, Manuguerra JC, Holmes EC, Sall AA. Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic. Nature. 2015 Aug 06; 524(7563):102-4. PMID: 26106863.
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    83. Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. 2015 Jun 18; 161(7):1516-26. PMID: 26091036; PMCID: PMC4503805.
    84. Geoghegan JL, Tan le V, Kühnert D, Halpin RA, Lin X, Simenauer A, Akopov A, Das SR, Stockwell TB, Shrivastava S, Ngoc NM, Uyen le TT, Tuyen NT, Thanh TT, Hang VT, Qui PT, Hung NT, Khanh TH, Thinh le Q, Nhan le NT, Van HM, Viet do C, Tuan HM, Viet HL, Hien TT, Chau NV, Thwaites G, Grenfell BT, Stadler T, Wentworth DE, Holmes EC, Van Doorn HR. Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam. J Virol. 2015 Sep; 89(17):8871-9. PMID: 26085170; PMCID: PMC4524079.
    85. 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. Lancet Infect Dis. 2015 Jul; 15(7):862-6. PMID: 26051887; PMCID: PMC4824166.
    86. Sintchenko V, Holmes EC. The role of pathogen genomics in assessing disease transmission. BMJ. 2015 May 11; 350:h1314. PMID: 25964672.
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    87. 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. J Virol. 2015 Jul; 89(13):6860-73. PMID: 25903329; PMCID: PMC4468500.
    88. 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. 2015; 10(4):e0122644. PMID: 25897755; PMCID: PMC4405500.
    89. 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. 2015 Apr 07; 6(2). PMID: 25852163; PMCID: PMC4453542.
    90. 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. Nat Commun. 2015 Mar 27; 6:6696. PMID: 25813399; PMCID: PMC4380236.
    91. Duchêne S, Duchêne D, Holmes EC, Ho SY. The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data. Mol Biol Evol. 2015 Jul; 32(7):1895-906. PMID: 25771196.
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    92. 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, Poon LL, Webby RJ, Smith DK, Leung GM, Peiris JS, Holmes EC, Guan Y, Zhu H. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature. 2015 Jun 04; 522(7554):102-5. PMID: 25762140.
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    93. Duchêne S, Ho SY, Holmes EC. Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models. BMC Evol Biol. 2015 Mar 11; 15:36. PMID: 25886870; PMCID: PMC4358783.
    94. Kerr PJ, Liu J, Cattadori I, Ghedin E, Read AF, Holmes EC. Myxoma virus and the Leporipoxviruses: an evolutionary paradigm. Viruses. 2015 Mar 06; 7(3):1020-61. PMID: 25757062; PMCID: PMC4379559.
    95. 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, Ha do Q, Qui PT, Viet do C, Tuan HM, Wong KT, Holmes EC, Chau NV, Thwaites G, van Doorn HR. A generic assay for whole-genome amplification and deep sequencing of enterovirus A71. J Virol Methods. 2015 Apr; 215-216:30-6. PMID: 25704598; PMCID: PMC4374682.
    96. 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 Pathog. 2015 Feb; 11(2):e1004664. PMID: 25679389; PMCID: PMC4334499.
    97. 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 Negl Trop Dis. 2015 Jan; 9(1):e0003442. PMID: 25635775; PMCID: PMC4311992.
    98. 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. 2015 Jan 29; 4. PMID: 25633976; PMCID: PMC4384744.
    99. 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. J Gen Virol. 2015 Jun; 96(Pt 6):1309-19. PMID: 25626685.
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    100. 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, Bošková V, Stadler T, Costa AM, Dwyer DE, Huang QS, Jennings LC, Rawlinson W, Sullivan SG, Hurt AC, Maurer-Stroh S, Wentworth DE, Smith GJ, Barr IG. The contrasting phylodynamics of human influenza B viruses. Elife. 2015 Jan 16; 4:e05055. PMID: 25594904; PMCID: PMC4383373.
    101. Holmes EC, Zhang YZ. The evolution and emergence of hantaviruses. Curr Opin Virol. 2015 Feb; 10:27-33. PMID: 25562117.
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    102. Parrish CR, Murcia PR, Holmes EC. Influenza virus reservoirs and intermediate hosts: dogs, horses, and new possibilities for influenza virus exposure of humans. J Virol. 2015 Mar; 89(6):2990-4. PMID: 25540375; PMCID: PMC4337525.
    103. 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. 2015 Feb; 476:37-42. PMID: 25506671.
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    104. 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. Am J Trop Med Hyg. 2015 Feb; 92(2):405-10. PMID: 25487727; PMCID: PMC4347348.
    105. Geoghegan JL, Walker PJ, Duchemin JB, Jeanne I, Holmes EC. Seasonal drivers of the epidemiology of arthropod-borne viruses in Australia. PLoS Negl Trop Dis. 2014 Nov; 8(11):e3325. PMID: 25412443; PMCID: PMC4239014.
    106. 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. 2015 Jan 01; 474:154-62. PMID: 25463613; PMCID: PMC4259830.
    107. Holmes EC. Freezing viruses in time. Proc Natl Acad Sci U S A. 2014 Nov 25; 111(47):16643-4. PMID: 25404311; PMCID: PMC4250107.
    108. 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, Dwyer DE, Asghar A, Booy R. Viral respiratory infections among Hajj pilgrims in 2013. Virol Sin. 2014 Dec; 29(6):364-71. PMID: 25413828.
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    109. 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, Parrish CR, Dwyer C. Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus. J Virol. 2015 Jan 15; 89(2):1389-403. PMID: 25392223; PMCID: PMC4300652.
    110. 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. 2015 Jan 01; 474:19-27. PMID: 25463600.
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    111. 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 Pathog. 2014 Nov; 10(11):e1004475. PMID: 25375184; PMCID: PMC4223063.
    112. Di Giallonardo F, Holmes EC. Viral biocontrol: grand experiments in disease emergence and evolution. Trends Microbiol. 2015 Feb; 23(2):83-90. PMID: 25455418; PMCID: PMC4323752.
    113. 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 Pathog. 2014 Oct; 10(10):e1004455. PMID: 25340642; PMCID: PMC4207809.
    114. 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. Vet Microbiol. 2014 Dec 05; 174(3-4):547-553. PMID: 25457369; PMCID: PMC4274224.
    115. 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. J Epidemiol Glob Health. 2015 Jun; 5(2):181-9. PMID: 25922328.
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    116. Wagner DM, Keim PS, Scholz HC, Holmes EC, Poinar H. Yersinia pestis and the three plague pandemics--authors' reply. Lancet Infect Dis. 2014 Oct; 14(10):919. PMID: 25253401.
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    117. 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. 2014 Nov; 468-470:104-12. PMID: 25155199.
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    118. 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. 2014 Sep; 464-465:415-423. PMID: 25146599; PMCID: PMC4598644.
    119. 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 Res. 2014 Oct 13; 191:51-8. PMID: 25087879.
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    120. 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 Evol Biol. 2014 Jul 30; 14:167. PMID: 25073875; PMCID: PMC4236549.
    121. Fourment M, Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evol Biol. 2014 Jul 24; 14:163. PMID: 25055743; PMCID: PMC4222489.
    122. Duchêne S, Holmes EC, Ho SY. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc Biol Sci. 2014 Jul 07; 281(1786). PMID: 24850916; PMCID: PMC4046420.
    123. 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. J Virol. 2014 Sep 01; 88(17):10110-9. PMID: 24965467; PMCID: PMC4136342.
    124. 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 Res. 2014 Aug 30; 189:114-20. PMID: 24874196.
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    125. Zhang YZ, Holmes EC. What is the time-scale of hantavirus evolution? Infect Genet Evol. 2014 Jul; 25:144-5. PMID: 24793564.
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    126. 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. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):6744-9. PMID: 24753611; PMCID: PMC4020047.
    127. Cui J, Schlub TE, Holmes EC. An allometric relationship between the genome length and virion volume of viruses. J Virol. 2014 Jun; 88(11):6403-10. PMID: 24672040; PMCID: PMC4093846.
    128. 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, Xu J, Plyusnin A, Holmes EC, Zhang YZ. Co-circulation of multiple hemorrhagic fever diseases with distinct clinical characteristics in Dandong, China. PLoS One. 2014; 9(2):e89896. PMID: 24587107; PMCID: PMC3937409.
    129. 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. J Virol. 2014 Apr; 88(8):4375-88. PMID: 24501401; PMCID: PMC3993777.
    130. 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, Earn DJ, Dewitte S, Rouillard JM, Grupe G, Wiechmann I, Bliska JB, Keim PS, Scholz HC, Holmes EC, Poinar H. Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis. Lancet Infect Dis. 2014 Apr; 14(4):319-26. PMID: 24480148.
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    131. 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. J Infect Dis. 2014 Jul 01; 210(1):121-5. PMID: 24446525; PMCID: PMC4162001.
    132. 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, Tesh RB. Arboretum and Puerto Almendras viruses: two novel rhabdoviruses isolated from mosquitoes in Peru. J Gen Virol. 2014 Apr; 95(Pt 4):787-92. PMID: 24421116; PMCID: PMC3973475.
    133. 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. N Engl J Med. 2014 Jan 23; 370(4):334-40. PMID: 24401020.
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    134. 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 Biol. 2014; 15(12):539. PMID: 25496498; PMCID: PMC4272516.
    135. 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. 2014 Feb; 450-451:106-13. PMID: 24503072; PMCID: PMC3984403.
    136. 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. 2014 Feb; 450-451:2-12. PMID: 24503062; PMCID: PMC3925403.
    137. 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. Mol Ecol. 2014 Feb; 23(2):408-20. PMID: 24251353; PMCID: PMC4595043.
    138. 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 Negl Trop Dis. 2013; 7(12):e2581. PMID: 24340118; PMCID: PMC3854975.
    139. 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. J Virol. 2014 Feb; 88(3):1525-35. PMID: 24227855; PMCID: PMC3911615.
    140. 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. 2014 Jan 05; 448:284-92. PMID: 24314659; PMCID: PMC3873333.
    141. 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 Negl Trop Dis. 2013; 7(10):e2484. PMID: 24147168; PMCID: PMC3798614.
    142. 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. Virol J. 2013 Oct 10; 10:304. PMID: 24107353; PMCID: PMC3852826.
    143. 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, McBride R, Carney PJ, Gilbert AT, Chang J, Guo Z, Davis CT, Paulson JC, Stevens J, Rupprecht CE, Holmes EC, Wilson IA, Donis RO. New world bats harbor diverse influenza A viruses. PLoS Pathog. 2013; 9(10):e1003657. PMID: 24130481; PMCID: PMC3794996.
    144. 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. 2013 Dec; 447(1-2):146-54. PMID: 24210109.
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    145. 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. J Virol. 2013 Dec; 87(23):12900-15. PMID: 24067966; PMCID: PMC3838154.
    146. 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. J Gen Virol. 2013 Dec; 94(Pt 12):2609-15. PMID: 24062532; PMCID: PMC3836499.
    147. 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. J Virol. 2013 Nov; 87(22):12447-56. PMID: 24027322; PMCID: PMC3807886.
    148. 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. J Virol. 2013 Nov; 87(22):12080-9. PMID: 23986601; PMCID: PMC3807925.
    149. 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 Pathog. 2013 Aug; 9(8):e1003543. PMID: 23966858.
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    150. 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. J Virol. 2013 Oct; 87(19):10904-7. PMID: 23885071; PMCID: PMC3807407.
    151. 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 Res. 2013 Sep; 176(1-2):232-40. PMID: 23845302.
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    152. 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. 2013 Sep; 444(1-2):80-9. PMID: 23773405; PMCID: PMC3755043.
    153. Simon-Loriere E, Holmes EC, Pagán I. The effect of gene overlapping on the rate of RNA virus evolution. Mol Biol Evol. 2013 Aug; 30(8):1916-28. PMID: 23686658; PMCID: PMC3708502.
    154. 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, Wentworth DN, Holmes EC, Davey R, Wentworth DE, Ghedin E. Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus. J Virol. 2013 Jul; 87(14):8064-74. PMID: 23678180; PMCID: PMC3700204.
    155. 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, Pham MP, Nguyen HT, Luong TT, Wills B, Nguyen CV, Wolbers M, Simmons CP. Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proc Natl Acad Sci U S A. 2013 May 28; 110(22):9072-7. PMID: 23674683; PMCID: PMC3670336.
    156. 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, Malekani J, Lindblade KA, Rostal MK, Ojeda-Flores R, Suzan G, Davis LB, Blau DM, Ogunkoya AB, Alvarez Castillo DA, Moran D, Ngam S, Akaibe D, Agwanda B, Briese T, Epstein JH, Daszak P, Rupprecht CE, Holmes EC, Lipkin WI. Bats are a major natural reservoir for hepaciviruses and pegiviruses. Proc Natl Acad Sci U S A. 2013 May 14; 110(20):8194-9. PMID: 23610427; PMCID: PMC3657805.
    157. 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. Infect Genet Evol. 2013 Jul; 17:202-9. PMID: 23603764.
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    158. 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. Infect Genet Evol. 2013 Aug; 18:367-78. PMID: 23548803.
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    159. Wang L, Yin Q, He G, Rossiter SJ, Holmes EC, Cui J. Ancient invasion of an extinct gammaretrovirus in cetaceans. Virology. 2013 Jun 20; 441(1):66-9. PMID: 23545142.
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    160. 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. 2013 Mar 27; 10:35. PMID: 23537098; PMCID: PMC3621094.
    161. Simon-Loriere E, Holmes EC. Gene duplication is infrequent in the recent evolutionary history of RNA viruses. Mol Biol Evol. 2013 Jun; 30(6):1263-9. PMID: 23486612.
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    162. 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. Virol J. 2013 Mar 04; 10:69. PMID: 23497016; PMCID: PMC3599451.
    163. Ke R, Aaskov J, Holmes EC, Lloyd-Smith JO. Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses. PLoS Pathog. 2013 Feb; 9(2):e1003193. PMID: 23468631; PMCID: PMC3585136.
    164. 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 Pathog. 2013 Feb; 9(2):e1003172. PMID: 23436995; PMCID: PMC3578757.
    165. 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 Pathog. 2013 Feb; 9(2):e1003159. PMID: 23408889; PMCID: PMC3567184.
    166. 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. J Virol. 2013 Apr; 87(8):4768-71. PMID: 23388708; PMCID: PMC3624384.
    167. Viboud C, Nelson MI, Tan Y, Holmes EC. Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Philos Trans R Soc Lond B Biol Sci. 2013 Mar 19; 368(1614):20120199. PMID: 23382422; PMCID: PMC3678324.
    168. 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, Scott TW, Jarman RG. Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand. PLoS Negl Trop Dis. 2013; 7(1):e1990. PMID: 23350000; PMCID: PMC3547850.
    169. Holmes EC. What can we predict about viral evolution and emergence? Curr Opin Virol. 2013 Apr; 3(2):180-4. PMID: 23273851; PMCID: PMC3626763.
    170. 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 Pathog. 2012 Dec; 8(12):e1003081. PMID: 23308065; PMCID: PMC3534375.
    171. 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, Tong S. Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. J Gen Virol. 2013 Apr; 94(Pt 4):738-48. PMID: 23239573.
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    172. 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. J Virol. 2013 Feb; 87(4):2342-7. PMID: 23221559; PMCID: PMC3571474.
    173. 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. Proc Biol Sci. 2013 Jan 07; 280(1750):20122173. PMID: 23135678; PMCID: PMC3574438.
    174. 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 Pathog. 2012; 8(10):e1002950. PMID: 23055928; PMCID: PMC3464225.
    175. Nielsen AC, Gyhrs ML, Holmes EC, Cui J. Co-circulation and persistence of genetically distinct saffold viruses, Denmark. Emerg Infect Dis. 2012 Oct; 18(10):1694-6. PMID: 23017727; PMCID: PMC3471643.
    176. 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. J Gen Virol. 2012 Dec; 93(Pt 12):2584-9. PMID: 22993190; PMCID: PMC4091293.
    177. 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. J Infect Dis. 2012 Nov 15; 206(10):1504-11. PMID: 22966122; PMCID: PMC3475640.
    178. 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. J Virol. 2012 Nov; 86(22):12411-3. PMID: 22951836; PMCID: PMC3486490.
    179. 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, Kung HF, Holmes EC, Cheng J. Epidemiological dynamics and phylogeography of influenza virus in southern China. J Infect Dis. 2013 Jan 01; 207(1):106-14. PMID: 22930808; PMCID: PMC3523792.
    180. 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, Parkhill J, Dougan G, Thomson NR. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet. 2012 Sep; 44(9):1056-9. PMID: 22863732; PMCID: PMC3442231.
    181. Nelson MI, Gramer MR, Vincent AL, Holmes EC. Global transmission of influenza viruses from humans to swine. J Gen Virol. 2012 Oct; 93(Pt 10):2195-203. PMID: 22791604; PMCID: PMC3541789.
    182. 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. J Virol. 2012 Aug; 86(16):8872-8. PMID: 22696653; PMCID: PMC3421719.
    183. Cui J, Tachedjian G, Tachedjian M, Holmes EC, Zhang S, Wang LF. Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats. J Gen Virol. 2012 Sep; 93(Pt 9):2037-45. PMID: 22694899.
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    184. 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 Pathog. 2012; 8(5):e1002730. PMID: 22693449; PMCID: PMC3364949.
    185. 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. J Gen Virol. 2012 Aug; 93(Pt 8):1831-40. PMID: 22592263.
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    186. 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. Mol Ecol. 2012 Jun; 21(12):3062-77. PMID: 22574738.
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    187. Cui J, Holmes EC. Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses. J Virol. 2012 Jul; 86(14):7688-91. PMID: 22553337; PMCID: PMC3416299.
    188. 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. 2012; 7(4):e34261. PMID: 22514627; PMCID: PMC3325999.
    189. Cui J, Holmes EC. Evidence for an endogenous papillomavirus-like element in the platypus genome. J Gen Virol. 2012 Jun; 93(Pt 6):1362-6. PMID: 22422067.
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    190. Cui J, Holmes EC. Endogenous RNA viruses of plants in insect genomes. Virology. 2012 Jun 05; 427(2):77-9. PMID: 22410578; PMCID: PMC3725393.
    191. Kachroo P, Pak PS, Sandha HS, Lee C, Elashoff D, Nelson SD, Chmielowski B, Selch MT, Cameron RB, Holmes EC, Eilber FC, Lee JM. Single-institution, multidisciplinary experience with surgical resection of primary chest wall sarcomas. J Thorac Oncol. 2012 Mar; 7(3):552-8. PMID: 22307013.
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    192. Pagán I, Holmes EC, Simon-Loriere E. Level of gene expression is a major determinant of protein evolution in the viral order Mononegavirales. J Virol. 2012 May; 86(9):5253-63. PMID: 22345453; PMCID: PMC3347393.
    193. 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. J Gen Virol. 2012 Apr; 93(Pt 4):817-22. PMID: 22238233.
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    194. Cui J, Holmes EC. Endogenous lentiviruses in the ferret genome. J Virol. 2012 Mar; 86(6):3383-5. PMID: 22238305; PMCID: PMC3302300.
    195. 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. J Virol. 2012 Feb; 86(3):1514-21. PMID: 22114336; PMCID: PMC3264339.
    196. 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, Simmons CP. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. J Virol. 2012 Jan; 86(2):835-43. PMID: 22090119; PMCID: PMC3255838.
    197. Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris JS, Riley S, Rambaut A, Holmes EC, Smith GJ. Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc Natl Acad Sci U S A. 2011 Nov 29; 108(48):19359-64. PMID: 22084096; PMCID: PMC3228450.
    198. 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. J Virol. 2012 Jan; 86(2):865-72. PMID: 22072763; PMCID: PMC3255849.
    199. Boni MF, Smith GJ, Holmes EC, Vijaykrishna D. No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Gene. 2012 Feb 25; 494(2):242-5. PMID: 22226809; PMCID: PMC3427013.
    200. Holmes EC. Genomics: Plague's progress. Nature. 2011 Oct 26; 478(7370):465-6. PMID: 22031436.
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    201. Holmes EC. The evolution of endogenous viral elements. Cell Host Microbe. 2011 Oct 20; 10(4):368-77. PMID: 22018237.
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    202. 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. Infect Genet Evol. 2012 Jan; 12(1):63-70. PMID: 22036789.
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    203. Cook S, Moureau G, Kitchen A, Gould EA, de Lamballerie X, Holmes EC, Harbach RE. Molecular evolution of the insect-specific flaviviruses. J Gen Virol. 2012 Feb; 93(Pt 2):223-34. PMID: 22012464; PMCID: PMC3352342.
    204. 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. Ecol Lett. 2012 Jan; 15(1):24-33. PMID: 22008513; PMCID: PMC3228906.
    205. Cattoli G, Fusaro A, Monne I, Coven F, Joannis T, El-Hamid HS, 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. 2011 Nov 21; 29(50):9368-75. PMID: 22001877.
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    206. Tra My PV, Rabaa MA, Vinh H, Holmes EC, Hoang NV, Vinh NT, Phuong le T, Tham NT, Bay PV, 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. Am J Trop Med Hyg. 2011 Oct; 85(4):768-75. PMID: 21976585; PMCID: PMC3183790.
    207. Torres-Pérez F, Palma RE, Hjelle B, Holmes EC, Cook JA. Spatial but not temporal co-divergence of a virus and its mammalian host. Mol Ecol. 2011 Oct; 20(19):4109-22. PMID: 21880089; PMCID: PMC3183239.
    208. 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. J Virol. 2011 Oct; 85(19):10279-85. PMID: 21795347; PMCID: PMC3196454.
    209. Simon-Loriere E, Holmes EC. Why do RNA viruses recombine? Nat Rev Microbiol. 2011 Jul 04; 9(8):617-26. PMID: 21725337; PMCID: PMC3324781.
    210. Fusaro A, Monne I, Salviato A, Valastro V, Schivo A, Amarin NM, Gonzalez C, Ismail MM, Al-Ankari AR, Al-Blowi MH, Khan OA, Maken Ali AS, Hedayati A, Garcia Garcia J, Ziay GM, Shoushtari A, Al Qahtani KN, Capua I, Holmes EC, Cattoli G. Phylogeography and evolutionary history of reassortant H9N2 viruses with potential human health implications. J Virol. 2011 Aug; 85(16):8413-21. PMID: 21680519; PMCID: PMC3147996.
    211. 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. Nat Rev Microbiol. 2011 Jun 13; 9(7):532-41. PMID: 21666708; PMCID: PMC3321645.
    212. Nelson MI, Lemey P, Tan Y, Vincent A, Lam TT, 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 Pathog. 2011 Jun; 7(6):e1002077. PMID: 21695237; PMCID: PMC3111536.
    213. Morens DM, Holmes EC, Davis AS, Taubenberger JK. Global rinderpest eradication: lessons learned and why humans should celebrate too. J Infect Dis. 2011 Aug 15; 204(4):502-5. PMID: 21653230; PMCID: PMC3144172.
    214. 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 Pathog. 2011 Jun; 7(6):e1002064. PMID: 21655108; PMCID: PMC3107208.
    215. 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. Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community. J Virol. 2011 Jul; 85(14):6923-9. PMID: 21593168; PMCID: PMC3126550.
    216. Holmes EC. What does virus evolution tell us about virus origins? J Virol. 2011 Jun; 85(11):5247-51. PMID: 21450811; PMCID: PMC3094976.
    217. Murcia PR, Wood JL, Holmes EC. Genome-scale evolution and phylodynamics of equine H3N8 influenza A virus. J Virol. 2011 Jun; 85(11):5312-22. PMID: 21430049; PMCID: PMC3094979.
    218. Liu WJ, Rourke MF, Holmes EC, Aaskov JG. Persistence of multiple genetic lineages within intrahost populations of Ross River virus. J Virol. 2011 Jun; 85(11):5674-8. PMID: 21430052; PMCID: PMC3094999.
    219. Bhatt S, Holmes EC, Pybus OG. The genomic rate of molecular adaptation of the human influenza A virus. Mol Biol Evol. 2011 Sep; 28(9):2443-51. PMID: 21415025; PMCID: PMC3163432.
    220. 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, St George K. Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance. J Infect Dis. 2011 Jan 15; 203(2):168-74. PMID: 21288815; PMCID: PMC3071067.
    221. 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. 2010 Dec 22; 5(12):e14357. PMID: 21203504; PMCID: PMC3008715.
    222. Kitchen A, Shackelton LA, Holmes EC. Family level phylogenies reveal modes of macroevolution in RNA viruses. Proc Natl Acad Sci U S A. 2011 Jan 04; 108(1):238-43. PMID: 21173251; PMCID: PMC3017157.
    223. Simmons HE, Holmes EC, Stephenson AG. Rapid turnover of intra-host genetic diversity in Zucchini yellow mosaic virus. Virus Res. 2011 Feb; 155(2):389-96. PMID: 21138748; PMCID: PMC3026904.
    224. 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, Musser JM. Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. J Virol. 2011 Jan; 85(2):828-34. PMID: 21068250; PMCID: PMC3020026.
    225. Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Nourlil J, Jalal N, Faouzi A, Echevarría JE, Vazquez Morón S, Rambaut A, Campiz N, Tatem AJ, Holmes EC, Bourhy H. Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog. 2010 Oct 28; 6(10):e1001166. PMID: 21060816; PMCID: PMC2965766.
    226. 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. J Virol. 2010 Dec; 84(24):12636-45. PMID: 20943966; PMCID: PMC3004329.
    227. Holmes EC. Malaria: The gorilla connection. Nature. 2010 Sep 23; 467(7314):404-5. PMID: 20864986.
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    228. Jahnke M, Holmes EC, Kerr PJ, Wright JD, Strive T. Evolution and phylogeography of the nonpathogenic calicivirus RCV-A1 in wild rabbits in Australia. J Virol. 2010 Dec; 84(23):12397-404. PMID: 20861266; PMCID: PMC2976393.
    229. Pagán I, Firth C, Holmes EC. Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus tobamovirus. J Mol Evol. 2010 Oct; 71(4):298-307. PMID: 20838783.
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    230. Rabaa MA, Ty Hang VT, Wills B, Farrar J, Simmons CP, Holmes EC. Phylogeography of recently emerged DENV-2 in southern Viet Nam. PLoS Negl Trop Dis. 2010 Jul 27; 4(7):e766. PMID: 20668540; PMCID: PMC2910671.
    231. 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, Simmons CP. 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 Negl Trop Dis. 2010 Jul 20; 4(7):e757. PMID: 20651932; PMCID: PMC2907417.
    232. 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, Caro V, Gessain A, Bourhy H. Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses. J Virol. 2010 Sep; 84(18):9557-74. PMID: 20610710; PMCID: PMC2937603.
    233. Romano CM, de Carvalho-Mello IM, Jamal LF, de Melo FL, Iamarino A, Motoki M, Pinho JR, Holmes EC, de Andrade Zanotto PM. Social networks shape the transmission dynamics of hepatitis C virus. PLoS One. 2010 Jun 23; 5(6):e11170. PMID: 20585651; PMCID: PMC2890415.
    234. 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. Arch Virol. 2010 Sep; 155(9):1401-12. PMID: 20549264.
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    235. Carpi G, Holmes EC, Kitchen A. The evolutionary dynamics of bluetongue virus. J Mol Evol. 2010 Jun; 70(6):583-92. PMID: 20526713.
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    236. Holmes EC. Virology. Helping the resistance. Science. 2010 Jun 04; 328(5983):1243-4. PMID: 20522766.
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    237. Holmes EC. The RNA virus quasispecies: fact or fiction? J Mol Biol. 2010 Jul 16; 400(3):271-3. PMID: 20493194.
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    238. 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, McCauley JW, McKinley TJ, Holmes EC, Grenfell BT, Wood JL. Intra- and interhost evolutionary dynamics of equine influenza virus. J Virol. 2010 Jul; 84(14):6943-54. PMID: 20444896; PMCID: PMC2898244.
    239. Boni MF, de Jong MD, van Doorn HR, Holmes EC. Guidelines for identifying homologous recombination events in influenza A virus. PLoS One. 2010 May 03; 5(5):e10434. PMID: 20454662; PMCID: PMC2862710.
    240. 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. J Virol. 2010 Jul; 84(13):6497-504. PMID: 20410280; PMCID: PMC2903258.
    241. Pagán I, Holmes EC. Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. J Virol. 2010 Jun; 84(12):6177-87. PMID: 20375155; PMCID: PMC2876656.
    242. 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. Mol Biol Evol. 2010 Sep; 27(9):2038-51. PMID: 20363828; PMCID: PMC3107591.
    243. 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. J Virol. 2010 Apr; 84(7):3726-7; author reply 3727-8. PMID: 20212326; PMCID: PMC2838117.
    244. Holmes EC. Does hepatitis C virus really form quasispecies? Infect Genet Evol. 2010 May; 10(4):431-2. PMID: 20304103.
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    245. 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, Spiro DJ, Holmes EC. Unseasonal transmission of H3N2 influenza A virus during the swine-origin H1N1 pandemic. J Virol. 2010 Jun; 84(11):5715-8. PMID: 20237080; PMCID: PMC2876599.
    246. 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. J Virol. 2010 May; 84(10):5329-35. PMID: 20219907; PMCID: PMC2863817.
    247. 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. J Virol. 2010 Apr; 84(7):3239-47. PMID: 20071565; PMCID: PMC2838112.
    248. Balmaseda A, Standish K, Mercado JC, Matute JC, Tellez Y, Saborío 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. J Infect Dis. 2010 Jan 01; 201(1):5-14. PMID: 19929380; PMCID: PMC3724236.
    249. Chen R, Holmes EC. Hitchhiking and the population genetic structure of avian influenza virus. J Mol Evol. 2010 Jan; 70(1):98-105. PMID: 20041240; PMCID: PMC2826789.
    250. Halloran ME, Holmes EC. Invited commentary: Evaluating vaccination programs using genetic sequence data. Am J Epidemiol. 2009 Dec 15; 170(12):1464-6; discussion 1467-8. PMID: 19910381; PMCID: PMC2800275.
    251. Sall AA, Faye O, Diallo M, Firth C, Kitchen A, Holmes EC. Yellow fever virus exhibits slower evolutionary dynamics than dengue virus. J Virol. 2010 Jan; 84(2):765-72. PMID: 19889759; PMCID: PMC2798388.
    252. 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, Viboud C, Holmes E, Henrickson K. The early diversification of influenza A/H1N1pdm. PLoS Curr. 2009 Nov 03; 1:RRN1126. PMID: 20029664.
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    253. Holmes EC. Evolution in health and medicine Sackler colloquium: The comparative genomics of viral emergence. Proc Natl Acad Sci U S A. 2010 Jan 26; 107 Suppl 1:1742-6. PMID: 19858482; PMCID: PMC2868293.
    254. Holmes EC, Grenfell BT. Discovering the phylodynamics of RNA viruses. PLoS Comput Biol. 2009 Oct; 5(10):e1000505. PMID: 19855824; PMCID: PMC2756585.
    255. Firth C, Charleston MA, Duffy S, Shapiro B, Holmes EC. Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J Virol. 2009 Dec; 83(24):12813-21. PMID: 19812157; PMCID: PMC2786836.
    256. 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. Emerg Infect Dis. 2009 Oct; 15(10):1630-2. PMID: 19861059; PMCID: PMC2866390.
    257. Kerr PJ, Kitchen A, Holmes EC. Origin and phylodynamics of rabbit hemorrhagic disease virus. J Virol. 2009 Dec; 83(23):12129-38. PMID: 19759153; PMCID: PMC2786765.
    258. Jones A, Lowry K, Aaskov J, Holmes EC, Kitchen A. Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy. J Gen Virol. 2010 Jan; 91(Pt 1):182-8. PMID: 19759236.
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    259. Grard G, Moureau G, Charrel RN, Holmes EC, Gould EA, de Lamballerie X. Genomics and evolution of Aedes-borne flaviviruses. J Gen Virol. 2010 Jan; 91(Pt 1):87-94. PMID: 19741066.
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    260. Holmes EC. RNA virus genomics: a world of possibilities. J Clin Invest. 2009 Sep; 119(9):2488-95. PMID: 19729846; PMCID: PMC2735898.
    261. Rambaut A, Holmes E. The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Curr. 2009 Aug 18; 1:RRN1003. PMID: 20025195; PMCID: PMC2762654.
    262. 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. J Gen Virol. 2009 Nov; 90(Pt 11):2669-78. PMID: 19656970; PMCID: PMC2885038.
    263. 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. J Virol. 2009 Sep; 83(17):8832-41. PMID: 19553313; PMCID: PMC2738154.
    264. 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. 2009 Aug 01; 390(2):289-97. PMID: 19501380; PMCID: PMC2753668.
    265. Cardosa J, Ooi MH, Tio PH, Perera D, Holmes EC, Bibi K, Abdul Manap Z. Dengue virus serotype 2 from a sylvatic lineage isolated from a patient with dengue hemorrhagic fever. PLoS Negl Trop Dis. 2009; 3(4):e423. PMID: 19399166; PMCID: PMC2669127.
    266. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Virology. 2009 Jun 05; 388(2):270-8. PMID: 19394063; PMCID: PMC2705899.
    267. Holmes EC, Tio PH, Perera D, Muhi J, Cardosa J. Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia. Virus Res. 2009 Jul; 143(1):1-5. PMID: 19463715.
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    268. 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. J Virol. 2009 Jun; 83(11):5485-94. PMID: 19297491; PMCID: PMC2681951.
    269. Duffy S, Holmes EC. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol. 2009 Jun; 90(Pt 6):1539-47. PMID: 19264617; PMCID: PMC4091138.
    270. Talbi C, Holmes EC, de Benedictis P, 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. J Gen Virol. 2009 Apr; 90(Pt 4):783-91. PMID: 19264663.
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    271. Franco ML, King CH, Culjat MO, Lewis CE, Bisley JW, Holmes EC, Grundfest WS, Dutson EP. An integrated pneumatic tactile feedback actuator array for robotic surgery. Int J Med Robot. 2009 Mar; 5(1):13-9. PMID: 19086011.
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    272. 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. J Virol. 2009 May; 83(9):4163-73. PMID: 19211734; PMCID: PMC2668455.
    273. de Graaf M, Osterhaus AD, Fouchier RA, Holmes EC. Evolutionary dynamics of human and avian metapneumoviruses. J Gen Virol. 2008 Dec; 89(Pt 12):2933-42. PMID: 19008378.
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    274. Chen R, Holmes EC. Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds. Virology. 2009 Jan 05; 383(1):156-61. PMID: 19000628; PMCID: PMC2633721.
    275. Bourhy H, Reynes JM, Dunham EJ, Dacheux L, Larrous F, Huong VT, Xu G, Yan J, Miranda ME, Holmes EC. The origin and phylogeography of dog rabies virus. J Gen Virol. 2008 Nov; 89(Pt 11):2673-81. PMID: 18931062; PMCID: PMC3326349.
    276. Ramsden C, Holmes EC, Charleston MA. Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol. 2009 Jan; 26(1):143-53. PMID: 18922760.
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    277. Hoelzer K, Shackelton LA, Holmes EC, Parrish CR. Within-host genetic diversity of endemic and emerging parvoviruses of dogs and cats. J Virol. 2008 Nov; 82(22):11096-105. PMID: 18768982; PMCID: PMC2573264.
    278. Chang GS, Hong Y, Ko KD, Bhardwaj G, Holmes EC, Patterson RL, van Rossum DB. Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13474-9. PMID: 18765810; PMCID: PMC2527991.
    279. Hoelzer K, Shackelton LA, Parrish CR, Holmes EC. Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses. J Gen Virol. 2008 Sep; 89(Pt 9):2280-9. PMID: 18753238; PMCID: PMC2735869.
    280. Parrish CR, Holmes EC, Morens DM, Park EC, Burke DS, Calisher CH, Laughlin CA, Saif LJ, Daszak P. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol Mol Biol Rev. 2008 Sep; 72(3):457-70. PMID: 18772285; PMCID: PMC2546865.
    281. Briese T, Renwick N, Venter M, Jarman RG, Ghosh D, Köndgen S, Shrestha SK, Hoegh AM, Casas I, Adjogoua EV, Akoua-Koffi C, Myint KS, Williams DT, Chidlow G, van den Berg R, Calvo C, Koch O, Palacios G, Kapoor V, Villari J, Dominguez SR, Holmes KV, Harnett G, Smith D, Mackenzie JS, Ellerbrok H, Schweiger B, Schønning K, Chadha MS, Leendertz FH, Mishra AC, Gibbons RV, Holmes EC, Lipkin WI. Global distribution of novel rhinovirus genotype. Emerg Infect Dis. 2008 Jun; 14(6):944-7. PMID: 18507910; PMCID: PMC2600308.
    282. Dugan VG, Chen R, Spiro DJ, Sengamalay N, Zaborsky J, Ghedin E, Nolting J, Swayne DE, Runstadler JA, Happ GM, Senne DA, Wang R, Slemons RD, Holmes EC, Taubenberger JK. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. 2008 May 30; 4(5):e1000076. PMID: 18516303; PMCID: PMC2387073.
    283. Shackelton LA, Holmes EC. The role of alternative genetic codes in viral evolution and emergence. J Theor Biol. 2008 Sep 07; 254(1):128-34. PMID: 18589455.
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    284. Chen R, Holmes EC. The evolutionary dynamics of human influenza B virus. J Mol Evol. 2008 Jun; 66(6):655-63. PMID: 18504518; PMCID: PMC3326418.
    285. Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, Bouchier C, Bourhy H. Genomic diversity and evolution of the lyssaviruses. PLoS One. 2008 Apr 30; 3(4):e2057. PMID: 18446239; PMCID: PMC2327259.
    286. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature. 2008 May 29; 453(7195):615-9. PMID: 18418375; PMCID: PMC2441973.
    287. Ramsden C, Melo FL, Figueiredo LM, Holmes EC, Zanotto PM. High rates of molecular evolution in hantaviruses. Mol Biol Evol. 2008 Jul; 25(7):1488-92. PMID: 18417484.
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    288. Simmons HE, Holmes EC, Stephenson AG. Rapid evolutionary dynamics of zucchini yellow mosaic virus. J Gen Virol. 2008 Apr; 89(Pt 4):1081-5. PMID: 18343852.
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    289. Jarman RG, Holmes EC, Rodpradit P, Klungthong C, Gibbons RV, Nisalak A, Rothman AL, Libraty DH, Ennis FA, Mammen MP, Endy TP. Microevolution of Dengue viruses circulating among primary school children in Kamphaeng Phet, Thailand. J Virol. 2008 Jun; 82(11):5494-500. PMID: 18367520; PMCID: PMC2395201.
    290. Boni MF, Zhou Y, Taubenberger JK, Holmes EC. Homologous recombination is very rare or absent in human influenza A virus. J Virol. 2008 May; 82(10):4807-11. PMID: 18353939; PMCID: PMC2346757.
    291. Pardini MI, Jamal LF, Durigon EL, Massad E, Perez JF, Pinho JR, Holmes EC, de Andrade Zanotto PM. Boosting virology in Brazil. PLoS Biol. 2008 Mar 11; 6(3):e57. PMID: 18336070; PMCID: PMC2265768.
    292. Romano CM, Zanotto PM, Holmes EC. Bayesian coalescent analysis reveals a high rate of molecular evolution in GB virus C. J Mol Evol. 2008 Mar; 66(3):292-7. PMID: 18320258; PMCID: PMC3324782.
    293. Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet. 2008 Apr; 9(4):267-76. PMID: 18319742.
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    294. Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, St George K, Taylor J, Spiro DJ, Sengamalay NA, Ghedin E, Taubenberger JK, Holmes EC. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. 2008 Feb 29; 4(2):e1000012. PMID: 18463694; PMCID: PMC2262849.
    295. Pomeroy LW, Bjørnstad ON, Holmes EC. The evolutionary and epidemiological dynamics of the paramyxoviridae. J Mol Evol. 2008 Feb; 66(2):98-106. PMID: 18217182; PMCID: PMC3334863.
    296. Holmes EC. Evolutionary history and phylogeography of human viruses. Annu Rev Microbiol. 2008; 62:307-28. PMID: 18785840.
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    297. Shackelton LA, Hoelzer K, Parrish CR, Holmes EC. Comparative analysis reveals frequent recombination in the parvoviruses. J Gen Virol. 2007 Dec; 88(Pt 12):3294-301. PMID: 18024898; PMCID: PMC3326350.
    298. Aaskov J, Buzacott K, Field E, Lowry K, Berlioz-Arthaud A, Holmes EC. Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient. J Gen Virol. 2007 Dec; 88(Pt 12):3334-40. PMID: 18024903; PMCID: PMC2884982.
    299. Holmes EC. When HIV spread afar. Proc Natl Acad Sci U S A. 2007 Nov 20; 104(47):18351-2. PMID: 18003901; PMCID: PMC2141781.
    300. Duffy S, Holmes EC. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J Virol. 2008 Jan; 82(2):957-65. PMID: 17977971; PMCID: PMC2224568.
    301. Romano CM, de Melo FL, Corsini MA, Holmes EC, Zanotto PM. Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys. PLoS One. 2007 Oct 10; 2(10):e1026. PMID: 17925874; PMCID: PMC2001186.
    302. Holmes EC. Viral evolution in the genomic age. PLoS Biol. 2007 Oct 02; 5(10):e278. PMID: 17914905; PMCID: PMC1994994.
    303. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog. 2007 Sep 14; 3(9):1220-8. PMID: 17941707; PMCID: PMC2323296.
    304. Duffy S, Holmes EC. Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World. Appl Environ Microbiol. 2007 Nov; 73(21):7114-7. PMID: 17827315; PMCID: PMC2074955.
    305. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI. A metagenomic survey of microbes in honey bee colony collapse disorder. Science. 2007 Oct 12; 318(5848):283-7. PMID: 17823314.
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    306. Sharp EL, Farrell HE, Borchers K, Holmes EC, Davis-Poynter NJ. Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates. J Gen Virol. 2007 Sep; 88(Pt 9):2450-62. PMID: 17698654.
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    307. Kalayanarooj S, Rimal HS, Andjaparidze A, Vatcharasaevee V, Nisalak A, Jarman RG, Chinnawirotpisan P, Mammen MP, Holmes EC, Gibbons RV. Clinical intervention and molecular characteristics of a dengue hemorrhagic fever outbreak in Timor Leste, 2005. Am J Trop Med Hyg. 2007 Sep; 77(3):534-7. PMID: 17827374.
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    308. Thümer L, Rethwilm A, Holmes EC, Bodem J. The complete nucleotide sequence of a New World simian foamy virus. Virology. 2007 Dec 05; 369(1):191-7. PMID: 17765280.
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    309. Barros de Freitas R, Durigon EL, Oliveira Dde S, Romano CM, Castro de Freitas MR, Linhares Ada C, Melo FL, Walshkeller L, Barbosa ML, Huatuco EM, Holmes EC, Zanotto PM. The "pressure pan" evolution of human erythrovirus B19 in the Amazon, Brazil. Virology. 2007 Dec 20; 369(2):281-7. PMID: 17698162.
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    310. Brault AC, Huang CY, Langevin SA, Kinney RM, Bowen RA, Ramey WN, Panella NA, Holmes EC, Powers AM, Miller BR. A single positively selected West Nile viral mutation confers increased virogenesis in American crows. Nat Genet. 2007 Sep; 39(9):1162-6. PMID: 17694056; PMCID: PMC2291521.
    311. Zhou Y, Holmes EC. Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J Mol Evol. 2007 Aug; 65(2):197-205. PMID: 17684696.
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    312. Vasilakis N, Holmes EC, Fokam EB, Faye O, Diallo M, Sall AA, Weaver SC. Evolutionary processes among sylvatic dengue type 2 viruses. J Virol. 2007 Sep; 81(17):9591-5. PMID: 17553878; PMCID: PMC1951459.
    313. Dunham EJ, Holmes EC. Inferring the timescale of dengue virus evolution under realistic models of DNA substitution. J Mol Evol. 2007 Jun; 64(6):656-61. PMID: 17541679.
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    314. Simonsen L, Viboud C, Grenfell BT, Dushoff J, Jennings L, Smit M, Macken C, Hata M, Gog J, Miller MA, Holmes EC. The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Mol Biol Evol. 2007 Aug; 24(8):1811-20. PMID: 17522084.
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    315. Bryant JE, Holmes EC, Barrett AD. Out of Africa: a molecular perspective on the introduction of yellow fever virus into the Americas. PLoS Pathog. 2007 May 18; 3(5):e75. PMID: 17511518; PMCID: PMC1868956.
    316. Sanjuán R, Cuevas JM, Furió V, Holmes EC, Moya A. Selection for robustness in mutagenized RNA viruses. PLoS Genet. 2007 Jun; 3(6):e93. PMID: 17571922; PMCID: PMC1892351.
    317. Holmes EC. Ancient lentiviruses leave their mark. Proc Natl Acad Sci U S A. 2007 Apr 10; 104(15):6095-6. PMID: 17404211; PMCID: PMC1851092.
    318. Schreiber MJ, Ong SH, Holland RC, Hibberd ML, Vasudevan SG, Mitchell WP, Holmes EC. DengueInfo: A web portal to dengue information resources. Infect Genet Evol. 2007 Jul; 7(4):540-1. PMID: 17350350.
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    319. Walker PR, Ketunuti M, Choge IA, Meyers T, Gray G, Holmes EC, Morris L. Polymorphisms in Nef associated with different clinical outcomes in HIV type 1 subtype C-infected children. AIDS Res Hum Retroviruses. 2007 Feb; 23(2):204-15. PMID: 17331028.
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    320. Nelson MI, Holmes EC. The evolution of epidemic influenza. Nat Rev Genet. 2007 03; 8(3):196-205. PMID: 17262054.
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    321. Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, Holmes EC. Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol Biol Evol. 2007 Mar; 24(3):845-52. PMID: 17218639.
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    322. Holmes EC, Drummond AJ. The evolutionary genetics of viral emergence. Curr Top Microbiol Immunol. 2007; 315:51-66. PMID: 17848060.
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    323. Snapinn KW, Holmes EC, Young DS, Bernard KA, Kramer LD, Ebel GD. Declining growth rate of West Nile virus in North America. J Virol. 2007 Mar; 81(5):2531-4. PMID: 17182695; PMCID: PMC1865964.
    324. Grard G, Moureau G, Charrel RN, Lemasson JJ, Gonzalez JP, Gallian P, Gritsun TS, Holmes EC, Gould EA, de Lamballerie X. Genetic characterization of tick-borne flaviviruses: new insights into evolution, pathogenetic determinants and taxonomy. Virology. 2007 Apr 25; 361(1):80-92. PMID: 17169393.
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    325. Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Ghedi E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC. Stochastic processes are key determinants of short-term evolution in influenza a virus. PLoS Pathog. 2006 Dec; 2(12):e125. PMID: 17140286; PMCID: PMC1665651.
    326. Grard G, Lemasson JJ, Sylla M, Dubot A, Cook S, Molez JF, Pourrut X, Charrel R, Gonzalez JP, Munderloh U, Holmes EC, de Lamballerie X. Ngoye virus: a novel evolutionary lineage within the genus Flavivirus. J Gen Virol. 2006 Nov; 87(Pt 11):3273-7. PMID: 17030860.
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    327. Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct. 2006 Oct 26; 1:34. PMID: 17067369; PMCID: PMC1647279.
    328. Aulicino PC, Holmes EC, Rocco C, Mangano A, Sen L. Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina. J Virol. 2007 Jan; 81(1):427-9. PMID: 17050594; PMCID: PMC1797267.
    329. Shackelton LA, Rambaut A, Pybus OG, Holmes EC. JC virus evolution and its association with human populations. J Virol. 2006 Oct; 80(20):9928-33. PMID: 17005670; PMCID: PMC1617318.
    330. Holmes EC, Lipman DJ, Zamarin D, Yewdell JW. Comment on "Large-scale sequence analysis of avian influenza isolates". Science. 2006 Sep 15; 313(5793):1573; author reply 1573. PMID: 16973862.
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    331. Zhou Y, Mammen MP, Klungthong C, Chinnawirotpisan P, Vaughn DW, Nimmannitya S, Kalayanarooj S, Holmes EC, Zhang C. Comparative analysis reveals no consistent association between the secondary structure of the 3'-untranslated region of dengue viruses and disease syndrome. J Gen Virol. 2006 Sep; 87(Pt 9):2595-603. PMID: 16894198.
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    332. Chen R, Holmes EC. Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol. 2006 Dec; 23(12):2336-41. PMID: 16945980.
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    333. Shapiro B, Rambaut A, Pybus OG, Holmes EC. A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Mol Biol Evol. 2006 Sep; 23(9):1724-30. PMID: 16774976.
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    334. Kuiken T, Holmes EC, McCauley J, Rimmelzwaan GF, Williams CS, Grenfell BT. Host species barriers to influenza virus infections. Science. 2006 Apr 21; 312(5772):394-7. PMID: 16627737.
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    335. Davis PL, Bourhy H, Holmes EC. The evolutionary history and dynamics of bat rabies virus. Infect Genet Evol. 2006 Nov; 6(6):464-73. PMID: 16621724.
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    336. Varki A, Holmes E, Yamada T, Agre P, Brenner S. Physician-scientists are needed now more than ever. Nature. 2006 Apr 06; 440(7085):740. PMID: 16598232.
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    337. Cook S, Bennett SN, Holmes EC, De Chesse R, Moureau G, de Lamballerie X. Isolation of a new strain of the flavivirus cell fusing agent virus in a natural mosquito population from Puerto Rico. J Gen Virol. 2006 Apr; 87(Pt 4):735-48. PMID: 16528021.
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    338. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, Beltran M, Vorndam V, Gubler DJ, McMillan WO. Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction. J Gen Virol. 2006 Apr; 87(Pt 4):885-93. PMID: 16528038.
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    339. Zhang C, Mammen MP, Chinnawirotpisan P, Klungthong C, Rodpradit P, Nisalak A, Vaughn DW, Nimmannitya S, Kalayanarooj S, Holmes EC. Structure and age of genetic diversity of dengue virus type 2 in Thailand. J Gen Virol. 2006 Apr; 87(Pt 4):873-83. PMID: 16528037.
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    340. Shackelton LA, Holmes EC. Phylogenetic evidence for the rapid evolution of human B19 erythrovirus. J Virol. 2006 Apr; 80(7):3666-9. PMID: 16537636; PMCID: PMC1440363.
    341. Holmes EC. The evolution of viral emergence. Proc Natl Acad Sci U S A. 2006 Mar 28; 103(13):4803-4. PMID: 16567658; PMCID: PMC1458749.
    342. Edwards CT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ. Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol Biol. 2006 Mar 23; 6:28. PMID: 16556318; PMCID: PMC1444934.
    343. Shackelton LA, Parrish CR, Holmes EC. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol. 2006 May; 62(5):551-63. PMID: 16557338.
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    344. Aaskov J, Buzacott K, Thu HM, Lowry K, Holmes EC. Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes. Science. 2006 Jan 13; 311(5758):236-8. PMID: 16410525.
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    345. Holmes EC. The evolutionary biology of dengue virus. Novartis Found Symp. 2006; 277:177-87; discussion 187-92, 251-3. PMID: 17319162.
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    346. Zhang C, Mammen MP, Chinnawirotpisan P, Klungthong C, Rodpradit P, Monkongdee P, Nimmannitya S, Kalayanarooj S, Holmes EC. Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J Virol. 2005 Dec; 79(24):15123-30. PMID: 16306584; PMCID: PMC1316048.
    347. Carrington CV, Foster JE, Pybus OG, Bennett SN, Holmes EC. Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. J Virol. 2005 Dec; 79(23):14680-7. PMID: 16282468; PMCID: PMC1287558.
    348. Milicic A, Edwards CT, Hué S, Fox J, Brown H, Pillay T, Drijfhout JW, Weber JN, Holmes EC, Fidler SJ, Zhang HT, Phillips RE. Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants. J Virol. 2005 Nov; 79(22):13953-62. PMID: 16254331; PMCID: PMC1280182.
    349. Pillay T, Zhang HT, Drijfhout JW, Robinson N, Brown H, Khan M, Moodley J, Adhikari M, Pfafferott K, Feeney ME, St John A, Holmes EC, Coovadia HM, Klenerman P, Goulder PJ, Phillips RE. Unique acquisition of cytotoxic T-lymphocyte escape mutants in infant human immunodeficiency virus type 1 infection. J Virol. 2005 Sep; 79(18):12100-5. PMID: 16140787; PMCID: PMC1212591.
    350. Holmes EC. On being the right size. Nat Genet. 2005 Sep; 37(9):923-4. PMID: 16132047.
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    351. Holmes EC, Taubenberger JK, Grenfell BT. Heading off an influenza pandemic. Science. 2005 Aug 12; 309(5737):989. PMID: 16099952.
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    352. Davis PL, Holmes EC, Larrous F, Van der Poel WH, Tjørnehøj K, Alonso WJ, Bourhy H. Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses. J Virol. 2005 Aug; 79(16):10487-97. PMID: 16051841; PMCID: PMC1182613.
    353. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005 Sep; 3(9):e300. PMID: 16026181; PMCID: PMC1180517.
    354. Edwards CT, Pfafferott KJ, Goulder PJ, Phillips RE, Holmes EC. Intrapatient escape in the A*0201-restricted epitope SLYNTVATL drives evolution of human immunodeficiency virus type 1 at the population level. J Virol. 2005 Jul; 79(14):9363-6. PMID: 15994836; PMCID: PMC1168780.
    355. Myat Thu H, Lowry K, Jiang L, Hlaing T, Holmes EC, Aaskov J. Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection. Virology. 2005 Jun 05; 336(2):163-72. PMID: 15892958.
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    356. Rodriguez-Roche R, Alvarez M, Holmes EC, Bernardo L, Kouri G, Gould EA, Halstead S, Guzman MG. Dengue virus type 3, Cuba, 2000-2002. Emerg Infect Dis. 2005 May; 11(5):773-4. PMID: 15898173; PMCID: PMC3320353.
    357. Goodarzi MO, Taylor KD, Guo X, Quiñones MJ, Cui J, Li X, Hang T, Yang H, Holmes E, Hsueh WA, Olefsky J, Rotter JI. Variation in the gene for muscle-specific AMP deaminase is associated with insulin clearance, a highly heritable trait. Diabetes. 2005 Apr; 54(4):1222-7. PMID: 15793265.
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    358. Switzer WM, Salemi M, Shanmugam V, Gao F, Cong ME, Kuiken C, Bhullar V, Beer BE, Vallet D, Gautier-Hion A, Tooze Z, Villinger F, Holmes EC, Heneine W. Ancient co-speciation of simian foamy viruses and primates. Nature. 2005 Mar 17; 434(7031):376-80. PMID: 15772660.
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    359. Pybus OG, Cochrane A, Holmes EC, Simmonds P. The hepatitis C virus epidemic among injecting drug users. Infect Genet Evol. 2005 Mar; 5(2):131-9. PMID: 15639745.
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    360. Cook S, Diallo M, Sall AA, Cooper A, Holmes EC. Mitochondrial markers for molecular identification of Aedes mosquitoes (Diptera: Culicidae) involved in transmission of arboviral disease in West Africa. J Med Entomol. 2005 Jan; 42(1):19-28. PMID: 15691004.
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    361. Shackelton LA, Parrish CR, Truyen U, Holmes EC. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc Natl Acad Sci U S A. 2005 Jan 11; 102(2):379-84. PMID: 15626758; PMCID: PMC544290.
    362. Walker PR, Pybus OG, Rambaut A, Holmes EC. Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. Infect Genet Evol. 2005 Apr; 5(3):199-208. PMID: 15737910.
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    363. Priest FG, Barker M, Baillie LW, Holmes EC, Maiden MC. Population structure and evolution of the Bacillus cereus group. J Bacteriol. 2004 Dec; 186(23):7959-70. PMID: 15547268; PMCID: PMC529064.
    364. A-Nuegoonpipat A, Berlioz-Arthaud A, Chow V, Endy T, Lowry K, Mai le Q, Ninh TU, Pyke A, Reid M, Reynes JM, Su Yun ST, Thu HM, Wong SS, Holmes EC, Aaskov J. Sustained transmission of dengue virus type 1 in the Pacific due to repeated introductions of different Asian strains. Virology. 2004 Nov 24; 329(2):505-12. PMID: 15518827.
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    365. Klungthong C, Zhang C, Mammen MP, Ubol S, Holmes EC. The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand. Virology. 2004 Nov 10; 329(1):168-79. PMID: 15476884.
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    366. Shackelton LA, Holmes EC. The evolution of large DNA viruses: combining genomic information of viruses and their hosts. Trends Microbiol. 2004 Oct; 12(10):458-65. PMID: 15381195.
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    367. Chare ER, Holmes EC. Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J Gen Virol. 2004 Oct; 85(Pt 10):3149-57. PMID: 15448378.
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    368. Urwin R, Russell JE, Thompson EA, Holmes EC, Feavers IM, Maiden MC. Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design. Infect Immun. 2004 Oct; 72(10):5955-62. PMID: 15385499; PMCID: PMC517544.
    369. de S Leal E, Holmes EC, Zanotto PM. Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy. Virology. 2004 Aug 01; 325(2):181-91. PMID: 15246258.
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    370. Holmes EC, Rambaut A. Viral evolution and the emergence of SARS coronavirus. Philos Trans R Soc Lond B Biol Sci. 2004 Jul 29; 359(1447):1059-65. PMID: 15306390; PMCID: PMC1693395.
    371. Oxenius A, Price DA, Trkola A, Edwards C, Gostick E, Zhang HT, Easterbrook PJ, Tun T, Johnson A, Waters A, Holmes EC, Phillips RE. Loss of viral control in early HIV-1 infection is temporally associated with sequential escape from CD8+ T cell responses and decrease in HIV-1-specific CD4+ and CD8+ T cell frequencies. J Infect Dis. 2004 Aug 15; 190(4):713-21. PMID: 15272399.
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    372. Draenert R, Le Gall S, Pfafferott KJ, Leslie AJ, Chetty P, Brander C, Holmes EC, Chang SC, Feeney ME, Addo MM, Ruiz L, Ramduth D, Jeena P, Altfeld M, Thomas S, Tang Y, Verrill CL, Dixon C, Prado JG, Kiepiela P, Martinez-Picado J, Walker BD, Goulder PJ. Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. J Exp Med. 2004 Apr 05; 199(7):905-15. PMID: 15067030; PMCID: PMC2211885.
    373. Sheridan I, Pybus OG, Holmes EC, Klenerman P. High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression. J Virol. 2004 Apr; 78(7):3447-54. PMID: 15016867; PMCID: PMC371055.
    374. Moya A, Holmes EC, González-Candelas F. The population genetics and evolutionary epidemiology of RNA viruses. Nat Rev Microbiol. 2004 Apr; 2(4):279-88. PMID: 15031727.
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    375. Holmes EC. The phylogeography of human viruses. Mol Ecol. 2004 Apr; 13(4):745-56. PMID: 15012753.
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    376. Barnett OE, Worobey M, Holmes EC, Cooper A. Detection of TT virus among chimpanzees in the wild using a noninvasive technique. J Wildl Dis. 2004 Apr; 40(2):230-7. PMID: 15362822.
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    377. Holmes EC. Virology. 1918 and all that. Science. 2004 Mar 19; 303(5665):1787-8. PMID: 15031487.
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    378. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC. Unifying the epidemiological and evolutionary dynamics of pathogens. Science. 2004 Jan 16; 303(5656):327-32. PMID: 14726583.
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    379. Rambaut A, Posada D, Crandall KA, Holmes EC. The causes and consequences of HIV evolution. Nat Rev Genet. 2004 Jan; 5(1):52-61. PMID: 14708016.
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    380. Holmes EC. Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 2003 Dec; 11(12):543-6. PMID: 14659685.
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    381. Mao JT, Roth MD, Serio KJ, Baratelli F, Zhu L, Holmes EC, Strieter RM, Dubinett SM. Celecoxib modulates the capacity for prostaglandin E2 and interleukin-10 production in alveolar macrophages from active smokers. Clin Cancer Res. 2003 Dec 01; 9(16 Pt 1):5835-41. PMID: 14676104.
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    382. Chare ER, Gould EA, Holmes EC. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol. 2003 Oct; 84(Pt 10):2691-703. PMID: 13679603.
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    383. Holmes EC. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol. 2003 Oct; 77(20):11296-8. PMID: 14512579; PMCID: PMC224983.
    384. Twiddy SS, Pybus OG, Holmes EC. Comparative population dynamics of mosquito-borne flaviviruses. Infect Genet Evol. 2003 Jul; 3(2):87-95. PMID: 12809802.
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    385. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, Beltran M, Vorndam V, Gubler DJ, McMillan WO. Selection-driven evolution of emergent dengue virus. Mol Biol Evol. 2003 Oct; 20(10):1650-8. PMID: 12832629.
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    386. Holmes EC, Roberts AF, Staines KA, Ellis SA. Evolution of major histocompatibility complex class I genes in Cetartiodactyls. Immunogenetics. 2003 Jul; 55(4):193-202. PMID: 12756505.
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    387. Holmes EC, Twiddy SS. The origin, emergence and evolutionary genetics of dengue virus. Infect Genet Evol. 2003 May; 3(1):19-28. PMID: 12797969.
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    388. Walker PR, Worobey M, Rambaut A, Holmes EC, Pybus OG. Epidemiology: Sexual transmission of HIV in Africa. Nature. 2003 Apr 17; 422(6933):679. PMID: 12700750.
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    389. Holmes EC. Molecular clocks and the puzzle of RNA virus origins. J Virol. 2003 Apr; 77(7):3893-7. PMID: 12634349; PMCID: PMC150674.
    390. Craig S, Thu HM, Lowry K, Wang XF, Holmes EC, Aaskov J. Diverse dengue type 2 virus populations contain recombinant and both parental viruses in a single mosquito host. J Virol. 2003 Apr; 77(7):4463-7. PMID: 12634407; PMCID: PMC150639.
    391. Isobe T, Holmes EC, Rudenko G. The transferrin receptor genes of Trypanosoma equiperdum are less diverse in their transferrin binding site than those of the broad-host range Trypanosoma brucei. J Mol Evol. 2003 Apr; 56(4):377-86. PMID: 12664158.
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    392. Jenkins GM, Holmes EC. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 2003 Mar; 92(1):1-7. PMID: 12606071.
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    393. Guyatt KJ, Twin J, Davis P, Holmes EC, Smith GA, Smith IL, Mackenzie JS, Young PL. A molecular epidemiological study of Australian bat lyssavirus. J Gen Virol. 2003 Feb; 84(Pt 2):485-96. PMID: 12560583.
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    394. Twiddy SS, Holmes EC. The extent of homologous recombination in members of the genus Flavivirus. J Gen Virol. 2003 Feb; 84(Pt 2):429-40. PMID: 12560576.
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    395. Twiddy SS, Holmes EC, Rambaut A. Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol. 2003 Jan; 20(1):122-9. PMID: 12519914.
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    396. Gould EA, de Lamballerie X, Zanotto PM, Holmes EC. Origins, evolution, and vector/host coadaptations within the genus Flavivirus. Adv Virus Res. 2003; 59:277-314. PMID: 14696332.
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    397. Woelk CH, Holmes EC. Reduced positive selection in vector-borne RNA viruses. Mol Biol Evol. 2002 Dec; 19(12):2333-6. PMID: 12446826.
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    398. Urwin R, Holmes EC, Fox AJ, Derrick JP, Maiden MC. Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB. Mol Biol Evol. 2002 Oct; 19(10):1686-94. PMID: 12270895.
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    399. Twiddy SS, Woelk CH, Holmes EC. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J Gen Virol. 2002 Jul; 83(Pt 7):1679-89. PMID: 12075087.
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    400. Twiddy SS, Farrar JJ, Vinh Chau N, Wills B, Gould EA, Gritsun T, Lloyd G, Holmes EC. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Virology. 2002 Jun 20; 298(1):63-72. PMID: 12093174.
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    401. Posada D, Crandall KA, Holmes EC. Recombination in evolutionary genomics. Annu Rev Genet. 2002; 36:75-97. PMID: 12429687.
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    402. Kurtenbach K, De Michelis S, Sewell HS, Etti S, Schäfer SM, Holmes E, Hails R, Collares-Pereira M, Santos-Reis M, Hanincová K, Labuda M, Bormane A, Donaghy M. The key roles of selection and migration in the ecology of Lyme borreliosis. Int J Med Microbiol. 2002 Jun; 291 Suppl 33:152-4. PMID: 12141740.
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    403. Fares MA, Holmes EC. A revised evolutionary history of hepatitis B virus (HBV). J Mol Evol. 2002 Jun; 54(6):807-14. PMID: 12029362.
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    404. Woelk CH, Pybus OG, Jin L, Brown DW, Holmes EC. Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections. J Gen Virol. 2002 Jun; 83(Pt 6):1419-30. PMID: 12029157.
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    405. Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol. 2002 Feb; 54(2):156-65. PMID: 11821909.
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    406. Brault AC, Powers AM, Holmes EC, Woelk CH, Weaver SC. Positively charged amino acid substitutions in the e2 envelope glycoprotein are associated with the emergence of venezuelan equine encephalitis virus. J Virol. 2002 Feb; 76(4):1718-30. PMID: 11799167; PMCID: PMC135911.
    407. Holmes EC, Woelk CH, Kassis R, Bourhy H. Genetic constraints and the adaptive evolution of rabies virus in nature. Virology. 2002 Jan 20; 292(2):247-57. PMID: 11878928.
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    408. Holmes EC, Moya A. Is the quasispecies concept relevant to RNA viruses? J Virol. 2002 Jan; 76(1):460-5. PMID: 11739715; PMCID: PMC135735.
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