Eddie Holmes
Location: Macleay Building, Room 203 | Phone: +61 2 9351 5591 | Email: edward.holmes@sydney.edu.au | Lab: Viral Evolution
NHMRC Australia Fellow Professor in Biology & Medicine (joint appointment with Sydney Medical School)
I am an evolutionary biologist who has worked on viruses and other microbes for over 20 years. My main research theme has been to determine the mechanisms by which viruses emerge in new host species, their patterns and dynamics of spread through populations, and their major mechanisms of evolutionary change. My main research tool has been the evolutionary (largely phylogenetic) analysis of gene sequence data. As case studies I have worked on a number of important viruses of humans and other animals, such as HIV, influenza, dengue, rabies and myxoma. I have also published on a number of bacterial diseases. A good summary of my research and ideas can be found in my book on viral evolution.
I joined the University of Sydney in October 2012. Prior to moving here, I worked at Penn State University (2005-2012), the University of Oxford, where I was also a Fellow of New College (1993-2004), the University of Edinburgh (1991-1993), and the University of California, Davis (1990-1991). My Ph.D. is from the University of Cambridge (1990), and I also have an undergraduate degree from University College London (1986).
I have spent most of my scientific career undertaking research aimed at revealing the principle patterns and processes of viral evolution and emergence. Although I still find work of this type fascinating, and I will continue to explore these themes, I want the molecular evolution and epidemiology I pursue to have a more direct and measurable impact on public and animal health. This will be my primary goal at the University of Sydney.
Please email me if you are interested in joining my research group or wish to discuss specific areas of my research program.
Publications
Due to copyright restrictions, please email me () if you would like a copy of any of these articles. You can also view my publications on PubMed.
Books
- Holmes EC. (2009). The Evolution and Emergence of RNA Viruses. Oxford Series in Ecology and Evolution (OSEE). Series edited by PH Harvey & RM May. Oxford University Press, Oxford.
- Page RDM & Holmes EC. (1998). Molecular Evolution: A Phylogenetic Approach. Blackwell Science Ltd, Oxford.
Peer Reviewed Journal Articles
Summary
- 341 published papers
- 19,327 total citations
- H-index = 72
In press
- 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. In Press).
- Wang L, Yin Q, He G, Rossiter SJ, Holmes EC & Cui J. Ancient invasion of an extinct gammaretrovirus in cetaceans. (Virology In Press).
Published
2013
1. Allison AB, Kohler DJ, Fox KA, Brown JD, Gerhold RW, Shearn-Bochsler VI, Dubovi EJ, Parrish CR & Holmes EC. (2013). Frequent cross-species transmission of parvoviruses among diverse carnivore hosts. J.Virol. 87, 2342-2347.
2. Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Guan Y, Wood JLN, Brown IH, Kellam P, Combating Swine Influenza Consortium & Pybus OG. (2013). The evolutionary dynamics of influenza A virus adaptation to mammalian hosts. Phil.Trans.Roy.Soc.Lond.B. 368 20120382; doi:10.1098/rstb.2012.0382.
3. Cheng X, Tan Y, He M, Lam TT-Y, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, Kung H-F, Holmes EC & Cheng J. (2013). Epidemiological dynamics and phylogeography of influenza virus in southern China. J.Infect.Dis. 207, 106-114.
4. Guo W-P, Lin X-D, Wang W, Tian J-H, Cong M-L, Zhang H-L, Wang M-R, Wang J-B, Zhou R-H, Wang J-B, Li M-H, Xu J, Holmes EC & Zhang Y-Z. (2013). Phylogeny and origins of hantaviruses harbored by bats, insectivores, and rodents. PLoS Pathog. 9:e1003159.
5. Hayward JA, Tachedjian M, Cui J, Field H, Holmes EC, Wang L-F & Tachedjian G. (2013). Identification of diverse full-length endogenous betaretroviruses in megabats and microbats. Retrovirology 10:35.
6. Holmes EC. (2013). What can we predict about viral evolution and emergence? Curr.Opin.Virol. Epub 28 December 2012.
7. Ke R, Aaskov J, Holmes EC & Lloyd-Smith JO. (2013). Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses. PLoS Pathog. 9:e1003193.
8. Murcia PR, Baillie GJ, Stack JC, Jervis C, Elton E, Mumford JA, Daly J, Kellam P, Grenfell BT, Holmes EC & Wood JL. (2013). Evolution of equine influenza virus in vaccinated horses. J.Virol. Epub 6 February 2013.
9. Nougairède A, de Fabritus L, Aubry F, Gould EA, Holmes EC & de Lamballerie X. (2013). Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. PLoS Pathog. 9:e1003172.
10. Rabaa MA, Klungthong C, Yoon I-K, Holmes EC, Chinnawirotpisan P, Thaisomboonsuk B, Srikiatkhachorn A, Rothman AL, Tannitisupawong D, Aldstadt J, Nisalak A, Mammen MP Jr., Thammapalo S, Gibbons RV, Endy TP, Fansiri T, Scott TW & Jarman RG. (2013). Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand. PLoS Neglect.Trop.Dis. 7:e1990.
11. Simon-Loriere E & Holmes EC. (2013). Gene duplication is infrequent in the recent evolutionary history of RNA viruses. Mol.Biol.Evol. 13 March 2013.
12. Stack JR, Murcia PR, Grenfell BT, Wood JLN & Holmes EC. (2013). Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic evolution. Proc.Roy.Soc.Lond.Lond.B. 280 20122173; doi:10.1098/rspb.2012.2173.
13. 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. (2013). Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. J.Gen.Virol. 94, 738-748.
14. Vasilakis N, Widen S, Travassos da Rosa AAPA, Wood TG, Walker PJ, Holmes EC & Tesh RB. (2013). Malpais Spring virus is a new species in the genus Vesiculovirus. Virol.J. 10:69.
15. Viboud C, Nelson MI, Tan Y & Holmes EC. (2013). Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Phil.Trans.Roy.Soc.Lond.B. 368 20120199; doi:10.1098/rstb.2012.0199.
2012
16. Allison AB, Harbison CE, Pagán I, Stucker KM, Kaelber JT, Brown JD, Ruder MG, Keel MK, Dubovi EJ, Holmes EC & Parrish CR. (2012).The role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus. J.Virol. 86, 865-872.
17. Allison AB, Holmes EC, Potgieter C, Wright IM, Sailleau C, Breard, E Ruder MG & Stallknecht DE. (2012). Segmental configuration and putative origin of the reassortant orbivirus, epizootic hemorrhagic disease virus serotype 6, strain Indiana. Virology 424, 67-75.
18. Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL & van Rossum DB. (2012). PHYRN: A novel method for the phylogenetic analysis of highly divergent sequences. PLoS One 7, e34261.
19. Boni MF, Smith GJD, Holmes EC & Vijaykrishna D. (2012). No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Gene 494, 242-245.
20. Cook S, Moureau G, Kitchen A, Gould EA, de Lamballerie X, Holmes EC & Harbach RE. (2012). Molecular evolution of the insect-specific flaviviruses. J.Gen.Virol. 93, 223-234.
21. Cui J & Holmes EC. (2012). Endogenous retroviruses in the ferret genome. J.Virol. 86, 3383-3385.
22. Cui J & Holmes EC. (2012). Endogenous RNA viruses of plants in insect genomes. Virology 427, 77-79.
23. Cui J & Holmes EC. (2012). Evidence for an endogenous papillomavirus-like element in the platypus genome. J.Gen.Virol. 93,1362-1366.
24. Cui J & Holmes EC. (2012). Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses. J.Virol. 86, 7688-7691.
25. Cui J, Tachedjian G, Tachedjian M, Holmes EC, Zhang S & Wang L-F. (2012). Identification of diverse groups of endogenous gammaretroviruses in mega and microbats. J.Gen.Virol. 93, 2037-2045.
26. Ghedin E, Holmes EC, DePasse JV, Pinilla LT, Fitch A, Hamelin M-E, Papenburg J & Boivin G. (2012). Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. J.Infect.Dis. 206, 1504-1511.
27. Holt KE, Baker S, Weill F-X, 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. (2012). Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat.Genet. 44, 1056-1059.
28. Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JLN, Holmes EC & Murcia PR. (2012). Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathog. 8:e1003081.
29. Kerr PJ, Ghedin E, DePasse JV, Fitch A, Cattadori IM, Hudson PJ, Tscharke DC, Read AF & Holmes EC. (2012). Evolutionary history and attenuation of myxoma virus on two continents. PLoS Pathog. 8:e1002950.
30. Lam TT-Y, Hon C-C, Lemey P, Pybus OG, Shi M, Tun HM, Li J, Jiang J, Holmes EC & Leung FC-C. (2012). Phylodynamics of H5N1 highly pathogenic avian influenza virus in Indonesia. Mol.Ecol. 21, 3062-3077.
31. Lam TT-Y, Ip HS, Ghedin E, Wentworth DE, Halpin RA, Stockwell TB, Spiro DJ, Dusek RJ, Bortner JB, Bales BD, Yparraguirre DR & Holmes EC.. (2012). Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecol.Lett. 15, 24-33.
32. Lam TT-Y, Zhu H, Smith DK, Guan Y, Holmes EC & Pybus OG. (2012). The recombinant origin of emerging human norovirus GII.4/2008: intra-genic exchange of the capsid P2 domain. J.Gen.Virol. 93, 817-822.
33. 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 JLN. (2012). Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathog. 8:e1002730.
34. Nelson MI, Detmer SE, Wentworth DE, Tan Y, Schwartzbard A, Halpin RA, Stockwell TB, Lin X, Vincent AL, Gramer MR & Holmes EC. (2012). Genomic reassortment of influenza A virus in North American swine, 1998-2011. J.Gen.Virol. 93, 2584-2589.
35. Nelson MI, Gramer MR, Vincent AL & Holmes EC. (2012). Global transmission of influenza viruses from humans to swine, 2009-2011. J.Gen.Virol. 93, 2195-2203.
36. Nelson MI, Vincent AL, Kitikoon P, Holmes EC & Gramer MR. (2012). Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011. J.Virol. 86, 8872-8878.
37. Nielsen ACY, Gyhrs ML, Holmes EC & Cui J. (2012). Co-circulation and persistence of genetically distinct Saffold viruses, Denmark. Emerg.Infect.Dis. 18, 1694-1696.
38. Pagán I, Holmes EC & Simon-Loriere E. (2012). Level of gene expression is a major determinant of protein evolution in the viral order Mononegavirales. J.Virol. 86, 5253-5263.
39. Panzarin V, Fusaro A, Monne I, Cappellozza E, Patarnello P, Bovo G, Capua I, Holmes EC & Cattoli G. (2012). Molecular epidemiology and evolutionary dynamics of betanodavirus in southern Europe. Infect.Genet.Evol. 12, 63-70.
40. Shi M, Jagger BW, Wise HM, Digard P, Holmes EC & Taubenberger JK. (2012). Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus. J.Virol. 86, 12411-12413.
41. Simmons HE, Dunham JP, Stack JC, Dickins BJA, Pagán I, Holmes EC & Stephenson AG. (2012). Deep sequencing reveals persistence of intra- and inter-host diversity in natural and greenhouse populations of Zucchini yellow mosaic virus. J.Gen.Virol. 93, 1831-1840.
42. Stucker KM, Pagán I, Cifuente JO, Kaelber JT, Lillie TD, Hafenstein S, Holmes EC & Parrish CR. (2012). The role of evolutionary intermediates in the host adaptation of canine parvovirus. J.Virol. 86, 1514-1521.
43. Thai KTD, 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. (2012). High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 identifies mixed infections. J.Virol. 86, 835-843.
2011
44. Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin R, Stockwell T, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris M, Riley S, Rambaut A, Holmes EC & Smith GJD. (2011). Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc.Natl.Acad.Sci.USA 108, 19359-19364.
45. Bhatt S, Holmes EC & Pybus OG. (2011). The genomic rate of molecular adaptation of the human influenza A virus. Mol.Biol.Evol. 28, 2443-2451.
46. Cattoli G, Fusaro A, Monne I, Coven F, Joannis F, Abd El-Hamid HS, Amarin NM, Mancin M, Holmes EC & Capua I. (2011). Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry. Vaccine 29, 9368-9375.
47. Fusaro A, Monne I, Salviato A, Valastro V, Schivo A, Amarin NM, Gonzalez C, Ismail MM, Al-ankari R-A, Al-Bowi MH, Khan OA, Ali ASM, Hedayati A, Garcia JG, Ziay GM, Shoushtari A, Al Qahtani KN, Capua I, Holmes EC & Cattoli G. (2011). Phylogeography and evolutionary history of reassortant H9N2 viruses with potential human health implications. J.Virol. 85, 8413-8421.
48. 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. (2011). Deep sequencing reveals mixed infection with pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance. J.Infect.Dis. 203, 168-174.
49. Holmes EC. (2011). What does virus evolution tell us about virus origins? J.Virol. 85, 5247-5251.
50. Holmes EC. (2011). The evolution of endogenous viral elements. Cell Host & Microbe 10, 368-377.
51. Holmes EC, Ghedin E, Halpin RA, Stockwell TB, Zhang X-Q, Fleming R, Davey R, Benson CA, Mehta S, Taplitz R, Liu Y-T, Brouwer KC, Wentworth DE, Lin X, INSIGHT FLU002 Study Group & Schooley RT. (2011). Extensive geographical mixing of human H1N1/09 influenza A virus in a single university community. J.Virol. 85, 6923-6929.
52. Kitchen A, Shackelton L & Holmes EC. (2011). Family level phylogenies reveal modes of macroevolution in RNA viruses. Proc.Natl.Acad.Sci.USA 108, 238-243.
53. Lam TT-Y, Zhu H, Wang J, Smith DK, Holmes EC, Webster RG, Webby R, Peiris JM & Guan Y. (2011). Reassortment events among swine influenza A viruses in China: Implications for the origin of the 2009 influenza pandemic. J.Virol. 85, 10279-10285.
54. Liu W, Rourke M, Holmes EC & Aaskov J. (2011). Persistence of multiple genetic lineages within intra-host populations of Ross River Virus. J.Virol. 85, 5674-5678.
55. Morens DM, Holmes EC, Davis AS & Taubenberger JK. (2011). Rinderpest eradication: why humans should celebrate too. J.Infect.Dis. 204, 502-505.
56. Murcia PR, Wood JLN, Holmes EC. (2011). Genome-scale evolution and phylodynamics of equine H3N8 influenza A virus. J.Virol. 85, 5312-5322.
57. My PVT, Rabaa MA, Vinh H, Holmes EC, Hoang NVM, Vinh NT, Phuong LT, Tham NT, Bay PVB, Campbell JI, Farrar J & Baker S. (2011). The emergence of rotavirus G12 and the prevalence of enteric viruses from hospitalised pediatric diarrheal patients in southern Vietnam. Am.J.Trop.Med.Hyg. 85, 768-775.
58. Nelson MI, Lemey P, Tan Y, Vincent A, Lam TT-Y, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC & Gramer M. (2011). Spatial dynamics of human-origin H1 influenza A virus in North American swine. PLoS Pathog. 7:e1002077.
59. Nelson MI, Tan Y, Ghedin E, Wentworth DE, St. George K, Edelman L, Beck ET, Fan J, Lam TT-Y, Kumar S, Spiro DJ, Simonsen L, Viboud C, Holmes EC, Henrickson KJ & Musser JM. (2011). Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. J.Virol. 85, 828-834.
60. Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR & Simmons CP. (2011). Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLoS Pathog. 7:e1002064.
61. Simmons HE, Holmes EC, Gildow FE, Bothe-Goralczyk ME & Stephenson AG. (2011). Experimental verification of seed transmission in Zucchini yellow mosaic virus. Plant Dis. 95, 751-754.
62. Simmons HE, Holmes EC & Stephenson AG. (2011). Rapid turnover of intra-host genetic diversity in zucchini yellow mosaic virus. Virus Res. 155, 389-396.
63. Simon-Loriere E & Holmes EC. (2011). Why do RNA viruses recombine? Nat.Rev.Micro. 9, 617-626.
64. Torres-Pérez F, Palma RE, Hjelle B, Holmes EC & Cook JA. (2011). Spatial but not temporal co-divergence of a virus and its mammalian host. Mol.Ecol. 20, 4109-4122.
65. Vasilakis N, Cardosa J, Hanley KA, Holmes EC & Weaver SC. (2011). Fever from the forest: prospects for continued emergence of sylvatic dengue virus and impact on public health. Nat.Rev.Micro. 9, 532-541.
2010
66. Balmaseda A, Standish K, Mercado JC, Matute JC, Tellez Y, Sabor'o S, Hammond SN, Nuñez A, Avilés W, Henn MR, Holmes EC, Gordon A, Coloma J, Kuan G & Harris E. (2010). Trends in patterns of dengue transmission over four years of a pediatric cohort study in Nicaragua. J.Infect.Dis. 201, 5-14.
67. Boni MF, de Jong MD, van Doorn HR & Holmes EC. (2010). Guidelines for identifying homologous recombination events in influenza A virus. PLoS One 5:e10434.
68. Bennett SN, Drummond AJ, Kapan DD, Muñoz JL, Pybus OG, Holmes EC & Gubler DJ. (2010). Epidemic dynamics revealed in dengue evolution. Mol.Biol.Evol. 27, 811-818.
69. Carpi G, Holmes EC & Kitchen A. (2010). The evolutionary dynamics of bluetongue virus. J.Mol.Evol. 70, 583-592.
70. Carrillo-Valenzo K, Danis-Lozano R, Velasco-Hernández JX, Sanchez-Burgos G, Alpuche C, Lopez I, Rosales C, Baronti C, de Lamballerie X, Holmes EC & Ramos-Castañeda J. (2010). Evolution of dengue virus in México is characterized by frequent lineage replacement. Arch.Virol. 155, 1401-1412.
71. Chen R & Holmes EC. (2010). Hitchhiking and the population genetic structure of avian influenza virus. J.Mol.Evol. 70, 98-105.
72. 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 J-C, Cole ST, Caro V, Gessain A & Bourhy H. (2010). Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses. J.Virol. 84, 9557-9574.
73. Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC & Rambaut A. (2010). Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol.Biol.Evol. 27, 2038-2051.
74. Fusaro A, Nelson MI, Joannis T, Bertolotti L, Monne I, Salviato A, Capua I, Holmes EC & Cattoli G. (2010). Evolutionary dynamics of multiple sublineages of H5N1 influenza viruses in Nigeria, 2006-2008. J.Virol. 84, 3239-3247.
75. Ghedin E, Wentworth D, Halpin RA, Lin X, Bera J, DePasse J, Fitch A, Griesemer S, Hine E, Katzel DA, Overton L, Proudfoot K, Sitz J, Szczypinski B, St. George K, Spiro DJ & Holmes EC. (2010). Unseasonal transmission of H3N2 Influenza A virus during the swine-origin H1N1 pandemic. J.Virol. 84, 5715-5718.
76. Grard G, Moureau G, Charrel RN, Holmes EC, Gould EA & de Lamballerie X. (2010). Genomics and evolution of Aedes-borne flaviviruses and related viruses. J.Gen.Virol. 91, 87-94.
77. Hayward JJ, Dubovi EJ, Scarlett JM, Janeczko S, Holmes EC & Parrish CR. (2010). Microevolution of canine influenza virus in shelters and its molecular epidemiology in the United States. J.Virol. 84, 12636-12645.
78. Hoelzer K, Murcia PR, Baillie GJ, Wood JLN, Metzger S, Osterrieder K, Dubovi EJ, Holmes EC & Parrish CR. (2010). Intra-host evolutionary dynamics of canine influenza virus in naïve and partially immune dogs. J.Virol. 84, 5329-5335.
79. Holmes EC. (2010). The comparative genomics of viral emergence. Proc.Natl.Acad.Sci.USA. 107, 1742-1746.
80. Holmes EC. (2010). Does hepatitis C virus really form quasispecies? Infect.Genet.Evol. 10, 431-432.
81. Holmes EC. (2010). The RNA virus quasispecies: fact or fiction? J.Mol.Biol. 400, 271-273.
82. Jahnke M, Holmes EC, Kerr PJ, Wright JD & Strive T. (2010). Evolution and phylogeography of the non-pathogenic calicivirus RCV-A1 in wild rabbits in Australia. J.Virol. 84, 12397-12404.
83. Jones A, Lowry K, Aaskov J, Holmes EC & Kitchen A. (2010). Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy. J.Gen.Virol. 91, 182-188.
84. Murcia PR, Baillie GJ, Daley 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, McKinley TJ, McCauley JW, Holmes EC, Grenfell BT & Wood JLN. (2010). The intra- and inter-host evolutionary dynamics of equine influenza virus. J.Virol. 84, 6943-6954.
85. Pagán I, Firth C & Holmes EC. (2010). Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus Tobamovirus. J.Mol.Evol. 71, 298-307.
86. Pagán I & Holmes EC. (2010). Long-term evolution of the Luteoviridae: time-scale and mode of virus speciation. J.Virol. 84, 6177-6187.
87. Rabaa M, Ty Hang VT, Wills B, Farrar J, Simmons C & Holmes EC. (2010). Phylogeography of DENV-2 in southern Viet Nam: anthropogenic aspects of viral dispersal. PLoS Neglect.Trop.Dis. 4:e766.
88. Romano CM, Mello IMG de C, Pinho JRP, Melo FR, Motoki M, Jamal L, Holmes EC, Zanotto PM de A & the VGDN Consortium. (2010). Social networks shape the transmission dynamics of hepatitis C virus. PLoS One 5:e11170.
89. Sall AA, Faye O, Diallo M, Firth C, Kitchen A & Holmes EC. (2010). Yellow fever virus exhibits slower evolutionary dynamics than dengue virus. J.Virol. 84, 765-772.
90. Singh R, Levitt AL, Rajotte EG, Holmes EC, Ostiguy N, van Engelsdorp D, Lipkin WI, de Pamphilis CW, Toth AL & Cox-Foster DL. (2010). RNA viruses in hymenopteran pollinators: evidence of inter-taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species. PLoS One 5:e14357.
91. Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Jalal N, Faouzi A, Echevarr'a JE, Morón SV, Rambaut A, Campiz N, Tatem AJ, Holmes EC & Bourhy H. (2010). Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog. 6:e1001166.
92. Ty Hang VT, Holmes EC, Veasna D, Nguyen TQ, Hien TT, Quail M, Churcher C, Parkhill J, Cardosa J, Farrar J, Willis B, Lennon NJ, Birren BW, Buchy P, Henn MR & Simmons CP. (2010). Emergence of the Asian I genotype of dengue virus serotype 2 in Viet Nam: In vivo fitness advantage and selectively mediated lineage replacement across South-East Asia. PLoS Neglect.Trop.Dis. 4:e757.
93. Vasilakis N, Cardosa J, Diallo M, Sall AA, Holmes EC, Hanley KA & Weaver SC. (2010). Sylvatic dengue viruses share the pathogenic potential of urban/endemic dengue viruses. J.Virol. 84, 3726-3728.
94. 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. (2010). Genome scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and varying evolutionary rates. J.Virol. 84, 6497-6504.
2009
95. Bahl J, Vijaykrishna D, Holmes EC, Smith GJC & Guan Y. (2009). Gene flow and competitive exclusion of avian influenza A in the natural reservoir hosts. Virology 390, 289-297.
96. Botosso VF, Zanotto PM de A, Ueda M, Arruda E, Gilio AE, Vieira SE, Stewien KE, Peret TC, Jamal LF, de M C Pardini MI, Pinho JR, Massad E, Sant'anna OA, Holmes EC, Durigon EL & the VGDN Consortium. (2009). Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus. PLoS Pathog. 5:e1000254.
97. Cardosa J, Ooi MH, Tio PH, Perera D, Holmes EC, Bibi K & Manap ZA. (2009). Dengue virus serotype 2 from a sylvatic linage isolated a patient with dengue haemorrhagic fever. PLoS Neglect.Trop.Dis. 3:e423.
98. Chen R & Holmes EC. (2009). Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds. Virology 383, 156-161.
99. Cook S, Moureau G, Harbach RE, Mukwaya L, Goodger K, Ssenfuka F, Gould EA, Holmes EC & de Lamballerie X. (2009). Isolation of a novel species of flavivirus and a novel strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda. J.Gen.Virol. 90, 2669-2678.
100. Dorji T, Yoon I-K, Holmes EC, Wangchuk S, Tobgay T, Nisalak A, Chinnawirotpisan P, Sangkachantaranon K, Gibbons RV & Jarman RG. (2009). Diversity and origin of dengue serotypes 1, 2 and 3 in Bhutan. Emerg.Infect.Dis. 5, 1630-1632.
101. Duffy S & Holmes EC. (2009). Validation of high rates of nucleotide substitution in geminiviruses: Phylogenetic evidence from East African cassava mosaic viruses. J.Gen.Virol. 90, 539-1547.
102. Dunham EJ, Dugan VG, Kaser EK, Perkins SE, Brown IH, Holmes EC & Taubenberger JK. (2009). Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses. J.Virol. 83, 5485-5494.
103. Firth C, Charleston MA, Duffy S, Shapiro B & Holmes EC. (2009). Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J.Virol. 83, 12813-12821.
104. Ghedin E, Fitch A, Boyne A, DePasse J, Bera J, Halpin RA, Griesemer S, Smit M, Jennings L, St. George K, Holmes EC & Spiro DI. (2009). Mixed infection and the genesis of influenza diversity. J.Virol. 83, 8832-8841.
105. Holmes EC. (2009). The evolutionary genetics of emerging viruses. Annu.Rev.Ecol.Evol.Syst. 40, 353-372.
106. Holmes EC. (2009). RNA virus genomics: a world possibilities. J.Clin.Invest. 119, 2488-2495.
107. Holmes EC & Grenfell BT. (2009). Discovering the phylodynamics of RNA viruses. PLoS Comput.Biol. 5:e1000505.
108. Holmes EC, Toi P-H, Perera D, Muhi J & Cardosa J. (2009). Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia. Virus Res. 143, 1-5.
109. Kerr PJ, Kitchen A & Holmes EC. (2009). The origin and phylodynamics of rabbit hemorrhagic disease virus. J.Virol. 83, 12129-12138.
110. Nelson MI, Simonsen L, Miller MA, Viboud C & Holmes EC. (2009). The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Virology 388, 270-278.
111. Nelson MI, Spiro DJ, Wentworth DE, Fan J, Beck ET, St. George K, Halpin RA, Bera J, Hine E, Proudfoot K, Stockwell TB, Lin X, Bose ME, Jurgens L, Kumar S, Viboud C, Holmes EC & Henrickson KJ. (2009). The early diversification of influenza A/H1N1pdm. PLoS Currents: Influenza. 10.1371/currents.RRN1126.
112. Rambaut A & Holmes EC. (2009). The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Currents: Influenza. 10.1371/currents.RRN1003.
113. Ramsden C, Holmes EC & Charleston MA. (2009). Hantavirus evolution in relation to its rodent and insectivore Hosts: No evidence for co-divergence. Mol.Biol.Evol. 26, 143-153.
114. Schreiber MJ, Holmes EC, Ong SH, Soh HSH, Liu W, Tanner L, Aw PPK, Tan HC, Ng LC, Leo YS, Low JGH, Ong A, Ooi EE, Vasudevan S & Hibberd ML. (2009). Genomic epidemiology of a dengue virus epidemic in urban Singapore. J.Virol. 83, 4163-4173.
115. Talbi C, Holmes EC, de Benedictis, Faye O, Nakouné E, Gamatié D, Diarra A, Elmamy BO, Sow A, Sangare O, Dundon WG, Capua I, Sall AA & Bourhy H. (2009). The evolutionary history and dynamics of dog rabies virus in West and Central Africa. J.Gen.Virol. 90, 783-791.
2008
116. Boni MF, Zhou Y, Taubenberger JK & Holmes EC. (2008). Homologous recombination is very rare or absent in human influenza A virus. J.Virol. 82, 4807-4811.
117. Bourhy H, Reynes J-M, Dunham EJ, Dacheux L, Larouss F, Hong VTQ, Xu G, Yan J, Miranda MEG & Holmes EC. (2008). The origin and phylogeography of dog rabies virus. J.Gen.Virol. 89, 2673-2681.
118. Briese T, Palacios G, Lipkin WI, Renwick N, Venter M, Jarman RG, Dominguez SR, Holmes KV & Holmes EC. (2008). Prior evidence of putative novel rhinovirus species, Australia response. Emerg.Infect.Dis. 14, 1824-1825.
119. Briese T, Renwick N, van den Berg M, Jarman J, Ghosh D, Köndgen S, Shrestha S, Hoegh AM, Flecha IC, Adjogoua EV, Akoua-Koffi C, Myint KS, Williams D, Chidlow G, Calvo C, Palacios G, Kapoor V, Joseph Villari J, Harnett G, Smith D, Mackenzie J, Ellerbrok H, Schweiger B, Schønning K, Chaddha M, Fabian H. Leendertz FH, Mishra AC, Gibbons R, Venter M, Holmes EC & Lipkin WI. (2008). Global distribution of novel rhinovirus genotype. Emerg.Infect.Dis. 14, 944-947.
120. Chang GS, Hoon Y, Ko KD, Bhardwaj G, Holmes EC, Patterson RL & van Rossum DB. (2008). Phylogenetic profiles reveal evolutionary relationships within the ‘twilight zone’ of sequence similarity. Proc.Natl.Acad.Sci.USA 105, 13474-13479.
121. Chen R & Holmes EC. (2008). The evolutionary dynamics of human influenza B virus. J.Mol.Evol. 66, 655-663.
122. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Kalkstein AL, Evans JD, Moran NA, Quan P-L, Geiser DM, Briese T, Hornig M, Hui J, van Engelsdorp D, Pettis JS & Lipkin WI. (2008). The latest buzz about colony collapse disorder. Science 319, 724-725.
123. de Graaf M, Osterhaus ADME, Fouchier RAM & Holmes EC. (2008). Evolutionary dynamics of human and avian metapneumoviruses. J.Gen.Virol. 89, 2933-2942.
124. Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, Bouchier C & Bourhy H. (2008). Genomic diversity and evolution of the lyssaviruses. PLoS One 3:e2057.
125. Duffy S & Holmes EC. (2008). Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato Yellow Leaf Curl Virus. J.Virol. 82, 957-965.
126. Duffy S, Shackelton LA & Holmes EC. (2008). Rates of evolutionary change in viruses: Patterns and determinants. Nat.Rev.Genet. 9, 267-276.
127. 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. (2008). The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. 4:e1000076.
128. Hoelzer K, Shackelton LA, Holmes EC & Parrish CR. (2008). Within-host genetic diversity of endemic and emerging parvoviruses of cats and dogs. J.Virol. 82, 11096-11105.
129. Hoelzer K, Shackelton LA, Parrish CR & Holmes EC. (2008). Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses. J.Gen.Virol. 89, 2280-2289.
130. Holmes EC. (2008). The evolutionary history and phylogeography of human viruses. Annu.Rev.Microbiol. 62, 307-328.
131. Jarman RG, Holmes EC, Rodpradit P, Klungthong C, Gibbons RV, Nisalak A, Rothman AI, Libraty DH, Ennis FA, Mammen MP Jr. & Endy TP. (2008). Microevolution of dengue viruses circulating among primary school Children in Kamphaeng Phet, Thailand. J.Virol. 82, 5494-5500.
132. Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, Halpin R, Ghedin E, Miller MA, Simonsen L, Viboud C & Holmes EC. (2008). Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States. PLoS Pathog. 4:e1000133.
133. 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. (2008). Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. 4:e1000012.
134. Palacios G, Hui J, Quan PL, Kalkstein A Honkavuori KS, Bussetti AV, Conlan S, Evans J, Chen YP, VanEngelsdoorp D, Efrat H, Pettis J, Cox-Foster D, Holmes EC, Briese T & Lipkin WI. (2008). Genetic analysis of Israel Acute Paralysis Virus: Distinct clusters are circulating in the United States. J.Virol. 82, 6209-6217.
135. Parrish CR, Holmes EC, Morens DM, Park E-C, Burke DS, Calisher CH, Laughlin CA, Saif LJ & Dazsak P. (2008). Cross-species viral transmission and the emergence of new epidemic diseases. Microbiol.Mol.Biol.Rev. 72, 457-470.
136. Pomeroy LW, Bjørnstad ON & Holmes EC. (2008). The evolutionary and epidemiological dynamics of the Paramyxoviridae. J.Mol.Evol. 66, 98-106.
137. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK & Holmes EC. (2008). The genomic and epidemiological dynamics of human influenza A virus. Nature 453, 615-619.
138. Ramsden C, Melo FL, Figueiredo LM, Holmes EC, Zanotto PM de A and the VGDN Consortium. (2008). High rates of molecular evolution in hantaviruses. Mol.Biol.Evol. 25, 1488-1492.
139. Romano CM, Zanotto PM de A & Holmes EC. (2008). Bayesian coalescent analysis reveals a high rate of molecular evolution in GB virus C. J.Mol.Evol. 66, 292-297.
140. Shackelton LA & Holmes EC. (2008). The role of alternative genetic codes in virus evolution and emergence. J.Theor.Biol. 254, 128-134.
141. Simmons HE, Holmes EC & Stephenson AG. (2008). Rapid evolutionary dynamics of zucchini yellow mosaic virus. J.Gen.Virol. 89, 1081-1085.
2007
142. Aaskov J, Buzacott K, Field E, Berlioz-Arthaud A & Holmes EC. (2007). Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient. J.Gen.Virol. 88, 3334-3340.
143. Aulicino PC, Holmes EC, Rocco C, Mangano AM & Sen L. (2007). Extremely rapid spread of HIV-1 BF recombinants in Argentina. J.Virol. 81, 427-429.
144. Brault AC, Huang C Y-H, Langevin SA, Kinney RM, Bowen RA, Ramey WN, Panella NA, Holmes EC, Powers AM & Miller BR. (2007). A single positively selected West Nile viral mutation confers increased avian virogenesis in American crows. Nat.Genet. 39, 1162-1166.
145. Bryant JE, Holmes EC & Barrett ADT. (2007). Out of Africa: A molecular perspective on the introduction of Yellow Fever Virus into the Americas. PLoS Pathog. 3:e75.
146. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan P-L, Briese T, Geiser DM, Martinson V, van Engelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchinson S, Simons JF, Egholm M, Pettis JS & Lipkin WI. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318, 283-287.
147. Davis PL, Rambaut A, Bourhy H & Holmes EC. (2007). The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa. Arch.Virol. 152, 1251-1258.
148. de Freitas RB, Durigon EL, Oliveira D de S, Romano CM, de Freitas MRC, Linhares A de C, Melo FL, Walshkeller L, Barbosa ML, Huatuco EMM, Holmes EC & Zanotto PM de A. (2007). The ‘pressure pan’ evolution of human erythrovirus B19 in the Amazon, Brazil. Virology 369, 281-287.
149. Duffy S & Holmes EC. (2007). Multiple introductions of the Old World begomovirus, tomato yellow leaf curl virus (TYLCV), in the New World. Appl.Environ.Micro. 73, 7114-7117.
150. Dunham EJ & Holmes EC. (2007). Inferring the time-scale of dengue virus evolution under realistic models of DNA substitution. J.Mol.Evol. 64, 656-661.
151. Grard G, Moureau G, Charrel RN, Lemasson J-J, Gonzalez J-P, Galllian P, Gritsun T, Holmes EC, Gould EA & de Lamballerie X. (2007). Genetic characterisation of tick-borne flaviviruses: New insights into evolution, pathogenetic determinants and taxonomy. Virology 361, 80-92.
152. Holmes EC. (2007). Viral evolution in the genomic age. PLoS Biol. 5:e278.
153. Holmes EC & Drummond AJ. (2007). The evolutionary genetics of viral emergence. Curr.Top.Micro.Immunol. 315, 51-66.
154. Kalayanarooj S, Rimal HS, Andjaparidze A, Vatcharasaevee V, Nisalak A, Jarman RG, Chinnawirotpisan P, Mammen MP, Holmes EC & Gibbons RV. (2007). Clinical investigation and molecular characteristics of dengue hemorrhagic fever outbreak in Timor-Leste, 2005. Am.J.Trop.Med.Hyg. 77, 534-537.
155. Nelson MI & Holmes EC. (2007). The evolution of epidemic influenza. Nat.Rev.Genet. 8, 196-205.
156. Nelson MI, Simonsen L, Viboud C, Miller MA & Holmes EC. (2007). Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog. 3:1220-1228.
157. Pybus OG, Rambaut A, Freckleton RP, Belshaw R, Drummond AJ & Holmes EC. (2007). Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol.Biol.Evol. 24, 845-852.
158. Romano CM, de Melo FL, Corsini MAB, Holmes EC & Zanotto PM de A. Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys. (2007). PLoS One 2:e1026.
159. Sanjuán R, Cuevas JM, Furió V, Holmes EC & Moya A. (2007). Selection for robustness in mutagenized RNA viruses. PLoS Genet. 3: e93.
160. Schreiber MJ, Ong SH, Holland RC, Hibberd ML, Vasudevan SG, Mitchell WP & Holmes EC. (2007). DengueInfo: A web portal to dengue information resources. Infect.Genet.Evol. 7, 540-541.
161. Shackelton LA, Hoelzer K, Parrish CR & Holmes EC. (2007). Comparative analysis reveals frequent recombination in parvoviruses. J.Gen.Virol. 88, 3294-3301.
162. Sharp EL, Farrell HE, Borchers K, Holmes EC & Davis-Poynter NJ. (2007). Sequence analysis of the Equid herpesvirus-2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates. J.Gen.Virol. 88, 2450-2462.
163. Simonsen L, Viboud C, Grenfell BT, Dushoff J, Jennings L, Smit M, Macken C, Hata M, Gog J, Miller MA & Holmes EC. (2007). The genesis and spread of reassortant human influenza A/H3N2 viruses conferring adamantane resistance. Mol.Biol.Evol. 24, 1811-1820.
164. Snapinn KW, Holmes EC, Young DS, Bernard KA, Kramer LD & Ebel GD. (2007). Declining growth rate of West Nile virus in North America. J.Virol. 81, 2531-2534.
165. Thümer L, Rethwilm A, Holmes EC & Bodem J. (2007). The complete nucleotide sequence of a New World simian foamy virus. Virology 369, 191-197.
166. Vasilakis N, Holmes EC, Fokam EB, Faye O, Diallo M, Sall AA & Weaver SC. (2007). Evolutionary processes among sylvatic dengue-2 viruses. J.Virol. 81, 9591-9595.
167. Walker PR, Ketunuti M, Choge IA, Meyers T, Gray G, Holmes EC & Morris L. (2007). Polymorphisms in Nef associated with different clinical outcomes in HIV-1 subtype C infected children. AIDS Res.Hum.Retro. 23, 204-215.
168. Zhou Y & Holmes EC. (2007). Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J.Mol.Evol. 65, 197-205.
2006
169. Aaskov J, Buzacott K, Thu HM, Lowry K & Holmes EC. (2006). Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes. Science 311, 236-238.
170. Adams B, Holmes EC, Zhang C, Mammen MP Jr, Nimmannitya S, Kalayanarooj S & Boots M. (2006). Cross-protective immunity can account for the alternating epidemic pattern of dengue virus serotypes circulating in Bangkok. Proc.Natl.Acad.Sci.USA 103, 14234-14239.
171. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, Beltran M, Vorndam V, Gubler DJ & McMillan WO. (2006). Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction. J.Gen.Virol. 87, 885-893.
172. Chare ER & Holmes EC. (2006). A phylogenetic survey of recombination frequency in plant RNA viruses. Arch.Virol. 151, 933-946.
173. Chen R & Holmes EC. (2006). Avian influenza virus exhibits rapid evolutionary dynamics. Mol.Biol.Evol. 23, 2336-2341.
174. Cook S, Bennett SN, Holmes EC, de Chesse R, Moureau G & de Lamballerie X. (2006). Isolation of a new strain of the flavivirus cell fusing agent virus in a natural mosquito population from Puerto Rico. J.Gen.Virol. 87, 735-748.
175. Cook S & Holmes EC. (2006). A multigene analysis of the phylogenetic relationships among the flaviviruses (family Flaviviridae) and the evolution of vector transmission. Arch.Virol. 151, 309-325.
176. Davis PL, Bourhy H & Holmes EC. (2006). The evolutionary history and dynamics of bat rabies virus. Infect.Genet.Evol. 6, 464-473.
177. Edwards CTT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE & Drummond AJ. (2006). Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection. Genetics 174, 1441-1453.
178. Edwards CTT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE & Drummond AJ. (2006). Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol.Biol. 6:28.
179. Frater AJ, Edwards CTT, McCarthy N, Fox J, Brown H, Milicic A, Mackie N, Pillay T, Drijfhout JW, Dunstan S, Clarke JR, Holmes EC, Zhang HT, Pfafferott K, Goulder PJ, McClure MO, Weber J, Phillips RE & Fidler S. (2006). Passive sexual transmission of HIV-1 variants and adaptation in new hosts. J.Virol. 80, 7226-7234.
180. Grard G, Lemasson J-J, Sylla M, Dudot A, Cook S, Molez J-F, Charrel RN, Gonzalez J-P, Munderloh U, Holmes EC & de Lamballerie X. (2006). Ngoye virus: A novel evolutionary lineage within the genus Flavivirus. J.Gen.Virol. 87, 3273-3277.
181. Holmes EC. (2006). Future issues in RNA virus evolution. Future Virol. 1, 243-249.
182. Holmes EC, Lipman DJ, Zamarin D & Yewdell JW. (2006). Comment on ‘Large-scale analysis of avian influenza isolates’. Science 313, 1573b.
183. Kuiken T, Holmes EC, McCauley J, Rimmelzwaan GF, Williams CS & Grenfell BT. (2006). Host species barriers to influenza virus infections. Science 312, 394-397.
184. Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, St. George K, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK & Holmes EC. (2006). Stochastic processes are key determinants of the short-term evolution of influenza A virus. PLoS Pathog. 2:e125.
185. Shackelton LA & Holmes EC. (2006). Phylogenetic evidence for the rapid evolution of human B19 erythrovirus. J.Virol. 80, 3666-3669.
186. Shackelton LA, Parrish CR & Holmes EC. (2006). Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J.Mol.Evol. 62, 551-563.
187. Shackelton LA, Rambaut A, Pybus OG & Holmes EC. (2006). JC virus evolution and its association with human populations. J.Virol. 80, 9928-9933.
188. Shapiro B, Rambaut A, Pybus OG, Drummond A & Holmes EC. (2006). A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Mol.Biol.Evol. 23, 1724-1730.
189. Wolf YI, Viboud C, Holmes EC, Koonin EV & Lipman DJ. (2006). Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol.Direct. 1:34.
190. Zhang C, Mammen MP Jr, Chinnawirotpisan P, Klungthong C, Rodpradit P, Nisalak A, Nimmannitya S, Kalayanarooj S, Vaughn DW & Holmes EC. (2006). Structure and age of genetic diversity of dengue virus type 2 in Thailand. J.Gen.Virol. 87, 873-883.
191. Zhou Y, Mammen MP Jr, Chinnawirotpisan P, Klungthong C, Vaughn DW, Nimmannitya S, Kalayanarooj S, Holmes EC & Zhang C. (2006). Comparative analysis reveals no consistent association between the secondary structure of the 3’UTR of dengue viruses and disease syndrome. J.Gen.Virol. 87, 2595-2603.
2005
192. Bourhy H, Cowley JA, Larrous F, Holmes EC & Walker P. (2005). Phylogenetic relationships among the rhabdoviruses inferred using the L polymerase gene. J.Gen.Virol. 86, 2849-2858.
193. Carrington CVF, Foster JE, Pybus OG, Bennett SN & Holmes EC. (2005). Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. J.Virol. 79, 14680-14687.
194. Cook S, Diallo M, Sall AA, Cooper A & Holmes EC. (2005). Mitochondrial markers for the molecular identification of Aedes mosquitoes (Diptera:Culicidae) involved in the transmission of arboviral disease in West Africa. J.Med.Entomol. 42, 19-28.
195. Davis PL, Holmes EC, Larrous F, Van de Poel WHM, Tjørnehøj K, Alonso WJ & Bourhy H. (2005). Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses. J.Virol. 79, 10487-10497.
196. Edwards CTT, Pfafferot KJ, Goulder PGR, Phillips RE & Holmes EC. (2005). Intrapatient escape in the A*0201-restricted epitope SLYNTVATL drives evolution of human immunodeficiency virus type 1 at the population level. J.Virol. 79, 9363-9366.
197. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St. George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ & Taubenberger JK. (2005). Whole genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS.Biol. 3(9), e300.
198. Milicic A, Edwards CTT, Hue S, Fox J, Brown H, Pillay T, Drijfhout JW, Weber JN, Holmes EC, Fidler SJ, Zhang H-T, & Phillips RE. (2005). Sexual transmission of single human immunodeficiency type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants. J.Virol. 79, 13953-13962.
199. Pillay T, Zhang H-T, Drijfhout JW, Robinson N, Brown H, Khan M, Moodley J, Adhikari M, Pfafferott K, Feeny ME, St. John A, Holmes EC, Coovadia HM, Klenerman P, Goulder PJR & Phillips RE. (2005). Unique acquisition of cytotoxic T-lymphocyte escape mutants in infant human immunodeficiency virus type 1 infection. J.Virol. 79, 12100-12105.
200. Pybus OG, Cochrane A, Holmes EC & Simmonds P. (2005). The hepatitis C virus epidemic among injecting drug users. Infect.Genet.Evol. 5, 131-139.
201. Rodr'guez-Roche R, Alvarez M, Holmes EC, Bernardo L, Kour' G, Gould EA & Guzman MG. (2005). Dengue virus type 3, Cuba 2000-2002. Emerg.Infect.Dis. 11, 773-774.
202. Shackelton LA, Parrish CR, Truyen U & Holmes EC. (2005). High rate of viral evolution associated with the emergence of canine parvoviruses. Proc.Natl.Acad.Sci.USA 102, 379-384.
203. Switzer WM, Salemi M, Shanmugam V, Gao F, Cong M-E, Kuiken C, Bhullar V, Beer B, Vallet D, Gautier-Hion A, Tooze A, Villinger F, Holmes EC & Heneine W. (2005). Ancient co-speciation of simian foamy viruses and primates. Nature 434, 376-380.
204. Thu HM, Lowry K, Jian L, Hlaing T, Holmes EC & Aaskov J. (2005). Lineage extinction and replacement in dengue type 1 virus populations is due to stochastic events rather than natural selection. Virology 336, 163-172.
205. Walker PR, Pybus OG, Rambaut A & Holmes EC. (2005). Comparative population dynamics of HIV-1 subtypes B and C: Subtype-specific differences in patterns of epidemic growth. Infect.Genet.Evol. 5, 199-208.
206. Zhang C, Mammen MP Jr, Chinnawirotpisan P, Klungthong C, Rodpradit P, Monkongdee P, Nimmannitya S, Kalayanarooj S & Holmes EC. (2005). Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J.Virol. 79, 15123-15130.
2004
207. A-Nuegoonpipat A, Berlioz-Arthaud A, Chow V, Endy T, Lowry K, Mai LQ, Ninh TU, Pyke A, Reid M, Reynes J-M, Yun STS, Thu HM, Wong S-S, Holmes EC & Aaskov J. (2004). Sustained transmission of dengue virus type 1 in the Pacific due to repeated introduction of different Asian genotypes. Virology 329, 505-512.
208. Barnett OE, Worobey M, Holmes EC & Cooper A. (2004). The detection of TT virus among wild chimpanzees via a non-invasive technique. J.Wildlife Dis. 40, 230-237.
209. Chare ER & Holmes EC. (2004). Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J.Gen.Virol. 85, 3149-3157.
210. Draenert R, LeGall 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, Goldberg AL, Martinez-Picado J, Walker B.D. & Goulder P.J.R. (2004). Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. J.Exp.Med. 199, 905-915.
211. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, Mumford JA & Holmes EC. (2004). Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303, 327-332.
212. Holmes EC. (2004). The phylogeography of human viruses. Mol.Ecol. 13, 745-756.
213. Holmes EC & Rambaut A. (2004). Viral evolution and the emergence of SARS coronavirus. Phil.Trans.Roy.Soc.Lond.B. 359, 1059-1065.
214. Klungthong C, Zhang C, Mammen Jr. MP, Ubol S & Holmes EC. (2004). The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand. Virology 329, 168-179.
215. Leal E de S, Holmes EC & Zanotto PM de A. (2004). Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy. Virology 325, 181-191.
216. Leslie AJ, Pfafferott KJ, Chetty P, Draenert R, Addo MM, Feeney M, Holmes EC, Allen T, Prado JG, Altfeld M, Brander C, Dixon C, Ramduth D, Jeena P, Thomas SA, St. John A, Roach TA, Kupfer B, Luzzi G, Edwards A, Taylor G, Lyall H, Tudor-Williams G, Novelli V, Martinez-Picado J, Kiepiela P, Walker BD & Goulder PJR. (2004). HIV evolution: CTL escape mutation and reversion following transmission. Nat.Med. 10, 282-289.
217. Moya A, Holmes EC & González-Candelas F. (2004). The population genetics and evolutionary epidemiology of RNA viruses. Nat.Rev.Microbiol. 2, 279-287.
218. Oxenius A, Price DA, Trkola A, Edwards C, Gostick E, Zhang H-T, Easterbrook PJ, Tun T, Johnson A, Waters A, Holmes EC & Phillips RE. (2004). Loss of viral control in early HIV-1 infection is temporally associated with decline of HIV-specific CD4+ and CD8+ T cell frequencies and sequential escape from CTL responses. J.Infect.Dis. 190, 713-721.
219. Priest FG, Barker M, Baillie LWJ, Holmes EC & Maiden MCJ. (2004). Population structure and evolution of the Bacillus cereus subgroup. J.Bact. 186, 7959-7970.
220. Rambaut A, Crandall KA, Posada D & Holmes EC. (2004). The causes and consequences of HIV evolution. Nat.Rev.Genet. 5, 52-61.
221. Shackelton LA & Holmes EC. (2004). The evolution of large DNA viruses: Combining genomic information of viruses and their hosts. Trends Microbiol. 12, 458-465.
222. Sheridan I, Pybus OG, Holmes EC & Klenerman P. (2004). High resolution phylogenetic analysis of Hepatitis C virus adaptation and its relationship to disease progression. J.Virol. 78, 3447-3454.
223. Urwin R, Russell JE, Thompson EAL, Holmes EC, Feavers IM & Maiden MCJ. (2004). Distribution of surface protein variants among hyper-invasive meningococci: Implications for vaccine design. Infect.Immun. 72, 5955-5962.
2003
224. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, Beltran M, Vorndam V, Gubler DJ & McMillan WO. (2003). Selection-driven evolution of emergent dengue virus. Mol.Biol.Evol. 20, 1650-1658.
225. Chare ER, Gould EA & Holmes EC. (2003). Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J.Gen.Virol. 84, 2691-2703.
226. Craig S, Thu HM, Lowry K, Wang X-F, Holmes EC & Aaskov J. (2003). Diverse dengue type 2 virus populations contain recombinant and both parental viruses in a single mosquito host. J.Virol. 77, 4463-4467.
227. Gould EA, de Lamballerie X, Zanotto PM de A & Holmes EC. (2003). Origins, evolution, and vector/host co-adaptations within the Genus Flavivirus. Adv.Vir.Res. 59, 277-314.
228. Guyatt KJ, Twin J, Davis P, Holmes EC, Smith GA, Smith IL, Mackenzie JS & Young PL. (2003). A molecular epidemiological study of Australian bat lyssavirus. J.Gen.Virol. 84, 485-496.
229. Holmes EC. (2003). Molecular clocks and the puzzle of RNA virus origins. J.Virol. 77, 3893-3897.
230. Holmes EC. (2003). Patterns of intra- and inter-host nonsynonymous variation reveal strong purifying selection in dengue virus. J.Virol. 77, 11296-11298.
231. Holmes EC. (2003). Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 11, 543-546.
232. Holmes EC, Roberts A, Staines KA & Ellis SA. (2003). Evolution of major histocompatibility complex class I genes in Cetartiodactyls. Immunogenetics 55, 193-202.
233. Holmes EC & Twiddy SS. (2003). The origin, emergence and evolutionary genetics of dengue virus. Infect.Genet.Evol. 3, 19-28.
234. Isobe T, Holmes EC & Rudenko G. (2003). 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. 56, 377-386.
235. Jenkins GM & Holmes EC. (2003). The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92, 1-7.
236. Starkman S, MacDonald DM, Lewis JCM, Holmes EC & Simmonds P. (2003). Geographic and species association of hepatitis B virus genotypes in non-human primates. Virology 314, 381-393.
237. Twiddy SS & Holmes EC. (2003). The extent of homologous recombination in the genus Flavivirus. J.Gen.Virol. 84, 429-440.
238. Twiddy SS, Holmes EC & Rambaut A. (2003). Inferring the rate and time-scale of dengue virus evolution. Mol.Biol.Evol. 20, 122-129.
239. Twiddy SS, Pybus OG & Holmes EC. (2003). Comparative population dynamics of mosquito-borne flaviviruses. Infect.Genet.Evol. 3, 87-95.
240. Uzcategui NY, Comach G, Camacho D, Salcedo M, Cabello de Quintana M, Jimenez M, Sierra G, Cuello de Uzcategui R, James WS, Turner S, Holmes EC & Gould EA. (2003). Molecular epidemiology of dengue virus type 3 in Venezuela. J.Gen.Virol. 84, 1569-1575.
241. Walker PR, Worobey M, Rambaut A, Holmes EC & Pybus OG. (2003). Sexual transmission of HIV in Africa. Nature 422, 679.
2002
242. Brault AC, Powers AM, Holmes EC, Woelk CH & Weaver SC. (2002). Positively charged amino acid substitutions in the E2 envelope glycoprotein are associated with the emergence of Venezuelan equine encephalitis virus. J.Virol. 76, 1718-1730.
243. de Lamballerie X, Crochu S, Billoir F, Neyts J, de Micco P, Holmes EC & Gould EA. (2002). Genome sequence analysis of Tamara bat virus and it’s relationship with the genus Flavivirus. J.Gen.Virol. 83, 2443-2454.
244. Fares MA & Holmes EC. (2002). A revised evolutionary history of hepatitis B virus (HBV). J.Mol.Evol. 54, 807-814.
245. Holmes EC & Moya A. (2002). Is the quasispecies concept relevant to RNA viruses? J.Virol. 76, 460-462.
246. Holmes EC, Woelk CH, Kassis R & Bourhy H. (2002). Genetic constraints and the adaptive evolution of rabies virus. Virology 292, 247-257.
247. Jenkins GM, Rambaut A, Pybus OG & Holmes EC. (2002). Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J.Mol.Evol. 54, 152-161.
248. Posada D, Crandall KA & Holmes EC. (2002). Recombination in evolutionary genomics. Annu.Rev.Genet. 36, 75-97.
249. Pybus OG, Rambaut A, Holmes EC & Harvey PH. (2002). New inferences from tree shape: numbers of missing taxa and population growth rates. Syst.Biol. 51, 881-888.
250. Twiddy SS, Farrar JF, Chau NV, Wills B, Gould EA, Gritsun T, Lloyd G & Holmes EC. (2002). Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Virology 298, 63-72.
251. Twiddy SS, Woelk CH & Holmes EC. (2002). Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J.Gen.Virol. 83, 1679-1689.
252. Urwin R, Holmes EC, Fox AJ, Derrick JP & Maiden MCJ. (2002). Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB. Mol.Biol.Evol. 19, 1686-1694.
253. Wittke V, Robb TE, Thu HM, Nimmannitya S, Kalayanrooj S, Vaughn DW, Endy TP, Holmes EC & Aaskov JG. (2002). Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period. Virology 301, 148-156.
254. Woelk CH & Holmes EC. (2002). Reduced positive selection in vector-borne RNA viruses. Mol.Biol.Evol. 19, 2333-2336.
255. Woelk CH, Pybus OG, Jin L, Brown DWG & Holmes EC. (2002). Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections. J.Gen.Virol. 83, 1419-1430.
2001
256. Ballingall KT, Waibochi L, Holmes EC, Woelk CH, MacHugh ND, Lutje V & McKeever DJ. (2001). The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive selection. Immunogenetics 52, 276-283.
257. Dumpis U, Holmes EC, Mendy M, Hill AVS, Thursz M, Hall A, Whittle H & Karayiannis P. (2001). Transmission of hepatitis B virus infection in Gambian families revealed by phylogenetic analysis. J.Hepatol. 35, 99-104.
258. Feil EJ, Holmes EC, Enright MC, Bessent D, Day NPJ, Chan M-S, Hood D, Zhou JJ & Spratt BG. (2001). Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc.Natl.Acad.Sci.USA 98, 182-187. (joint first author).
259. Gould EA, de Lamballerie X, Zanotto PM de A & Holmes EC. (2001). Evolution, epidemiology and dispersal of flaviviruses revealed by molecular phylogenies. Adv.Vir.Res. 57, 71-103.
260. Goulder PJR, Pasquier C, Holmes EC, Liang B, Tang Y, Rosenberg ES, Burchett SK, McIntosh K, Barnardo M, Bunce M, Walker BD, Brander C & Phillips RE. (2001). Mother-to-child transmission of HIV infection and CTL escape through HLA-A2-SLYNTVATL epitope sequence variation. Immunol.Let. 79, 109-116.
261. Hayman A, Moss T, Simmons G, Arnold C, Holmes EC, Naylor-Adamson L, Hawkswell J, Allen K, Radford J, Nguyen-Van-Tam L & Balfe P. (2001). Phylogenetic analysis of multiple heterosexual transmission events of subtype B of HIV-1. AIDS Res.Hum.Retro. 17, 689-695.
262. Holmes EC. (2001). On the origin and evolution of the human immunodeficiency virus (HIV). Biol.Rev. 76, 239-254.
263. Jenkins GM, Pagel M, Gould EA, Zanotto P M de A & Holmes EC. (2001). Evolution of base composition and codon usage bias in the genus Flavivirus. J.Mol.Evol. 52, 383-390.
264. Jenkins GM, Worobey M, Woelk CH & Holmes EC. (2001). Evidence for the non-quasispecies evolution of RNA viruses. Mol.Biol.Evol. 18, 987-994.
265. Kelleher AD, Long C, Holmes EC, Allen RL, Wilson J, Conlon C, Workman C, Shaunak S, Wulfestieg K, Goulder P, Brander C, Ogg G, Sullivan JS, Dyer W, Jones I, McMichael AJ, Rowland-Jones S & Phillips RE. (2001). Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27 restricted CTL responses. J.Exp.Med. 193, 375-385.
266. Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC & Harvey PH. (2001). The epidemic behaviour of the hepatitis C virus. Science 292, 2323-2325.
267. Rambaut A, Robertson DL, Pybus OG, Peeters M & Holmes EC. (2001). Phylogeny and the origin of HIV-1. Nature 410, 1047-1048. [With accompanying News & Views].
268. Uzcategui NY, Camacho D, Comach G, Holmes EC & Gould EA. (2001). Molecular epidemiology of dengue-2 virus in Venezuela: evidence for in situ viral evolution and recombination. J.Gen.Virol. 82, 2945-2953.
269. Woelk CH & Holmes EC. (2001). Variable immune driven natural selection in the attachment (G) glycoprotein of respiratory syncytial virus (RSV). J.Mol.Evol. 52, 182-192.
270. Woelk CH, Jin L, Holmes EC & Brown DWG. (2001). Immune and artificial selection in the hemagglutin (H) glycoprotein of measles virus. J.Gen.Virol. 82, 2463-2474.
271. Worobey M & Holmes EC. (2001). Homologous recombination and the molecular evolution of GB virus C/hepatitis G virus. Mol.Biol.Evol. 18, 254-261.
2000
272. De Michelis S, Sewell H-S, Collares-Pereira M, Santos-Reis M, Schouls LM, Benes V, Holmes EC & Kurtenbach K. (2000). Genetic diversity of Borrelia burgdorferi sensu lato in ticks from mainland Portugal. J.Clin.Micro. 38, 2128-2133.
273. Holmes EC & Burch SS. (2000). The causes and consequences of genetic variation in dengue virus. Trends Microbiol. 8, 74-77.
274. Jenkins GM, Woelk C, Rambaut A & Holmes EC. (2000). Testing the extent of sequence similarity among viroids, satellite RNAs and HDV. J.Mol.Evol. 50, 98-102.
275. Macdonald DM, Holmes EC, Lewis JCM & Simmonds P. (2000). Detection of hepatitis B virus infection in wild caught chimpanzees (Pan troglodytes verus); phylogenetic relationships with human and other primate genotypes. J.Virol. 74, 4253-4257.
276. Mooers AØ & Holmes EC. (2000). The evolution of base composition and phylogenetic inference. Trends Ecol.Evol. 15, 365-369.
1999
277. Bollyky PL & Holmes EC. (1999). Reconstructing the complex evolutionary history of hepatitis B virus. J.Mol.Evol. 49, 130-141.
278. Bourhy H, Kissi B, Audry L, Smreczak M, Sadkowska-Todys M, Kulonen K, Tordo N, Zmudzinski JF & Holmes EC. (1999). Ecology and evolution of rabies virus in Europe. J.Gen.Virol. 80, 2545-2558.
279. Ellis SA, Holmes EC, Staines KA, Smith KB, Stear MJ, McKeever DJ, MacHugh ND & Morrison WI. (1999). Variation in the number of expressed MHC genes in different cattle class I haplotypes. Immunogenetics 50, 319-328.
280. Grassly NC, Harvey PH & Holmes EC. (1999). Population dynamics of HIV-1 inferred from gene sequences. Genetics 151, 427-438.
281. Holmes EC & Ellis SA. (1999). Evolutionary history of MHC class I genes in the mammalian order Perissodactyla. J.Mol.Evol. 49, 316-324.
282. Holmes EC, Urwin R & Maiden MCJ. (1999). The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol.Biol.Evol. 16, 741-749.
283. Holmes EC, Worobey M & Rambaut A. (1999). Phylogenetic evidence for recombination in dengue virus. Mol.Biol.Evol. 16, 405-409.
284. Proutski V, Gritsun TS, Gould EA & Holmes EC. (1999). Biological consequences of deletions within the 3’-UTR of flaviviruses may be due to rearrangements of RNA secondary structure. Virus Res. 64, 107-123.
285. Pybus OG, Holmes EC & Harvey PH. (1999). The mid-depth method and HIV-1: a practical approach to testing hypotheses of viral epidemic history. Mol.Biol.Evol. 16, 953-959.
286. Smith NH, Holmes EC, Donovan GM, Carpenter GA & Spratt BG. (1999). Networks and groups within the genus Neisseria: analysis of argF, recA, rho and 16S rRNA sequences from human Neisseria species. Mol.Biol.Evol. 16, 773-783.
287. Worobey M & Holmes EC. (1999). Evolutionary aspects of recombination in RNA viruses. J.Gen.Virol. 80, 2535-2544.
288. Worobey M, Rambaut A & Holmes EC. (1999). Widespread intra-serotype recombination in natural populations of dengue virus. Proc.Natl.Acad.Sci.USA. 96, 7352-7357.
289. Zanotto PM de A, Kallas EG, de Souza RF & Holmes EC. (1999). Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153, 1077-1089.
1998
290. Holmes EC. (1998). Human immunodeficiency virus, DNA and statistics. J.Roy.Stat.Soc.A 161, 199-208.
291. Holmes EC. (1998). The molecular epidemiology and evolution of emerging infectious diseases. Brit.Med.Bull. 54, 531-541.
292. Holmes EC. (1998). The molecular epidemiology of dengue virus: the time for big science. Trop.Med.Int.Health. 3, 855-856.
293. Holmes EC & Zanotto PM de A. (1998). Genetic drift of human immunodeficiency virus type 1? J.Virol. 72, 886-887.
294. McGuire K, Holmes EC, Gao GF, Reid HW & Gould EA. (1998). Tracing the origins of Louping-ill virus by molecular phylogenetic analysis. J.Gen.Virol. 79, 981-988.
295. Proutski V & Holmes EC. (1998). SWAN: sliding window analysis of nucleotide sequence variability. Bioinformatics 14, 467-468.
1997
296. Gao GF, Zanotto PM de A, Holmes EC, Reid HW & Gould EA. (1997). Molecular variation, evolution and geographical distribution of Louping ill virus. Acta Virol. 41, 259-268.
297. Grassly NC & Holmes EC. (1997). A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol.Biol.Evol. 14, 239-247.
298. Gritsun TS, Venugopal K, Zanotto PM de A, Mikhailov MV, Sall AA, Holmes EC, Polkinghorne I, Frolova TV, Pogodina VV, Lashkevich VA & Gould EA. (1997). Complete sequence of two tick-borne flaviviruses isolated from Siberia and the United Kingdom: analysis and significance of the 5’UTR and 3’UTR’s. Virus Res. 49, 27-39.
299. Proutski V, Gaunt MW, Gould EA & Holmes EC. (1997). Secondary structure of the 3’-untranslated region of yellow fever virus: implications for virulence, attenuation and vaccine development. J.Gen.Virol. 78, 1543-1549.
300. Proutski V, Gould EA & Holmes EC. (1997). Secondary structure of the 3’-untranslated region of flaviviruses: similarities and differences. Nuc.Acids Res. 25, 1194-1202.
1996
301. Bollyky PL, Rambaut A, Harvey PH & Holmes EC. (1996). Recombination between sequences of hepatitis B virus from different genotypes. J.Mol.Evol. 42, 97-102.
302. Garnett GP & Holmes EC. (1996). The ecology of emergent infectious disease. Bioscience 46, 127-135.
303. Kearsey SE, Maiorano D, Holmes EC & Todorov IT. (1996). The role of MCM proteins in the cell cycle control of genome duplication. BioEssays 18, 183-190.
304. Proutski V & Holmes EC. (1996). Primer Master: A new program for the design and analysis of PCR primers. CABIOS 12, 253-255.
305. Simmonds P, Mellor JM, Sakuldamrongpanich T, Nuchaprayoon C, Tanprasert S, Holmes EC & Smith DB. (1996). Evolutionary analysis of variants of hepatitis C virus found in South East Asia: comparison with classification based on sequence similarity. J.Gen.Virol. 77, 3013-3024.
306. Zanotto PM de A, Gibbs MJ, Gould EA & Holmes EC. (1996). A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J.Virol. 70, 6083-6096.
307. Zanotto PM de A, Gould EA, Gao GF, Harvey PH & Holmes EC. (1996). Population dynamics of flaviviruses revealed by molecular phylogenies. Proc.Natl.Acad.Sci.USA 93, 548-553.
308. Zanotto PM de A, Gould EA & Holmes EC. (1996). The limits of molecular phylogeny: the case of the genus Flavivirus in the family Flaviviridae. Brazil.J.Virus Res. 1, 29-38.
1995
309. Boner W, Schlicht H-J, Hanrieder K, Holmes EC & Carman WF. (1995). Further characterisation of two types of precore variant HBV isolates from Hong Kong. J.Infect.Dis. 171, 1461-1467.
310. Bonhoeffer S, Holmes EC & Nowak MA. (1995). Causes of HIV diversity. Nature 376, 125.
311. Ellis SA, Martin AJ, Holmes EC & Morrison WI. (1995). At least four MHC class I genes are transcribed in the horse: phylogenetic analysis suggests an unusual evolutionary history for the MHC in this species. Eur.J.Immunogenet. 22, 249-260.
312. Gritsun TS, Holmes EC & Gould EA. (1995). Analysis of flavivirus envelope proteins reveals domains that may determine their antigenicity, tropism and pathogenesis. Virus Res. 35, 307-321.
313. Healey CJ, Smith DB, Walker J, Holmes EC, Fleming KA, Chapman RWG & Simmonds P. (1995). Acute hepatitis C infection following sexual exposure: A case report. Gut 36, 148-150.
314. Holmes EC, Nee S, Rambaut A, Garnett GP & Harvey PH. (1995). Revealing the history of infectious disease epidemics using phylogenetic trees. Phil.Trans.Roy.Soc.Lond.B 349, 33-40.
315. Holmes EC, Zhang LQ, Robertson P, Cleland A, Harvey E, Simmonds P & Leigh Brown AJ (1995). The molecular epidemiology of HIV-1 in Edinburgh, Scotland. J.Infect.Dis. 171, 45-53.
316. Kasper P, Simmonds P, Schneweis KE, Kasier R, Matz B, Oldenburg J, Brackmann H-H & Holmes EC. (1995). The genetic diversification of the HIV-1 gag p17 gene in patients infected from a common source. AIDS Res.Hum.Retro. 11, 1197-1201.
317. McClure MO, Bieniasz PD, Weber JN, Tedder RS, O'Shea S, Banatvala JE, Tudor-Williams G, Simmonds P & Holmes EC. (1995). HIV clearance in an infant. Nature 375, 637.
318. Mellor J, Holmes EC, Jarvis LM, Yap PL, Simmonds P& The International HCV Collaborative Study Group. (1995). Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. J.Gen.Virol. 76, 2493-2507.
319. Nee S, Holmes EC, Rambaut A & Harvey PH. (1995). Inferring population history from molecular phylogenies. Phil.Trans.Roy.Soc.B. 349, 25-31.
320. Power JP, Lawlor E, Davidson F, Holmes EC, Yap PL & Simmonds P. (1995). Molecular epidemiology of an outbreak of infection with hepatitis C virus in recipients of anti-D immunoglobulin. Lancet 345, 1211-1213.
1994
321. Ball JK, Holmes EC, Whitwell H & Desselberger U. (1994). Genomic variation of HIV-1: molecular analyses of HIV-1 in sequential blood samples and various organs obtained at autopsy. J.Gen.Virol. 75, 867-879.
322. Donaldson YK, Bell JE, Holmes EC, Hughes ES, Brown HK & Simmonds P. (1994). In vivo distribution and cytopathology of variants of HIV-1 showing restricted sequence variability in the V3 loop. J.Virol. 68, 5991-6005.
323. Harvey PH, Holmes EC & Nee S. (1994). Model phylogenies to explain the real world. BioEssays 16, 767-770.
324. Holmes EC & Garnett GP. (1994). Genes, trees and infections: molecular evidence in epidemiology. Trends Ecol.Evol. 9, 256-260.
325. Jeffs PS, Holmes EC & Ashburner M. (1994). The molecular evolution of the Alcohol dehydrogenase and Alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup. Mol.Biol.Evol. 11, 287-304.
326. Leigh Brown AJ & Holmes EC. (1994). The evolutionary biology of human immunodeficiency virus. Ann.Rev.Ecol.Syst. 25, 127-165.
327. Nee S, Holmes EC, May RM & Harvey PH. (1994). Extinction rates can be estimated from molecular phylogenies. Phil.Trans.Roy.Soc.B. 344, 77-82.
328. Simmonds P, Alberti A, Alter HJ, Bonino F, Bradley DW, Brechot C, Brouwer JT, Holmes EC et al. (1994). A proposed system for the nomenclature of genotypes of hepatitis C virus genotypes. Hepatology 19, 1321-1324.
329. Simmonds P, Smith DB, McOmish F, Yap PL, Kolberg J, Urdea MS & Holmes EC (1994). Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions. J.Gen.Virol. 75, 1053-1061.
1993
330. Holmes EC, Simmonds P & Leigh Brown AJ. (1993). Sequence data as evidence. Nature 364, 766.
331. Holmes EC, Zhang LQ, Simmonds P, Rogers AS, & Leigh Brown AJ. (1993). Molecular investigation of HIV infection in a patient of an HIV-infected surgeon. J.Infect.Dis. 167, 1411-1414.
332. Rice PS, Simmonds P, Smith DB & Holmes EC. (1993). Heterosexual transmission of hepatitis C virus. Lancet. 342, 1052-1053.
333. Rigby MA, Holmes EC, Pistello M, Mackay N, Leigh Brown AJ & Neil J. (1993). Evolution of structural proteins of feline immunodeficiency virus; molecular epidemiology and evidence of selection for change. J.Gen.Virol. 74, 425-436.
334. Rogers AS, Froggatt JW, Townsend T, Gordon T, Leigh Brown AJ, Holmes EC, Zhang LQ & Moses H. (1993). Investigation of potential HIV transmission to the patients of an HIV-infected surgeon. JAMA 269, 1795-1801.
335. Simmonds P, Holmes EC, Cha TA, Chan S-W, McOmish F, Irvine B, Beall E, Yap PL, Kolberg J & Urdea MS. (1993). Classification of hepatitis C virus into 6 major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J.Gen.Virol. 74, 2391-2399.
336. Simmonds P, McOmish F, Yap PL, Chan S-W, Lin CK, Dusheiko G, Saeed AA & Holmes EC. (1993). Sequence variability in the 5' non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. J.Gen.Virol. 74, 661-668.
337. Zhang LQ, Leigh Brown AJ, Holmes EC, Cleland A, Mckenzie P & Simmonds P. (1993). Selection for specific sequences in the external envelope protein of HIV-1 upon primary infection. J.Virol. 67, 3345-3356.
1992
338. Chan S-W, McOmish F, Holmes EC, Dow B, Peutherer JF, Follet E, Yap PL & Simmonds P. (1992). Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. J.Gen.Virol. 73, 1131-1141.
339. Holmes EC, Zhang LQ, Simmonds P, Ludlam CA & Leigh Brown AJ. (1992). Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc.Natl.Acad.Sci.USA 89,4835-4839.
1991
340. Holmes EC. (1991). Different rates of substitution may produce different phylogenies of the eutherian mammals. J.Mol.Evol. 33, 209-215.
1989
341. Holmes EC, Pesole G & Saccone C. (1989). Stochastic models of molecular evolution and the estimation of phylogeny and rates of nucleotide substitution in the hominoid primates. J.Hum.Evol. 18, 775-794.
Book Chapters
1. Holmes EC. Virus evolution. In Fields Virology, 6th Edition. (Ed. DM Knipe & PM Howley). Lippincott Williams & Wilkins, Philadelphia. (In Press).
2. Holmes EC. (2008). Comparative studies of RNA virus evolution. In Origin and Evolution of Viruses, 2nd Edition. (Ed. E. Domingo, CR Parrish & JJ Holland). pp. 119-134. Academic Press, London, UK.
3. Holmes EC. (2007). The evolution of viral emergence. In Novel and Re-Emerging Respiratory Viral Diseases. Novartis Symposium 290. pp. 17-31. John Wiley & Sons, Chichester, UK.
4. Holmes EC. (2006). The evolutionary biology of dengue virus. In New Treatment Strategies for Dengue and other Flaviviral Diseases. Novartis Symposium 277. pp. 177-187 (Discussion 187-192). John Wiley & Sons, Chichester, UK.
5. Holmes EC & Rambaut A. (2005). Evolutionary genetics and the emergence of SARS coronavirus. In SARS: A Case Study in Emerging Infections. (Ed. AR McLean, RM May, J Pattison & RA Weiss). pp 16-23. Oxford University Press, Oxford.
6. Holmes EC. The evolution of virulence in AIDS viruses. (2004). In Evolution: From Molecules to Ecosystems. (Ed. A Moya & E. Font). pp. 69-81. Oxford University Press, Oxford.
7. Holmes EC. (2003). Evolutionary genetics and emergence of RNA virus diseases. In The Evolution of Population Biology. (Ed. RS Singh & MK Uyenoyama). pp. 391-410. Cambridge University Press, Cambridge.
8. Holmes EC. (2002). Acquired Immune Deficiency Syndrome: Origins and Phylogeny of HIV. In Encyclopedia of Evolution. pp. 1-6. (Ed. M Pagel). Oxford University Press, New York.
9. Holmes EC. (2002). Viruses. In Encyclopedia of Evolution. (Ed. M Pagel). pp. 1136-1141. Oxford University Press, New York.
10. Ellis SA, Holmes EC, Staines KA & Morrison WI. (2000). The evolution of MHC class I genes in cattle. In Major Histocompatibility Complex. (Ed. M Kasahara). pp. 273-278. Springer-Verlag, Tokyo.
11. Holmes EC & Zanotto PM de A. (2000). The ecology and evolution of human hepatitis viruses. In Molecular Epidemiology of Infectious Diseases (Ed. RCA Thompson). pp. 181-193. Arnold Publishers, London.
12. Holmes EC. (1999). Molecular phylogenies and the genetic structure of viral populations. In Evolution in Health & Disease. (Ed. S Stearns). pp. 173-182. Oxford University Press.
13. Holmes EC, Pybus OG & Harvey PH. (1999). The molecular population dynamics of HIV-1. In The Evolution of HIV. (Ed. KA Crandall). pp. 177-207. John Hopkins University Press.
14. Read AF, Aaby P, Antia R, Ebert D, Ewald PW, Gupta S, Holmes EC, Sasaki A, Shields D, Taddei F & Moxon R. (1999). What can evolutionary biology contribute to understanding virulence? In Evolution in Health & Disease. (Ed. S Stearns). pp. 205-215. Oxford University Press.
15. Holmes EC, Bartley LM & Garnett GP. (1998). The emergence of dengue: past, present and future. In Emerging Infections (Ed. RM Krause). pp. 301-325. Academic Press.
16. Gould EA, Zanotto PM de A & Holmes EC. (1997). The genetic evolution of flaviviruses. In Factors in the Emergence of Arbovirus Disease. (Ed. JF Saluzzo & B Dodet). pp. 51-63. Elsevier, Paris.
17. Holmes EC, Bollyky PL, Nee S, Rambaut A, Garnett GP & Harvey PH. (1996). Using phylogenetic trees to reconstruct the history of infectious disease epidemics. In New Uses for New Phylogenies (Ed. PH Harvey, AJ Leigh Brown, J Maynard Smith & S Nee). pp. 169-186. Oxford University Press.
18. Holmes EC, Gould EA & Zanotto PM de A. (1996). An RNA virus tree of life? In Evolution of Microbial Life (Ed. DMcL Roberts, P Sharp, G Alderson & MA Collins). pp. 127-144. Society for General Microbiology Symposium 54, Cambridge University Press.
19. Nee S, Holmes EC, Rambaut A & Harvey PH. (1996). Inferring population history from molecular phylogenies. In New Uses for New Phylogenies (Ed. PH Harvey, AJ Leigh Brown, J Maynard Smith & S Nee). pp. 66-80. Oxford University Press.
20. Nee S, Holmes EC, May RM & Harvey PH. (1995). Estimating extinction from molecular phylogenies. In Estimating Extinction Rates. (Ed. JL Lawton & RM May). pp. 164-182. Oxford University Press.
21. Harvey PH, Holmes EC, Mooers AØ & Nee S. (1994). Inferring evolutionary processes from molecular phylogenies. In Models in Phylogeny Reconstruction. (Ed. RW Scotland, DJ Siebert & DM Williams). Systematics Association Special Volume Series 52, 313-333.
22. Holmes EC, Simmonds P, Cha T-A, Chan S-W, McOmish F, Irvine B, Beall E, Yap PL, Kolberg J & Urdea MS. (1994). Derivation of a rational nomenclature for hepatitis C virus by phylogenetic analysis of the NS-5 region. In Viral Hepatitis and Liver Disease. (Ed. K Nishioka, H Suzuki, S Mishiro & T Oda). Spinger-Velag.
Commentaries & Other Publications
1. Holmes EC. (2011). Genomics: Plague’s progress (News & Views). Nature 478, 465-466.
2. Holmes EC. (2010). Emerging Viruses: Past, Present and Future. medicSA (Magazine of the Australian Medical Association (South Australia) Inc. Nov/Dec. 2010, 19-20.
3. Holmes EC. (2010). Malaria: The gorilla connection (News & Views). Nature 467, 404-405.
4. Holmes EC. (2010). Perspectives: Helping the resistance. Science 328, 1243-1244.
5. Halloran ME & Holmes EC. (2009). Invited commentary: Evaluating vaccination programs using genetic sequence data. Am.J.Epi. 170, 1464-1466.
6. Holmes EC. (2009). Preface to The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd Edition. Edited by P. Lemey, M. Salemi & A-M Vandamme. Cambridge University Press.
7. Pardini MI de MC, Jamal JF, Durigon EJ, Massad E, Perez JF, Pinho JRR, Holmes EC & Zanotto PM de A. (2008). Boosting virology in Brazil. PLoS Biol. 6:e57.
8. Holmes EC. (2007). When HIV spread afar. Proc.Natl.Acad.Sci.USA. 104, 18351-18352.
9. Holmes EC. (2007). Ancient lentiviruses leave their mark. Proc.Natl.Acad.Sci.USA 104, 6095-6096.
10. Holmes EC. (2006). The evolution of viral emergence. Proc.Natl.Acad.Sci.USA 103, 4803-4804.
11. Holmes EC. (2005). On being the right size (News & Views). Nat.Genet. 37, 923-924.
12. Holmes EC, Taubenberger JK & Grenfell BT. (2005). Editorial: Heading off an influenza pandemic. Science 309, 989.
13. Holmes EC. (2004). Adaptation and immunity. PLoS Biology 2, 1267-1269.
14. Holmes EC. (2004). Los virus emergentes (in Spanish). Pasajes 14, 5-12.
15. Holmes EC. (2004). Perspectives: 1918 and all that. Science 303, 1787-1788.
16. Holmes EC. (2001). Human immunodeficiency virus (In ‘Evolution in the century of biology’). Am.Nat. 158, S13.
17. Holmes EC. (1999). Genomics, phylogenetics and epidemiology. Microbiology Today 26, 162-163.
18. Holmes EC. (1998). The molecular archaeology of infectious disease. SGM Quart. 25, 56-57.
19. Holmes EC. (1996). Reconstructing the history of viral epidemics. Biologist 43, 54-57.
20. Holmes EC & Harvey PH. (1994). Spinning the web of life. Current Biology 4, 841-843.
21. Holmes EC & Harvey PH. (1993). Fitting the bill. Current Biology 3, 776-777.
Book Reviews
1. The Viral Storm: The Dawn of a New Pandemic Age. (2011). By Nathan Wolfe. Nature 478, 319-320.
2. Inferring Phylogenies. (2004). By J Felsenstein. Quart.Rev.Biol.
3. Japanese Encephalitis and West Nile Viruses. Current Topics in Microbiology and Immunology, vol. 267. (2002). Edited by JS Mackenzie, ADT Barrett & V Deubel. Microbiol.Today.
4. Evolution: An Introduction. (2001). By SC Stearns & RF Hoekstra. J.Biogeog.
5. Origin and Evolution of Viruses. (2000). Edited by E Domingo, R Webster & JH Holland. Quart.Rev.Biol.
6. Molecular Basis of Virus Evolution. (1995). Edited by A Gibbs, CH Calisher & F Garcîa-Arenal. SGM Quarterly.
7. The Evolutionary Biology of Viruses. (1995). Edited by SS Morse. Quart.Rev.Biol.
8. Molecular Ecology In Focus. (1992). By AR Hoezel & GA Dover. Genetical.Res.Camb.
9. The Fundamentals of Molecular Evolution. (1991). By W-H Li & D Graur. Am.J.Phys.Anth.
Conference Abstracts & Proceedings
1. Holmes EC. (2009). The evolutionary genomics of dengue virus. In Arbovirus Research in Australia (Ed. P Ryan, J Aaskov & R Russell). Vol. 10, 69.
2. Jarman RG, Klungthong C, Holmes EC, Chinnawirotpisan P, Rodpradit P, Pimgate C, Scott TW, Rothman AL, Yoon IK & Gibbons RV. (2008). Genetic analysis of dengue viruses collected from mosquitoes and humans during dengue cluster investigations in Thailand. Am.J.Trop.Med.Hyg. 79, S37.
3. Allicock OM, Auguste AJ Dunham EJ, Pybus OG, Holmes EC & Carrington CV. (2007). Genetic diversity and positive selection in Eastern equine encephalitis virus. Am.J.Trop.Med.Hyg. 77, S176.
4. Auguste AJ, Dunham EJ, Pybus OG, Holmes EC & Carrington CV. (2007). Migration and transmission history of St. Louis encephalitis virus. Am.J.Trop.Med.Hyg. 77, S197.
5. Holmes EC. (2007). The evolution and epidemiology of dengue virus. Salud Pública de México 49, E296-E300.
6. Rodriguez-Roche R, Alvarez M, Holmes EC, Bernardo L, Flores GK, Halstead SB & Guzman MG. (2006). Dengue hemorrhagic fever caused by sequential dengue 1-3 infections at a long interval: Havana epidemic, 2001-2002. Am.J.Trop.Med.Hyg. 75, S30.
7. Zhang C, Mammen MP, Klungthong C, Chinnawirotpisan P, Rodpradit P, Kalayanarooj S & Holmes EC. (2005). The structure of genetic diversity and the evolutionary processes of dengue viruses circulating in Thailand. Am.J.Trop.Med.Hyg. 73, S5.
8. Kurtenbach K, De Michelis S, Sewell HS, Etti S, Schafer SM, Holmes EC, Hails R, Collares-Pereira M, Santos-Reis M, Hanincova K, Labuda M, Bormane A & Donaghy M. (2002). The key roles of selection and migration in the ecology of Lyme borreliosis. Int.J.Med.Micro. 291 (Suppl. 33.), 152-154.
9. Grassly NC & Holmes EC. (1998). The use of Monte Carlo simulation to infer population dynamic history from DNA sequence data. In Proceedings of the Trinational Workshop on Molecular Evolution. (Ed. MK Uyenoyama, N Takahata & A von Haeseler). pp. 91-112. Duke Publications Group, Durham, NC.
10. Bollyky PL, Rambaut A, Grassly N, Carman WF & Holmes EC. (1997). Hepatitis B virus has a recent new world evolutionary origin. Hepatology 26, 765.
11. Bollyky PL, Yasmin M, Holmes EC, Trautwein C, Fagan EA & Carman WF. (1997). Viruses from unrelated fulminant hepatitis B cases cluster in phylogenetically distinct lineages, each containing unique motifs of nucleotide and Hbx variants which have increased transcriptional activity in vitro. J.Hepatology 26 (Suppl. 1), 67.
12. Yasmin M, Bollyky PL, Holmes EC, Carman WF & Fagan EA. (1997). Genotype D variants with high replication efficiency predict good prognosis in fulminant hepatitis B. J.Hepatol. 26, S761.
13. Bonhoeffer S, Holmes EC & Nowak MA. (1995). Varying selection pressure in HIV-1 infection. J.Acquir.Immun.Def.Synd.Hum.Retro. 10, 85.
14. Harvey PH, Holmes EC, Rambaut A & Nee S. (1995). How to reveal viral population history from gene sequence data. In Immunobiology of Viral Infection. Proceedings 3rd International Congress of Veterinary Virology. (Ed. M Schwyzer, M Ackermann, G Bertoni, R Kocherhans, K McCullough, M Engels, R Wittek & R Zanoni).
15. Simmonds P, Hughes ES, Livingstone WJ, Donaldson YK, Holmes EC, Brown HK & Bell JE. (1995). Restricted sequence variability of the HIV-1 V3 loop in vivo. J. Cell. Biochem. S21, 244.
16. Holmes EC. (1993). The pattern and process of base substitution in immunodeficiency viruses. Binary 5, 189.
17. Leigh Brown AJ, Zhang LQ, Holmes EC & Simmonds P. (1993). Selection onV3 loop sequences in early HIV infection. AIDS Res.Hum.Retro. 9 (S1), 100.
18. Leigh Brown AJ, Zhang LQ, Robertson P, Cleland A, Holmes EC & Simmonds P. (1993). Studies on virus load and sequence in HIV transmission. J.Cell.Biochem. S17, 4.
19. Leigh Brown AJ, Zhang LQ, Holmes EC & Simmonds P. (1992). Selection for specific V3 loop sequences on transmission of HIV. J.Cell.Biochem. S16, 51.
20. Holmes EC. (1987). The phylogenetic position of the primates within the eutheria: molecular evidence. (Abstract issue for XXII congress of the International Primatological Society) Int.J.Primat. 8, 235.