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Edward Holmes

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TOP 3
Etienne Simon-Loriere; Edward C Holmes
Gene duplication is infrequent in the recent evolutionary history of RNA viruses.
Edward C Holmes
What can we predict about viral evolution and emergence?
S Bhatt; T A Bowden; I H Brown; Y Guan; Edward C Holmes; P Kellam; T T Lam; Andrew J Leigh Brown; S J Lycett; J L N Wood; O G Pybus
The evolutionary dynamics of influenza A virus adaptation to mammalian hosts.

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All Publications

2013: Etienne Simon-Loriere; Edward C Holmes
Gene duplication is infrequent in the recent evolutionary history of RNA viruses.
Molecular biology and evolution 2013;30(6):1263-9.
2013: Edward C Holmes
What can we predict about viral evolution and emergence?
Current opinion in virology 2013;3(2):180-4.
2013: S Bhatt; T A Bowden; I H Brown; Y Guan; Edward C Holmes; P Kellam; T T Lam; Andrew J Leigh Brown; S J Lycett; J L N Wood; O G Pybus
The evolutionary dynamics of influenza A virus adaptation to mammalian hosts.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368(1614):20120382.
2013: Cécile Viboud; Martha I Nelson; Yi Tan; Edward C Holmes
Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368(1614):20120199.
2013: Andrew B Allison; Justin D Brown; Edward J Dubovi; Karen A Fox; Richard W Gerhold; Dennis J Kohler; Colin R Parrish; Valerie I Shearn-Bochsler; Edward C Holmes
Frequent cross-species transmission of parvoviruses among diverse carnivore hosts.
Journal of virology 2013;87(4):2342-7.
2013: J Conrad Stack; James L N Wood; Bryan T Grenfell; Pablo R Murcia; Edward C Holmes
Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation.
Proceedings. Biological sciences / The Royal Society 2013;280(1750):20122173.
2013: Nikos Vasilakis; Peter J Walker; Steven Widen; Thomas G Wood; Edward C Holmes; Amelia P A Travassos da Rosa; Robert B Tesh
Malpais spring virus is a new species in the genus vesiculovirus.
Virology journal 2013;10():69.
2013: Maia A Rabaa; Alan L Rothman; Thomas W Scott; Anon Srikiatkhachorn; Darunee Tannitisupawong; Butsaya Thaisomboonsuk; In-Kyu Yoon; Jared Aldstadt; Piyawan Chinnawirotpisan; Timothy Endy; Thanyalak Fansiri; Robert V Gibbons; Edward C Holmes; Chonticha Klungthong; Mammen P Mammen; Ananda Nisalak; Rick G Jarman
Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand.
PLoS neglected tropical diseases 2013;7(1):e1990.
2013: Xiaowen Cheng; Shishong Fang; Jianfan He; Mingliang He; Edward C Holmes; Hsiang-Fu Kung; Tommy Tsan-Yuk Lam; Jianhua Lu; Xing Lu; Hanwu Ma; Martha I Nelson; Yi Tan; Cécile Viboud; Xin Wang; Chunli Wu; Xu Xie; Shunxiang Zhang; Jinquan Cheng
Epidemiological dynamics and phylogeography of influenza virus in southern China.
The Journal of infectious diseases 2013;207(1):106-14.
2012: Martha I Nelson; Aaron Schwartzbard; Timothy B Stockwell; Yi Tan; Amy L Vincent; David E Wentworth; Susan E Detmer; Marie R Gramer; Rebecca Halpin; Xudong Lin; Edward C Holmes
Genomic reassortment of influenza A virus in North American swine, 1998-2011.
The Journal of general virology 2012;93(Pt 12):2584-9.
2012: Mang Shi; Paul Digard; Edward C Holmes; Brett W Jagger; Helen M Wise; Jeffery K Taubenberger
Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus.
Journal of virology 2012;86(22):12411-3.
2012: Martha I Nelson; Amy L Vincent; Marie R Gramer; Edward C Holmes
Global transmission of influenza viruses from humans to swine.
The Journal of general virology 2012;93(Pt 10):2195-203.
2012: Jie Cui; Edward C Holmes; Gilda Tachedjian; Mary Tachedjian; Shuyi Zhang; Lin-Fa Wang
Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats.
The Journal of general virology 2012;93(Pt 9):2037-45.
2012: Martha I Nelson; Amy L Vincent; Edward C Holmes; Pravina Kitikoon; Marie R Gramer
Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011.
Journal of virology 2012;86(16):8872-8.
2012: H E Simmons; J C Stack; B J A Dickins; J P Dunham; Edward C Holmes; I Pagán; Andrew G Stephenson
Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus.
The Journal of general virology 2012;93(Pt 8):1831-40.
2012: Jie Cui; Edward C Holmes
Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses.
Journal of virology 2012;86(14):7688-91.
2012: Jie Cui; Edward C Holmes
Endogenous RNA viruses of plants in insect genomes.
Virology 2012;427(2):77-9.
2012: Tommy Tsan-Yuk Lam; Philippe Lemey; Edward C Holmes; Chung Chau Hon; Jingwei Jiang; Jun Li; Oliver G Pybus; Mang Shi; Hein Min Tun; Frederick Chi-Ching Leung
Phylodynamics of H5N1 avian influenza virus in Indonesia.
Molecular ecology 2012;21(12):3062-77.
2012: Jie Cui; Edward C Holmes
Evidence for an endogenous papillomavirus-like element in the platypus genome.
The Journal of general virology 2012;93(Pt 6):1362-6.
2012: Tommy Tsan-Yuk Lam; Yi Guan; Edward C Holmes; David K Smith; Huachen Zhu; Oliver G Pybus
The recombinant origin of emerging human norovirus GII.4/2008: intra-genotypic exchange of the capsid P2 domain.
The Journal of general virology 2012;93(Pt 4):817-22.
2012: Gaurav Bhardwaj; Sree V Chintapalli; Foram Dave; Matthew Gotlin; David Nicholas Hartranft; Ngai Lam Ho; Edward C Holmes; Yoojin Hong; Lindsay A Kline; Kyung Dae Ko; Morgen E Patterson; Randen L Patterson; Evan J Smith; Zhenhai Zhang; Damian B van Rossum
PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.
PloS one 2012;7(4):e34261.
2011: J Bahl; Kwok H Chan; Rubing Chen; Elodie Ghedin; Yi Guan; Rebecca Halpin; Edward C Holmes; Xudong Lin; Martha I Nelson; J S Malik Peiris; Andrew Rambaut; Steven Riley; Timothy B Stockwell; Dhanasekaran Vijaykrishna; David E Wentworth; Gavin J D Smith
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(48):19359-64.
2011: Edward C Holmes
The evolution of endogenous viral elements.
Cell host & microbe 2011;10(4):368-77.
2011: Samir Bhatt; Edward C Holmes; Oliver G Pybus
The genomic rate of molecular adaptation of the human influenza A virus.
Molecular biology and evolution 2011;28(9):2443-51.
2011: Edward C Holmes; Xudong Lin; Yu-Tseung Liu; Sanjay Mehta; Robert T Schooley; Timothy B Stockwell; Randy Taplitz; David E Wentworth; Xing-Quan Zhang; Constance A Benson; Kimberly C Brouwer; Richard Davey; Regina Fleming; Elodie Ghedin; Rebecca Halpin
Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community.
Journal of virology 2011;85(14):6923-9.
2011: Martha I Nelson; Andrew Rambaut; Marc A Suchard; Yi Tan; Cécile Viboud; Amy Vincent; Susan Detmer; Edward C Holmes; Tommy Tsan-Yuk Lam; Philippe Lemey; Marie Gramer
Spatial dynamics of human-origin H1 influenza A virus in North American swine.
PLoS pathogens 2011;7(6):e1002077.
2011: Edward C Holmes
What does virus evolution tell us about virus origins?
Journal of virology 2011;85(11):5247-51.
2011: Wen J Liu; Michelle F Rourke; Edward C Holmes; John Aaskov
Persistence of multiple genetic lineages within intrahost populations of Ross River virus.
Journal of virology 2011;85(11):5674-8.
2011: Heather E Simmons; Edward C Holmes; Andrew G Stephenson
Rapid turnover of intra-host genetic diversity in Zucchini yellow mosaic virus.
Virus research 2011;155(2):389-96.
2011: Elodie Ghedin; Jennifer Laplante; Jay DePasse; David E Wentworth; Roberto P Santos; Martha L Lepow; Joanne Porter; Kathleen Stellrecht; Xudong Lin; Darwin Operario; Sara Griesemer; Adam Fitch; Rebecca A Halpin; Timothy B Stockwell; David J Spiro; Edward C Holmes; Kirsten St George
Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance.
The Journal of infectious diseases 2011;203(2):168-74.
2011: Andrew Kitchen; Laura A Shackelton; Edward C Holmes
Family level phylogenies reveal modes of macroevolution in RNA viruses.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(1):238-43.
2010: Jessica J Hayward; Edward J Dubovi; Janet M Scarlett; Stephanie Janeczko; Edward C Holmes; Colin R Parrish
Microevolution of canine influenza virus in shelters and its molecular epidemiology in the United States.
Journal of virology 2010;84(24):12636-45.
2010: Israel Pagán; Cadhla Firth; Edward C Holmes
Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus tobamovirus.
Journal of molecular evolution 2010;71(4):298-307.
2010: Laurent Dacheux; Nicolas Berthet; Gabriel Dissard; Edward C Holmes; Olivier Delmas; Florence Larrous; Ghislaine Guigon; Philip Dickinson; Ousmane Faye; Amadou A Sall; Iain G Old; Katherine Kong; Giulia C Kennedy; Jean-Claude Manuguerra; Stewart T Cole; Valérie Caro; Antoine Gessain; Hervé Bourhy
Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses.
Journal of virology 2010;84(18):9557-74.
2010: Cadhla Firth; Andrew Kitchen; Beth Shapiro; Marc A Suchard; Edward C Holmes; Andrew Rambaut
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses.
Molecular biology and evolution 2010;27(9):2038-51.
2010: Edward C Holmes
The RNA virus quasispecies: fact or fiction?
Journal of molecular biology 2010;400(3):271-3.
2010: Edward C Holmes
Virology. Helping the resistance.
Science (New York, N.Y.) 2010;328(5983):1243-4.
2010: Israel Pagán; Edward C Holmes
Long-term evolution of the Luteoviridae: time scale and mode of virus speciation.
Journal of virology 2010;84(12):6177-87.
2010: Edward C Holmes
Evolution in health and medicine Sackler colloquium: The comparative genomics of viral emergence.
Proceedings of the National Academy of Sciences of the United States of America 2010;107 Suppl 1():1742-6.
2010: Chiraz Talbi; Philippe Lemey; Marc A Suchard; Elbia Abdelatif; Mehdi Elharrak; Jalal Nourlil; Nourlil Jalal; Abdellah Faouzi; Juan E Echevarría; Sonia Vazquez Morón; Andrew Rambaut; Nicholas Campiz; Andrew J Tatem; Edward C Holmes; Hervé Bourhy
Phylodynamics and human-mediated dispersal of a zoonotic virus.
PLoS pathogens 2010;6(10):e1001166.
2010: Maia A Rabaa; Vu Thi Ty Hang; Bridget Wills; Jeremy Farrar; Cameron P Simmons; Edward C Holmes
Phylogeography of recently emerged DENV-2 in southern Viet Nam.
PLoS neglected tropical diseases 2010;4(7):e766.
2010: Rubing Chen; Edward C Holmes
Hitchhiking and the population genetic structure of avian influenza virus.
Journal of molecular evolution 2010;70(1):98-105.
2010: Anita Jones; Kym Lowry; John Aaskov; Edward C Holmes; Andrew Kitchen
Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy.
The Journal of general virology 2010;91(Pt 1):182-8.
2010: Gilda Grard; Gregory Moureau; Remi CHARREL; Edward C Holmes; Ernest A Gould; Xavier de Lamballerie
Genomics and evolution of Aedes-borne flaviviruses.
The Journal of general virology 2010;91(Pt 1):87-94.
2009: Cadhla Firth; Michael A Charleston; Siobain Duffy; Beth Shapiro; Edward C Holmes
Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2.
Journal of virology 2009;83(24):12813-21.
2009: Tandin Dorji; In-Kyu Yoon; Edward C Holmes; Sonam Wangchuk; Tashi Tobgay; Ananda Nisalak; Piyawan Chinnawirotpisan; Kanittha Sangkachantaranon; Robert V Gibbons; Rick G Jarman
Diversity and origin of dengue virus serotypes 1, 2, and 3, Bhutan.
Emerging infectious diseases 2009;15(10):1630-2.
2009: Edward C Holmes; Bryan T Grenfell
Discovering the phylodynamics of RNA viruses.
PLoS computational biology 2009;5(10):e1000505.
2009: Edward C Holmes
RNA virus genomics: a world of possibilities.
The Journal of clinical investigation 2009;119(9):2488-95.
2009: Edward C Holmes; Phaik Hooi Tio; David Perera; Jamail Muhi; Jane Cardosa
Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia.
Virus research 2009;143(1):1-5.
2009: Siobain Duffy; Edward C Holmes
Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses.
The Journal of general virology 2009;90(Pt 6):1539-47.
2009: Chiraz Talbi; Edward C Holmes; Paola de Benedictis; Ousmane Faye; E Nakouné; Djibo Gamatié; Abass Diarra; Bezeid Ould Elmamy; Adama Sow; Edgard Valery Adjogoua; Oumou Sangare; William G Dundon; Ilaria Capua; Amadou A Sall; Hervé Bourhy
Evolutionary history and dynamics of dog rabies virus in western and central Africa.
The Journal of general virology 2009;90(Pt 4):783-91.
2009: Rubing Chen; Edward C Holmes
Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds.
Virology 2009;383(1):156-61.
2008: Hervé Bourhy; Jean-Marc Reynes; Eleca J Dunham; Laurent Dacheux; Florence Larrous; VT Huong; Gelin Xu; Jiaxin Yan; Mary Elizabeth Miranda; Edward C Holmes
The origin and phylogeography of dog rabies virus.
The Journal of general virology 2008;89(Pt 11):2673-81.
2008: Karin Hoelzer; Laura A Shackelton; Edward C Holmes; Colin R Parrish
Within-host genetic diversity of endemic and emerging parvoviruses of dogs and cats.
Journal of virology 2008;82(22):11096-105.
2008: Laura A Shackelton; Edward C Holmes
The role of alternative genetic codes in viral evolution and emergence.
Journal of theoretical biology 2008;254(1):128-34.
2008: Colin R Parrish; Edward C Holmes; David M Morens; Eun-Chung Park; Donald S. Burke; Charles H Calisher; Catherine A Laughlin; Linda J Saif; Peter Daszak
Cross-species virus transmission and the emergence of new epidemic diseases.
Microbiology and molecular biology reviews : MMBR 2008;72(3):457-70.
2008: Karin Hoelzer; Laura A Shackelton; Colin R Parrish; Edward C Holmes
Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses.
The Journal of general virology 2008;89(Pt 9):2280-9.
2008: Cadhla Ramsden; Fernando L Melo; Luiz M Figueiredo; Edward C Holmes; Paolo M A Zanotto
High rates of molecular evolution in hantaviruses.
Molecular biology and evolution 2008;25(7):1488-92.
2008: Rubing Chen; Edward C Holmes
The evolutionary dynamics of human influenza B virus.
Journal of molecular evolution 2008;66(6):655-63.
2008: Rick G Jarman; Edward C Holmes; Prinyada Rodpradit; Chonticha Klungthong; Robert V Gibbons; Ananda Nisalak; Alan L Rothman; Daniel H Libraty; Irene Bosch; Mammen P Mammen; Timothy Endy
Microevolution of Dengue viruses circulating among primary school children in Kamphaeng Phet, Thailand.
Journal of virology 2008;82(11):5494-500.
2008: Heather E Simmons; Edward C Holmes; Andrew G Stephenson
Rapid evolutionary dynamics of zucchini yellow mosaic virus.
The Journal of general virology 2008;89(Pt 4):1081-5.
2008: Siobain Duffy; Laura A Shackelton; Edward C Holmes
Rates of evolutionary change in viruses: patterns and determinants.
Nature reviews. Genetics 2008;9(4):267-76.
2008: Martha I Nelson; Cécile Viboud; Lone Simonsen; Ryan T Bennett; Sara B Griesemer; Kirsten St George; Jill Taylor; David Spiro; Naomi A Sengamalay; Elodie Ghedin; Jeffery Taubenberger; Edward C Holmes
Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918.
PLoS pathogens 2008;4(2):e1000012.
2008: Laura W Pomeroy; Ottar N Bjørnstad; Edward C Holmes
The evolutionary and epidemiological dynamics of the paramyxoviridae.
Journal of molecular evolution 2008;66(2):98-106.
2008: Edward C Holmes
Evolutionary history and phylogeography of human viruses.
Annual review of microbiology 2008;62():307-28.
2008: Martha I Nelson; Laurel Edelman; David Spiro; Alex R Boyne; Jayati Bera; Rebecca Halpin; Naomi Sengamalay; Elodie Ghedin; mark miller; Lone Simonsen; Cécile Viboud; Edward C Holmes
Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States.
PLoS pathogens 2008;4(8):e1000133.
2008: Olivier Delmas; Edward C Holmes; Chiraz Talbi; Florence Larrous; Laurent Dacheux; Christiane Bouchier; Hervé Bourhy
Genomic diversity and evolution of the lyssaviruses.
PloS one 2008;3(4):e2057.
2008: Siobain Duffy; Edward C Holmes
Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus.
Journal of virology 2008;82(2):957-65.
2007: John Aaskov; Katie Buzacott; Emma Field; Kym Lowry; Alain Berlioz-Arthaud; Edward C Holmes
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient.
The Journal of general virology 2007;88(Pt 12):3334-40.
2007: Laura A Shackelton; Karin Hoelzer; Colin R Parrish; Edward C Holmes
Comparative analysis reveals frequent recombination in the parvoviruses.
The Journal of general virology 2007;88(Pt 12):3294-301.
2007: Edward C Holmes
When HIV spread afar.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(47):18351-2.
2007: Siobain Duffy; Edward C Holmes
Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World.
Applied and environmental microbiology 2007;73(21):7114-7.
2007: Diana Cox-Foster; Sean Conlan; Edward C Holmes; Gustavo Palacios; Jay Evans; Nancy Moran; Phenix-Lan Quan; Thomas Briese; Mady Hornig; David M Geiser; Vince Martinson; Dennis vanEngelsdorp; Abby L Kalkstein; Andrew Drysdale; Jeffrey Hui; Junhui Zhai; Liwang Cui; Stephen K Hutchison; Jan Fredrik Simons; Michael Egholm; Jeffery S Pettis; W Ian Lipkin
A metagenomic survey of microbes in honey bee colony collapse disorder.
Science (New York, N.Y.) 2007;318(5848):283-7.
2007: Edward C Holmes
Viral evolution in the genomic age.
PLoS biology 2007;5(10):e278.
2007: Martha I Nelson; Lone Simonsen; Cécile Viboud; mark miller; Edward C Holmes
Phylogenetic analysis reveals the global migration of seasonal influenza A viruses.
PLoS pathogens 2007;3(9):1220-8.
2007: Siripen Kalayanarooj; Hem Sagar Rimal; Alex Andjaparidze; Varunee Vatcharasaevee; Ananda Nisalak; Rick G Jarman; Piyawan Chinnawirotpisan; Mammen P Mammen; Edward C Holmes; Robert V Gibbons
Clinical intervention and molecular characteristics of a dengue hemorrhagic fever outbreak in Timor Leste, 2005.
The American journal of tropical medicine and hygiene 2007;77(3):534-7.
2007: Nikos Vasilakis; Edward C Holmes; Eric B Fokam; Ousmane Faye; Mawlouth Diallo; Amadou A Sall; Scott C Weaver
Evolutionary processes among sylvatic dengue type 2 viruses.
Journal of virology 2007;81(17):9591-5.
2007: Yang Zhou; Edward C Holmes
Bayesian estimates of the evolutionary rate and age of hepatitis B virus.
Journal of molecular evolution 2007;65(2):197-205.
2007: Eleca J Dunham; Edward C Holmes
Inferring the timescale of dengue virus evolution under realistic models of DNA substitution.
Journal of molecular evolution 2007;64(6):656-61.
2007: Juliet E Bryant; Edward C Holmes; Alan D T Barrett
Out of Africa: a molecular perspective on the introduction of yellow fever virus into the Americas.
PLoS pathogens 2007;3(5):e75.
2007: Gilda Grard; Gregory Moureau; Remi CHARREL; Jean-Jacques Lemasson; jean paul gonzalez; Pierre Gallian; Tamara S Gritsun; Edward C Holmes; Ernest A Gould; Xavier de Lamballerie
Genetic characterization of tick-borne flaviviruses: new insights into evolution, pathogenetic determinants and taxonomy.
Virology 2007;361(1):80-92.
2007: Edward C Holmes
Ancient lentiviruses leave their mark.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(15):6095-6.
2007: Martha I Nelson; Edward C Holmes
The evolution of epidemic influenza.
Nature reviews. Genetics 2007;8(3):196-205.
2007: Oliver G Pybus; Andrew Rambaut; Robert Belshaw; Robert P Freckleton; Alexei J Drummond; Edward C Holmes
Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.
Molecular biology and evolution 2007;24(3):845-52.
2007: Katherine W Snapinn; Edward C Holmes; David S Young; Kristen A Bernard; Laura D Kramer; Gregory Ebel
Declining growth rate of West Nile virus in North America.
Journal of virology 2007;81(5):2531-4.
2007: Polly R Walker; Melissa Ketunuti; Isaac A Choge; Tammy Meyers; Glenda Gray; Edward C Holmes; Lynn Morris
Polymorphisms in Nef associated with different clinical outcomes in HIV type 1 subtype C-infected children.
AIDS research and human retroviruses 2007;23(2):204-15.
2007: Edward C Holmes; A J Drummond
The evolutionary genetics of viral emergence.
Current topics in microbiology and immunology 2007;315():51-66.
2007: Patricia L Davis; A Rambaut; Hervé Bourhy; Edward C Holmes
The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa.
Archives of virology 2007;152(7):1251-8.
2006: Martha I Nelson; Lone Simonsen; Cécile Viboud; mark miller; Jill Taylor; Kirsten St George; Sara B Griesemer; Elodie Ghedin; Elodie Ghedi; Naomi A Sengamalay; David Spiro; Igor Volkov; Bryan T Grenfell; David Lipman; Jeffery Taubenberger; Edward C Holmes
Stochastic processes are key determinants of short-term evolution in influenza a virus.
PLoS pathogens 2006;2(12):e125.
2006: Rubing Chen; Edward C Holmes
Avian influenza virus exhibits rapid evolutionary dynamics.
Molecular biology and evolution 2006;23(12):2336-41.
2006: Gilda Grard; Jean-Jacques Lemasson; Massamba Sylla; Audrey Dubot; Shelley Cook; Jean-François Molez; Xavier Pourrut; Remi CHARREL; jean paul gonzalez; Ulrike Munderloh; Edward C Holmes; Xavier de Lamballerie
Ngoye virus: a novel evolutionary lineage within the genus Flavivirus.
The Journal of general virology 2006;87(Pt 11):3273-7.
2006: Charles T T Edwards; Edward C Holmes; Oliver G Pybus; Daniel J Wilson; Raphael P Viscidi; E J Abrams; Rodney E Phillips; Alexei J Drummond
Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.
Genetics 2006;174(3):1441-53.
2006: Patricia L Davis; Hervé Bourhy; Edward C Holmes
The evolutionary history and dynamics of bat rabies virus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2006;6(6):464-73.
2006: Laura A Shackelton; Andrew Rambaut; Oliver G Pybus; Edward C Holmes
JC virus evolution and its association with human populations.
Journal of virology 2006;80(20):9928-33.
2006: B Adams; Edward C Holmes; C Zhang; Mammen P Mammen; Suchitra Nimmannitya; Siripen Kalayanarooj; Michael Boots
Cross-protective immunity can account for the alternating epidemic pattern of dengue virus serotypes circulating in Bangkok.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(38):14234-9.
2006: Edward C Holmes; David Lipman; Dmitriy Zamarin; jon yewdell
Comment on "Large-scale sequence analysis of avian influenza isolates".
Science (New York, N.Y.) 2006;313(5793):1573; author reply 1573.
2006: Yang Zhou; Mammen P Mammen; Chonticha Klungthong; Piyawan Chinnawirotpisan; David W Vaughn; Suchitra Nimmannitya; Siripen Kalayanarooj; Edward C Holmes; Chunlin Zhang
Comparative analysis reveals no consistent association between the secondary structure of the 3'-untranslated region of dengue viruses and disease syndrome.
The Journal of general virology 2006;87(Pt 9):2595-603.
2006: Beth Shapiro; Andrew Rambaut; Oliver G Pybus; Edward C Holmes
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.
Molecular biology and evolution 2006;23(9):1724-30.
2006: John Frater; Charles T T Edwards; N McCarthy; Julie Fox; Helen Brown; Anita Milicic; Nicola E Mackie; Tilly Pillay; Jan Wouter Drijfhout; Simon Dustan; John R Clarke; Edward C Holmes; Hua-Tang Zhang; Katja Pfafferott; Philip J R Goulder; Myra O McClure; Jonathan Weber; Rodney E Phillips; Sarah Fidler
Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts.
Journal of virology 2006;80(14):7226-34.
2006: Laura A Shackelton; Colin R Parrish; Edward C Holmes
Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses.
Journal of molecular evolution 2006;62(5):551-63.
2006: Elizabeth R Chare; Edward C Holmes
A phylogenetic survey of recombination frequency in plant RNA viruses.
Archives of virology 2006;151(5):933-46.
2006: Laura A Shackelton; Edward C Holmes
Phylogenetic evidence for the rapid evolution of human B19 erythrovirus.
Journal of virology 2006;80(7):3666-9.
2006: Chunlin Zhang; Mammen P Mammen; Piyawan Chinnawirotpisan; Chonticha Klungthong; Prinyada Rodpradit; Ananda Nisalak; David W Vaughn; Suchitra Nimmannitya; Siripen Kalayanarooj; Edward C Holmes
Structure and age of genetic diversity of dengue virus type 2 in Thailand.
The Journal of general virology 2006;87(Pt 4):873-83.
2006: Shelley Cook; Shannon N Bennett; Edward C Holmes; Reine de Chesse; Gregory Moureau; Xavier de Lamballerie
Isolation of a new strain of the flavivirus cell fusing agent virus in a natural mosquito population from Puerto Rico.
The Journal of general virology 2006;87(Pt 4):735-48.
2006: Edward C Holmes
The evolution of viral emergence.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(13):4803-4.
2006: S Cook; Edward C Holmes
A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission.
Archives of virology 2006;151(2):309-25.
2006: John Aaskov; Katie Buzacott; Hlaing Myat Thu; Kym Lowry; Edward C Holmes
Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes.
Science (New York, N.Y.) 2006;311(5758):236-8.
2006: Edward C Holmes
The evolutionary biology of dengue virus.
Novartis Foundation symposium 2006;277():177-87; discussion 187-92, 251-3.
2006: Charles T T Edwards; Edward C Holmes; Daniel J Wilson; Raphael P Viscidi; Elaine J Abrams; Rodney E Phillips; Alexei J Drummond
Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.
BMC evolutionary biology 2006;6():28.
2005: Chunlin Zhang; Mammen P Mammen; Piyawan Chinnawirotpisan; Chonticha Klungthong; Prinyada Rodpradit; Patama Monkongdee; Suchitra Nimmannitya; Siripen Kalayanarooj; Edward C Holmes
Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence.
Journal of virology 2005;79(24):15123-30.
2005: Anita Milicic; Charles T T Edwards; Stéphane Hué; Julie Fox; Helen Brown; Tilly Pillay; Jan Wouter Drijfhout; Jonathan N Weber; Edward C Holmes; Sarah Fidler; Hua-Tang Zhang; Rodney E Phillips
Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants.
Journal of virology 2005;79(22):13953-62.
2005: Hervé Bourhy; Jeff A Cowley; Florence Larrous; Edward C Holmes; Peter J Walker
Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene.
The Journal of general virology 2005;86(Pt 10):2849-58.
2005: Tilly Pillay; Hua-Tang Zhang; Jan Wouter Drijfhout; Nicola Robinson; Helen Brown; Munira Khan; Jack Moodley; Miriam Adhikari; Katja Pfafferott; Margaret E Feeney; Anne St John; Edward C Holmes; Hoosen M Coovadia; Paul Klenerman; Philip J R Goulder; Rodney E Phillips
Unique acquisition of cytotoxic T-lymphocyte escape mutants in infant human immunodeficiency virus type 1 infection.
Journal of virology 2005;79(18):12100-5.
2005: Edward C Holmes; Elodie Ghedin; Naomi Miller; Jill Taylor; Yiming Bao; Kirsten St George; Bryan T Grenfell; Steven L Salzberg; Claire M Fraser-Liggett; David Lipman; Jeffery Taubenberger
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.
PLoS biology 2005;3(9):e300.
2005: Patricia L Davis; Edward C Holmes; Florence Larrous; Wim H M van der Poel; Kirsten Tjørnehøj; Wladimir J Alonso; Hervé Bourhy
Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses.
Journal of virology 2005;79(16):10487-97.
2005: Charles T T Edwards; Katja Pfafferott; Philip J R Goulder; Rodney E Phillips; Edward C Holmes
Intrapatient escape in the A*0201-restricted epitope SLYNTVATL drives evolution of human immunodeficiency virus type 1 at the population level.
Journal of virology 2005;79(14):9363-6.
2005: Hlaing Myat Thu; Kym Lowry; Limin Jiang; Thaung Hlaing; Edward C Holmes; John Aaskov
Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection.
Virology 2005;336(2):163-72.
2005: Polly R Walker; Oliver G Pybus; Andrew Rambaut; Edward C Holmes
Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2005;5(3):199-208.
2005: Oliver G Pybus; Alexandra Cochrane; Edward C Holmes; Peter Simmonds
The hepatitis C virus epidemic among injecting drug users.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2005;5(2):131-9.
2005: Laura A Shackelton; Colin R Parrish; Uwe Truyen; Edward C Holmes
High rate of viral evolution associated with the emergence of carnivore parvovirus.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(2):379-84.
2005: Shelley Cook; Mawlouth Diallo; Amadou A Sall; Alan Cooper; Edward C Holmes
Mitochondrial markers for molecular identification of Aedes mosquitoes (Diptera: Culicidae) involved in transmission of arboviral disease in West Africa.
Journal of medical entomology 2005;42(1):19-28.
2004: Atchareeya A-nuegoonpipat; Alain Berlioz-Arthaud; Vincent Chow; Timothy Endy; Kym Lowry; Le Quynh Mai; Truong Uyen Ninh; Alyssa Pyke; Mark Reid; Jean-Marc Reynes; Se-Thoe Su Yun; Hlaing Myat Thu; Sook-San Wong; Edward C Holmes; John Aaskov
Sustained transmission of dengue virus type 1 in the Pacific due to repeated introductions of different Asian strains.
Virology 2004;329(2):505-12.
2004: Chonticha Klungthong; Chunlin Zhang; Mammen P Mammen; Sukathida Ubol; Edward C Holmes
The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand.
Virology 2004;329(1):168-79.
2004: Elizabeth R Chare; Edward C Holmes
Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission.
The Journal of general virology 2004;85(Pt 10):3149-57.
2004: Rachel Urwin; Joanne E Russell; Emily A L Thompson; Edward C Holmes; Ian M Feavers; Martin C J Maiden
Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design.
Infection and immunity 2004;72(10):5955-62.
2004: Laura A Shackelton; Edward C Holmes
The evolution of large DNA viruses: combining genomic information of viruses and their hosts.
Trends in microbiology 2004;12(10):458-65.
2004: Edward C Holmes
Adaptation and immunity.
PLoS biology 2004;2(9):E307.
2004: Edward C Holmes; Andrew Rambaut
Viral evolution and the emergence of SARS coronavirus.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2004;359(1447):1059-65.
2004: Rika Draenert; Sylvie Le Gall; Katja Pfafferott; Alasdair Leslie; Polan Chetty; Christian Brander; Edward C Holmes; Shih-Chung Chang; Margaret E Feeney; Marylyn M Addo; Lidia Ruiz; Danni Ramduth; Prakash Jeena; Marcus Altfeld; Stephanie Thomas; Yanhua Tang; Cori L Verrill; Catherine Dixon; Julia G Prado; Photini Kiepiela; Javier Martinez-Picado; Bruce D Walker; Philip J R Goulder
Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection.
The Journal of experimental medicine 2004;199(7):905-15.
2004: Oliver E Barnett; Michael Worobey; Edward C Holmes; Alan Cooper
Detection of TT virus among chimpanzees in the wild using a noninvasive technique.
Journal of wildlife diseases 2004;40(2):230-7.
2004: Isabelle Sheridan; Oliver G Pybus; Edward C Holmes; Paul Klenerman
High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression.
Journal of virology 2004;78(7):3447-54.
2004: Edward C Holmes
The phylogeography of human viruses.
Molecular ecology 2004;13(4):745-56.
2004: Edward C Holmes
Virology. 1918 and all that.
Science (New York, N.Y.) 2004;303(5665):1787-8.
2004: Alasdair Leslie; Katja Pfafferott; Polan Chetty; Rika Draenert; Marylyn M Addo; Margaret E Feeney; Yanhua Tang; Edward C Holmes; Todd Allen; Julia G Prado; Marcus Altfeld; Christian Brander; C Dixon; Danni Ramduth; Prakash Jeena; S A Thomas; A St John; Timothy Roach; B Kupfer; Graz Luzzi; Anne Edwards; G Taylor; Hermione Lyall; Gareth Tudor-Williams; Vas Novelli; Javier Martinez-Picado; Photini Kiepiela; Bruce D Walker; Philip J R Goulder
HIV evolution: CTL escape mutation and reversion after transmission.
Nature medicine 2004;10(3):282-9.
2004: Andrew Rambaut; David Posada; Keith A Crandall; Edward C Holmes
The causes and consequences of HIV evolution.
Nature reviews. Genetics 2004;5(1):52-61.
2003: Edward C Holmes
Error thresholds and the constraints to RNA virus evolution.
Trends in microbiology 2003;11(12):543-6.
2003: Edward C Holmes
Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus.
Journal of virology 2003;77(20):11296-8.
2003: Elizabeth R Chare; Ernest A Gould; Edward C Holmes
Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses.
The Journal of general virology 2003;84(Pt 10):2691-703.
2003: S Susanna Twiddy; Oliver G Pybus; Edward C Holmes
Comparative population dynamics of mosquito-borne flaviviruses.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2003;3(2):87-95.
2003: Edward C Holmes; Ann F C Roberts; Karen Staines; Shirley A Ellis
Evolution of major histocompatibility complex class I genes in Cetartiodactyls.
Immunogenetics 2003;55(4):193-202.
2003: Edward C Holmes; S Susanna Twiddy
The origin, emergence and evolutionary genetics of dengue virus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2003;3(1):19-28.
2003: Polly R Walker; Michael Worobey; Andrew Rambaut; Edward C Holmes; Oliver G Pybus
Epidemiology: Sexual transmission of HIV in Africa.
Nature 2003;422(6933):679.
2003: Tomoko Isobe; Edward C Holmes; Gloria Rudenko
The transferrin receptor genes of Trypanosoma equiperdum are less diverse in their transferrin binding site than those of the broad-host range Trypanosoma brucei.
Journal of molecular evolution 2003;56(4):377-86.
2003: Scott Craig; Hlaing Myat Thu; Kym Lowry; Xiao-fang Wang; Edward C Holmes; John Aaskov
Diverse dengue type 2 virus populations contain recombinant and both parental viruses in a single mosquito host.
Journal of virology 2003;77(7):4463-7.
2003: Edward C Holmes
Molecular clocks and the puzzle of RNA virus origins.
Journal of virology 2003;77(7):3893-7.
2003: Gareth M Jenkins; Edward C Holmes
The extent of codon usage bias in human RNA viruses and its evolutionary origin.
Virus research 2003;92(1):1-7.
2003: S Susanna Twiddy; Edward C Holmes
The extent of homologous recombination in members of the genus Flavivirus.
The Journal of general virology 2003;84(Pt 2):429-40.
2003: Ernest A Gould; Xavier de Lamballerie; Pablo M Zanotto; Edward C Holmes
Origins, evolution, and vector/host coadaptations within the genus Flavivirus.
Advances in virus research 2003;59():277-314.
2003: S Susanna Twiddy; Edward C Holmes; Andrew Rambaut
Inferring the rate and time-scale of dengue virus evolution.
Molecular biology and evolution 2003;20(1):122-9.
2002: Oliver G Pybus; Andrew Rambaut; Edward C Holmes; Paul H Harvey
New inferences from tree shape: numbers of missing taxa and population growth rates.
Systematic biology 2002;51(6):881-8.
2002: Rachel Urwin; Edward C Holmes; Andrew J Fox; Jeremy P Derrick; Martin C J Maiden
Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB.
Molecular biology and evolution 2002;19(10):1686-94.
2002: V Wittke; T E Robb; Hlaing Myat Thu; Ananda Nisalak; Suchitra Nimmannitya; S Kalayanrooj; David W Vaughn; Timothy Endy; Edward C Holmes; John Aaskov
Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period.
Virology 2002;301(1):148-56.
2002: S Susanna Twiddy; Christopher H Woelk; Edward C Holmes
Phylogenetic evidence for adaptive evolution of dengue viruses in nature.
The Journal of general virology 2002;83(Pt 7):1679-89.
2002: S Susanna Twiddy; Jeremy J Farrar; Nguyen Vinh Chau; Bridget Wills; Ernest A Gould; Tamara S Gritsun; Graham Lloyd; Edward C Holmes
Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus.
Virology 2002;298(1):63-72.
2002: Christopher H Woelk; Oliver G Pybus; Li Jin; David W G Brown; Edward C Holmes
Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections.
The Journal of general virology 2002;83(Pt 6):1419-30.
2002: Gareth M Jenkins; Andrew Rambaut; Oliver G Pybus; Edward C Holmes
Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.
Journal of molecular evolution 2002;54(2):156-65.
2002: Aaron C Brault; Ann M Powers; Edward C Holmes; C H Woelk; Scott C Weaver
Positively charged amino acid substitutions in the e2 envelope glycoprotein are associated with the emergence of venezuelan equine encephalitis virus.
Journal of virology 2002;76(4):1718-30.
2002: Edward C Holmes; Christopher H Woelk; Raid Kassis; Hervé Bourhy
Genetic constraints and the adaptive evolution of rabies virus in nature.
Virology 2002;292(2):247-57.
2002: David Posada; Keith A Crandall; Edward C Holmes
Recombination in evolutionary genomics.
Annual review of genetics 2002;36():75-97.
2001: Philip J R Goulder; C Pasquier; Edward C Holmes; B Liang; Y Tang; J Izopet; K Saune; E S Rosenberg; S K Burchett; K McIntosh; M C N M Barnardo; M Bunce; Bruce D Walker; Christian Brander; Rodney E Phillips
Mother-to-child transmission of HIV infection and CTL escape through HLA-A2-SLYNTVATL epitope sequence variation.
Immunology letters 2001;79(1-2):109-16.
2001: Christopher H Woelk; Li Jin; Edward C Holmes; David W G Brown
Immune and artificial selection in the haemagglutinin (H) glycoprotein of measles virus.
The Journal of general virology 2001;82(Pt 10):2463-74.
2001: Oliver G Pybus; Michael A Charleston; Sunetra Gupta; Andrew Rambaut; Edward C Holmes; Paul H Harvey
The epidemic behavior of the hepatitis C virus.
Science (New York, N.Y.) 2001;292(5525):2323-5.
2001: Gareth M Jenkins; Michael Worobey; Christopher H Woelk; Edward C Holmes
Evidence for the non-quasispecies evolution of RNA viruses [corrected].
Molecular biology and evolution 2001;18(6):987-94.
2001: Edward C Holmes
On the origin and evolution of the human immunodeficiency virus (HIV).
Biological reviews of the Cambridge Philosophical Society 2001;76(2):239-54.
2001: Andrew Rambaut; David L Robertson; Oliver G Pybus; M Peeters; Edward C Holmes
Human immunodeficiency virus. Phylogeny and the origin of HIV-1.
Nature 2001;410(6832):1047-8.
2001: Gareth M Jenkins; M Pagel; Ernest A Gould; P M de A Zanotto; Edward C Holmes
Evolution of base composition and codon usage bias in the genus Flavivirus.
Journal of molecular evolution 2001;52(4):383-90.
2001: Anthony D Kelleher; C Long; Edward C Holmes; Rachel Allen; J Wilson; Christopher Conlon; Cassy Workman; Sunil Shaunak; Kara Olson; Philip J R Goulder; Christian Brander; Graham S Ogg; John Sullivan; Wayne B Dyer; I Jones; Andrew J McMichael; Sarah Rowland-Jones; Rodney E Phillips
Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses.
The Journal of experimental medicine 2001;193(3):375-86.
2001: Christopher H Woelk; Edward C Holmes
Variable immune-driven natural selection in the attachment (G) glycoprotein of respiratory syncytial virus (RSV).
Journal of molecular evolution 2001;52(2):182-92.
2001: Michael Worobey; Edward C Holmes
Homologous recombination in GB virus C/hepatitis G virus.
Molecular biology and evolution 2001;18(2):254-61.
2001: Edward J Feil; Edward C Holmes; Debra E Bessen; Man-Suen Chan; Nicholas P J Day; Mark Enright; Richard Goldstein; Derek W Hood; Awdhesh Kalia; Catrin E Moore; J Zhou; Brian G Spratt
Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(1):182-7.
2001: Ernest A Gould; Xavier de Lamballerie; Pablo M Zanotto; Edward C Holmes
Evolution, epidemiology, and dispersal of flaviviruses revealed by molecular phylogenies.
Advances in virus research 2001;57():71-103.
2001: Keith T Ballingall; L Waibochi; Edward C Holmes; C H Woelk; Niall D MacHugh; Vittoria Lutje; Declan J McKeever
The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive natural selection.
Immunogenetics 2001;52(3-4):276-83.
2000: Simona De Michelis; Henna-Sisko Sewell; Maria Luisa Jorge Vieira; Margarida Santos-Reis; L M Schouls; V Benes; Edward C Holmes; Klaus Kurtenbach
Genetic diversity of Borrelia burgdorferi sensu lato in ticks from mainland Portugal.
Journal of clinical microbiology 2000;38(6):2128-33.
2000: Edward C Holmes; S S Burch
The causes and consequences of genetic variation in dengue virus.
Trends in microbiology 2000;8(2):74-7.
2000: Gareth M Jenkins; Christopher H Woelk; Andrew Rambaut; Edward C Holmes
Testing the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta virus.
Journal of molecular evolution 2000;50(1):98-102.
1999: Shirley A Ellis; Edward C Holmes; Karen Staines; K B Smith; Michael J Stear; Declan J McKeever; Niall D MacHugh; W Ivan Morrison
Variation in the number of expressed MHC genes in different cattle class I haplotypes.
Immunogenetics 1999;50(5-6):319-28.
1999: V Proutski; Tamara S Gritsun; Ernest A Gould; Edward C Holmes
Biological consequences of deletions within the 3'-untranslated region of flaviviruses may be due to rearrangements of RNA secondary structure.
Virus research 1999;64(2):107-23.
1999: Michael Worobey; Edward C Holmes
Evolutionary aspects of recombination in RNA viruses.
The Journal of general virology 1999;80 ( Pt 10)():2535-43.
1999: Edward C Holmes; Shirley A Ellis
Evolutionary history of MHC class I genes in the mammalian order Perissodactyla.
Journal of molecular evolution 1999;49(3):316-24.
1999: Oliver G Pybus; Edward C Holmes; Paul H Harvey
The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history.
Molecular biology and evolution 1999;16(7):953-9.
1999: P L Bollyky; Edward C Holmes
Reconstructing the complex evolutionary history of hepatitis B virus.
Journal of molecular evolution 1999;49(1):130-41.
1999: Michael Worobey; Andrew Rambaut; Edward C Holmes
Widespread intra-serotype recombination in natural populations of dengue virus.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(13):7352-7.
1999: Edward C Holmes; Rachel Urwin; Martin C J Maiden
The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis.
Molecular biology and evolution 1999;16(6):741-9.
1999: Edward C Holmes; Michael Worobey; Andrew Rambaut
Phylogenetic evidence for recombination in dengue virus.
Molecular biology and evolution 1999;16(3):405-9.
1999: NC Grassly; Paul H Harvey; Edward C Holmes
Population dynamics of HIV-1 inferred from gene sequences.
Genetics 1999;151(2):427-38.
1998: Edward C Holmes
Molecular epidemiology and evolution of emerging infectious diseases.
British medical bulletin 1998;54(3):533-43.
1997: G F Gao; Pablo M Zanotto; Edward C Holmes; Hugh W Reid; Ernest A Gould
Molecular variation, evolution and geographical distribution of louping ill virus.
Acta virologica 1997;41(5):259-68.
1997: V Proutski; M W Gaunt; Ernest A Gould; Edward C Holmes
Secondary structure of the 3'-untranslated region of yellow fever virus: implications for virulence, attenuation and vaccine development.
The Journal of general virology 1997;78 ( Pt 7)():1543-9.
1997: Tamara S Gritsun; K Venugopal; Pablo M Zanotto; Michael V Mikhailov; Amadou A Sall; Edward C Holmes; I Polkinghorne; TV Frolova; VV Pogodina; VA Lashkevich; Ernest A Gould
Complete sequence of two tick-borne flaviviruses isolated from Siberia and the UK: analysis and significance of the 5' and 3'-UTRs.
Virus research 1997;49(1):27-39.
1997: V Proutski; Ernest A Gould; Edward C Holmes
Secondary structure of the 3' untranslated region of flaviviruses: similarities and differences.
Nucleic acids research 1997;25(6):1194-202.
1997: NC Grassly; Edward C Holmes
A likelihood method for the detection of selection and recombination using nucleotide sequences.
Molecular biology and evolution 1997;14(3):239-47.
1996: Pablo M Zanotto; M J Gibbs; Ernest A Gould; Edward C Holmes
A reevaluation of the higher taxonomy of viruses based on RNA polymerases.
Journal of virology 1996;70(9):6083-96.
1996: V Proutski; Edward C Holmes
Primer Master: a new program for the design and analysis of PCR primers.
Computer applications in the biosciences : CABIOS 1996;12(3):253-5.
1996: Stephen E Kearsey; Domenico Maiorano; Edward C Holmes; I T Todorov
The role of MCM proteins in the cell cycle control of genome duplication.
BioEssays : news and reviews in molecular, cellular and developmental biology 1996;18(3):183-90.
1996: P L Bollyky; Andrew Rambaut; Paul H Harvey; Edward C Holmes
Recombination between sequences of hepatitis B virus from different genotypes.
Journal of molecular evolution 1996;42(2):97-102.
1996: Pablo M Zanotto; Ernest A Gould; G F Gao; P H Harvey; Edward C Holmes
Population dynamics of flaviviruses revealed by molecular phylogenies.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(2):548-53.
1995: Edward C Holmes; Sean Nee; Andrew Rambaut; Geoff P Garnett; Paul H Harvey
Revealing the history of infectious disease epidemics through phylogenetic trees.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1995;349(1327):33-40.
1995: Sean Nee; Edward C Holmes; Andrew Rambaut; Paul H Harvey
Inferring population history from molecular phylogenies.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1995;349(1327):25-31.
1994: Paul H Harvey; Edward C Holmes; Sean Nee
Model phylogenies to explain the real world.
BioEssays : news and reviews in molecular, cellular and developmental biology 1994;16(10):767-70.
1994: Edward C Holmes; Geoff P Garnett
Genes, trees and infections: Molecular evidence in epidemiology.
Trends in ecology & evolution 1994;9(7):256-60.
1994: Sean Nee; Edward C Holmes; Robert M May; Paul H Harvey
Extinction rates can be estimated from molecular phylogenies.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1994;344(1307):77-82.