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Papers authored by Pybus OG

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Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection.

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Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Gaudieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, and Barnes E

Journal of virology 83(22):11456-66, 2009 Nov - Who cited this? | PubMed ID: 19740991 | Fulltext

Macroevolution of complex retroviruses.

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Katzourakis A, Gifford RJ, Tristem M, Gilbert MT, and Pybus OG

Science (New York, N.Y.) 325(5947):1512, 2009 Sep 18 - Who cited this? | PubMed ID: 19762636 | Fulltext

Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa.

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Markov PV, Pepin J, Frost E, Deslandes S, Labbé AC, and Pybus OG

The Journal of general virology 90(Pt 9):2086-96, 2009 Sep - Who cited this? | PubMed ID: 19474244 | Fulltext

Phylodynamic analysis of the dissemination of HIV-1 CRF01_AE in Vietnam.

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Liao H, Tee KK, Hase S, Uenishi R, Li XJ, Kusagawa S, Thang PH, Hien NT, Pybus OG, and Takebe Y

Virology 391(1):51-6, 2009 Aug 15 - Who cited this? | PubMed ID: 19540543 | Fulltext

Evolutionary analysis of the dynamics of viral infectious disease.

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Pybus OG and Rambaut A

Nature reviews. Genetics 10(8):540-50, 2009 Aug - Who cited this? | PubMed ID: 19564871 | Fulltext

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.

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Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvão-Castro B, Vandamme AM, and de Oliveira T

Nucleic acids research 37(Web Server issue):W634-42, 2009 Jul 1 - Who cited this? | PubMed ID: 19483099 | Fulltext

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.

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Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, and Rambaut A

Nature 459(7250):1122-5, 2009 Jun 25 - Who cited this? | PubMed ID: 19516283 | Fulltext

Pandemic potential of a strain of influenza A (H1N1): early findings.

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Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM,

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Science (New York, N.Y.) 324(5934):1557-61, 2009 Jun 19 - Who cited this? | PubMed ID: 19433588 | Fulltext

HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering.

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Matthews PC, Leslie AJ, Katzourakis A, Crawford H, Payne R, Prendergast A, Power K, Kelleher AD, Klenerman P, Carlson J, Heckerman D, Ndung'u T, Walker BD, Allen TM, Pybus OG, and Goulder PJ

Journal of virology 83(9):4605-15, 2009 May - Who cited this? | PubMed ID: 19244334 | Fulltext

Estimating the date of origin of an HIV-1 circulating recombinant form.

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Tee KK, Pybus OG, Parker J, Ng KP, Kamarulzaman A, and Takebe Y

Virology 387(1):229-34, 2009 Apr 25 - Who cited this? | PubMed ID: 19272628 | Fulltext

Adaptation of HIV-1 to human leukocyte antigen class I.

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Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A,

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Nature 458(7238):641-5, 2009 Apr 2 - Who cited this? | PubMed ID: 19242411 | Fulltext

Genetic history of hepatitis C virus in East Asia.

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Pybus OG, Barnes E, Taggart R, Lemey P, Markov PV, Rasachak B, Syhavong B, Phetsouvanah R, Sheridan I, Humphreys IS, Lu L, Newton PN, and Klenerman P

Journal of virology 83(2):1071-82, 2009 Jan - Who cited this? | PubMed ID: 18971279 | Fulltext

From the Cover: A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.

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Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, and Shafer RW

Proceedings of the National Academy of Sciences of the United States of America 105(51):20362-7, 2008 Dec 23 - Who cited this? | PubMed ID: 19075221 | Fulltext

High prevalence of hepatitis C virus infection and predominance of genotype 4 in rural Gabon.

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Ndong-Atome GR, Makuwa M, Ouwe-Missi-Oukem-Boyer O, Pybus OG, Branger M, Le Hello S, Boye-Cheik SB, Brun-Vezinet F, Kazanji M, Roques P, and Bisser S

Journal of medical virology 80(9):1581, 2008 Sep - Who cited this? | PubMed ID: 18649323 | Fulltext

Variable epidemic histories of hepatitis C virus genotype 2 infection in West Africa and Cameroon.

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Pouillot R, Lachenal G, Pybus OG, Rousset D, and Njouom R

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 8(5):676-81, 2008 Sep - Who cited this? | PubMed ID: 18599380 | Fulltext

Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u.

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Xia X, Zhao W, Tee KK, Feng Y, Takebe Y, Li Q, Pybus OG, and Lu L

Journal of medical virology 80(10):1740, 2008 Aug 19 - Who cited this? | PubMed ID: 18712831 | Fulltext

Evolution and dispersal of St. Louis encephalitis virus in the Americas.

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Auguste AJ, Pybus OG, and Carrington CV

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2008 Jul 29 - Who cited this? | PubMed ID: 18708161 | Fulltext

Temporal and Spatial Dynamics of the Human Immunodeficiency Virus Type 1 Circulating Recombinant Forms 08_BC and 07_BC in Asia.

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Tee KK, Pybus OG, Li XJ, Han X, Shang H, Kamarulzaman A, and Takebe Y

Journal of virology, 2008 Jul 2 - Who cited this? | PubMed ID: 18596096 | Fulltext

The genomic and epidemiological dynamics of human influenza A virus.

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Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, and Holmes EC

Nature 453(7195):615, 2008 May 29 - Who cited this? | PubMed ID: 18418375 | Fulltext

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty.

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Parker J, Rambaut A, and Pybus OG

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 8(3):239-46, 2008 May - Who cited this? | PubMed ID: 17921073 | Fulltext

Impact of HIV on Host-Virus Interactions during Early Hepatitis C Virus Infection.

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Danta M, Semmo N, Fabris P, Brown D, Pybus OG, Sabin CA, Bhagani S, Emery VC, Dusheiko GM, and Klenerman P

The Journal of infectious diseases, 2008 Apr 17 - Who cited this? | PubMed ID: 18419344 | Fulltext

Analysis of the evolutionary forces in an immunodominant CD8 epitope in hepatitis C virus at a population level.

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Neumann-Haefelin C, Frick DN, Wang JJ, Pybus OG, Salloum S, Narula GS, Eckart A, Biezynski A, Eiermann T, Klenerman P, Viazov S, Roggendorf M, Thimme R, Reiser M, and Timm J

Journal of virology 82(7):3438-51, 2008 Apr - Who cited this? | PubMed ID: 18216107 | Fulltext

Pacing a small cage: mutation and RNA viruses.

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Belshaw R, Gardner A, Rambaut A, and Pybus OG

Trends in ecology & evolution (Personal edition) 23(4):188-93, 2008 Apr - Who cited this? | PubMed ID: 18295930 | Fulltext

Chronology of the HIV-1 CRF07_BC expansion in East Asia.

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Tee KK, Pybus OG, Liao H, Uenishi R, Hase S, Kamarulzaman A, Li XJ, and Takebe Y

AIDS (London, England) 22(1):156-8, 2008 Jan 2 - Who cited this? | PubMed ID: 18090407 | Fulltext

Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia.

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Lam TT, Hon CC, Pybus OG, Kosakovsky Pond SL, Wong RT, Yip CW, Zeng F, and Leung FC

PLoS pathogens 4(8), 2008 - Who cited this? | PubMed ID: 18725937 | Fulltext

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.

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Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D, and

Journal of virology 81(23):13050, 2007 Dec - Who cited this? | PubMed ID: 17898057 | Fulltext

Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin.

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Paraskevis D, Magiorkinis E, Magiorkinis G, Sypsa V, Paparizos V, Lazanas M, Gargalianos P, Antoniadou A, Panos G, Chrysos G, Sambatakou H, Karafoulidou A, Skoutelis A, Kordossis T, Koratzanis G, Theodoridou M,

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The Journal of infectious diseases 196(8):1167-76, 2007 Oct 15 - Who cited this? | PubMed ID: 17955435 | Fulltext

The evolution of genome compression and genomic novelty in RNA viruses.

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Belshaw R, Pybus OG, and Rambaut A

Genome research 17(10):1496, 2007 Oct - Who cited this? | PubMed ID: 17785537 | Fulltext

Investigating the endemic transmission of the hepatitis C virus.

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Pybus OG, Markov PV, Wu A, and Tatem AJ

International journal for parasitology 37(8-9):839-49, 2007 Jul - Who cited this? | PubMed ID: 17521655 | Fulltext

Recent epidemic of acute hepatitis C virus in HIV-positive men who have sex with men linked to high-risk sexual behaviours.

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Danta M, Brown D, Bhagani S, Pybus OG, Sabin CA, Nelson M, Fisher M, Johnson AM, Dusheiko GM, and HIV and Acute HCV (HAAC) group

AIDS (London, England) 21(8):983-91, 2007 May 11 - Who cited this? | PubMed ID: 17457092 | Fulltext

Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses.

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Lu L, Li C, Fu Y, Thaikruea L, Thongswat S, Maneekarn N, Apichartpiyakul C, Hotta H, Okamoto H, Netski D, Pybus OG, Murphy D, Hagedorn CH, and Nelson KE

The Journal of general virology 88(Pt 5):1505, 2007 May - Who cited this? | PubMed ID: 17412980 | Fulltext

Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6.

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Lu L, Li C, Fu Y, Gao F, Pybus OG, Abe K, Okamoto H, Hagedorn CH, and Murphy D

The Journal of general virology 88(Pt 5):1519-25, 2007 May - Who cited this? | PubMed ID: 17412981 | Fulltext

The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types.

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Recker M, Pybus OG, Nee S, and Gupta S

Proceedings of the National Academy of Sciences of the United States of America 104(18):7711-6, 2007 May 1 - Who cited this? | PubMed ID: 17460037 | Fulltext

Discovery and analysis of the first endogenous lentivirus.

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Katzourakis A, Tristem M, Pybus OG, and Gifford RJ

Proceedings of the National Academy of Sciences of the United States of America 104(15):6261-5, 2007 Apr 10 - Who cited this? | PubMed ID: 17384150 | Fulltext

Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.

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Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, and Holmes EC

Molecular biology and evolution 24(3):845, 2007 Mar - Who cited this? | PubMed ID: 17218639 | Fulltext

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

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Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, and Rambaut A

PLoS computational biology 3(2):e29, 2007 Feb 16 - Who cited this? | PubMed ID: 17305421 | Fulltext

Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages.

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Saarma U, Ho SY, Pybus OG, Kaljuste M, Tumanov IL, Kojola I, Vorobiev AA, Markov NI, Saveljev AP, Valdmann H, Lyapunova EA, Abramov AV, Männil P, Korsten M, Vulla E, Pazetnov SV,

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Molecular ecology 16(2):401-13, 2007 Jan - Who cited this? | PubMed ID: 17217353 | Fulltext

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak.

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de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D'Arrigo R, Amicosante M, Perrin L, Colizzi V, Perno CF, and Benghazi Study Group

Nature 444(7121):836-7, 2006 Dec 14 - Who cited this? | PubMed ID: 17171825 | Fulltext

Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.

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Edwards CT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, and Drummond AJ

Genetics 174(3):1441-53, 2006 Nov - Who cited this? | PubMed ID: 16951087 | Fulltext

JC virus evolution and its association with human populations.

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Shackelton LA, Rambaut A, Pybus OG, and Holmes EC

Journal of virology 80(20):9928-33, 2006 Oct - Who cited this? | PubMed ID: 17005670 | Fulltext

A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.

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Shapiro B, Rambaut A, Pybus OG, and Holmes EC

Molecular biology and evolution 23(9):1724-30, 2006 Sep - Who cited this? | PubMed ID: 16774976 | Fulltext

Investigating the origin and spread of hepatitis C virus genotype 5a.

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Verbeeck J, Maes P, Lemey P, Pybus OG, Wollants E, Song E, Nevens F, Fevery J, Delport W, Van der Merwe S, and Van Ranst M

Journal of virology 80(9):4220-6, 2006 May - Who cited this? | PubMed ID: 16611881 | Fulltext

Model selection and the molecular clock.

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Pybus OG

PLoS biology 4(5):e151, 2006 May - Who cited this? | PubMed ID: 16683863 | Fulltext

Do antiviral CD8+ T cells select hepatitis C virus escape mutants? Analysis in diverse epitopes targeted by human intrahepatic CD8+ T lymphocytes.

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Komatsu H, Lauer G, Pybus OG, Ouchi K, Wong D, Ward S, Walker B, and Klenerman P

Journal of viral hepatitis 13(2):121-30, 2006 Feb - Who cited this? | PubMed ID: 16436130 | Fulltext

Population genetic history of hepatitis C virus 1b infection in China.

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Nakano T, Lu L, He Y, Fu Y, Robertson BH, and Pybus OG

The Journal of general virology 87(Pt 1):73-82, 2006 Jan - Who cited this? | PubMed ID: 16361419 | Fulltext

HIV evolutionary dynamics within and among hosts.

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Lemey P, Rambaut A, and Pybus OG

AIDS reviews 8(3):125-40, 2006 - Who cited this? | PubMed ID: 17078483 | Fulltext

Invasion and maintenance of dengue virus type 2 and type 4 in the Americas.

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Carrington CV, Foster JE, Pybus OG, Bennett SN, and Holmes EC

Journal of virology 79(23):14680-7, 2005 Dec - Who cited this? | PubMed ID: 16282468 | Fulltext

The evolutionary dynamics of endogenous retroviruses.

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Katzourakis A, Rambaut A, and Pybus OG

Trends in microbiology 13(10):463-8, 2005 Oct - Who cited this? | PubMed ID: 16109487 | Fulltext

Host switch leads to emergence of Plasmodium vivax malaria in humans.

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Mu J, Joy DA, Duan J, Huang Y, Carlton J, Walker J, Barnwell J, Beerli P, Charleston MA, Pybus OG, and Su XZ

Molecular biology and evolution 22(8):1686-93, 2005 Aug - Who cited this? | PubMed ID: 15858201 | Fulltext

Bayesian coalescent inference of past population dynamics from molecular sequences.

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Drummond AJ, Rambaut A, Shapiro B, and Pybus OG

Molecular biology and evolution 22(5):1185-92, 2005 May - Who cited this? | PubMed ID: 15703244 | Fulltext

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