Room C31

Department of Zoology

University of Oxford

South Parks Road

Oxford

OX1 3PS, UK

(Email)

I investigate the evolutionary and ecological dynamics of infectious diseases, particularly pathogenic RNA viruses. My current research concerns (i) the molecular epidemiology and epidemic history of HIV and the hepatitis C virus, (ii) viral adaptation and natural selection, (iii) the evolutionary behaviour of influenza, (iv) the evolution of endogenous retroviruses, and (v) phylogenetic and population genetic methods of gene sequence analysis. More generally, I am interested in topics at the interface between ecology and evolution including adaptive radiation, speciation, and molecular ecology.

I am Tutor in Biological Sciences at New College.

I am an editor of PLoS Pathogens, Molecular Biology & Evolution, and Methods in Ecology & Evolution.

I have been awarded the Scientific Medal of the Zoological Society of London and the Daiwa Adrian Prize for my research.

2012

Pybus OG*, Perrins CM*, Manvell RJ*, Schulenburg B, Sheldon B, Brown IH. The age structure of a highly pathogenic avian influenza virus outbreak in wild mute swans. Parasitology In press

Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A, Pybus OG. The origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b. Journal of Virology In press

Lam TTY, Zhu H, Smith DK, Guan Y, Holmes EC, Pybus OG. The recombinant origin of emerging human norovirus GII.4/2008: intra-genotypic exchange of the capsid P2 domain. Journal of General Virology In press

Baille GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, Palser AL, Watson SJ, Hedge J, Underwood A, Platt S, Mclean E, Pebody RG, Rambaut A, Green J, Daniels R, Pybus OG*, Kellam P*, Zambon M*. Evolutionary dynamics of local pandemic H1N1/09 influenza lineages revealed by whole genome analysis. Journal of Virology 86:11-8

Allicock OM, Lemey P, Tatum AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CVF. Phylogeography and population dynamics of Dengue viruses in the Americas. Molecular Biology & Evolution In press

Lavoie M, Sharp CP, Pépin J, Pennington C, Njouom R, Pybus OG, Foupouapouognigni Y, Simmonds P. Epidemiology of human parvovirus-4 infection, Cameroon. Emerging Infectious Diseases In press

2011

Vijaykrishna D*, Smith GJD*, Pybus OG*, Zhu H, Bhatt S, Poon LLM, Riley S, Bahl J, Ma SK, Cheung CL, Perera RAP, Chen H, Shortridge KF, Webby RJ, Webster RG, Guan Y, Peiris J. Long-term evolution and transmission dynamics of swine influenza A virus. Nature 473:519-222

Bhatt S, Holmes EC, Pybus OG. The genomic rate of molecular adaptation of the human influenza A virus. Molecular Biology & Evolution 28:2443-51

Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131

Belshaw R, Sanjuan R, Pybus OG. Viral mutation and substitution: units and levels. Current Opinion in Virology 1:430-5

Barnes I, Duda A, Pybus OG, Thomas MG. Ancient urbanisation predicts genetic resistance to tuberculosis. Evolution 65:842-8

Gray RR, Tatem AJ, Johnson JA, Alexseyenko AV, Pybus OG, Suchard MA, Salemi M. Testing spatiotemporal hypotheses of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework. Molecular Biology & Evolution 28:1593-603

Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A Bayesian phylogenetic method to estimate unknown sequence ages. Molecular Biology & Evolution 28:879-87

Nakano T, Takahashi K, Pybus OG, Hashimoto N, Kato H, Okano H, Kobayashi M, Fujita N, Shiraki K, Takei Y, Ayada M, Arai M, Okamoto H, Mishiro S. New findings regarding the epidemic history and population dynamics of Japan-indigenous genotype 3 hepatitis E virus inferred by molecular evolution. Liver International In press

Gray RR, Pybus OG, Salemi M. Measuring the temporal structure in serially-sampled phylogenies. Methods in Ecology & Evolution 2:437-45

Fu Y, Wang Y, Xia W, Pybus OG, Qin W, Lu L, Nelson K. New trends of HCV infection in China revealed by genetic analysis of viral sequences determined from first-time volunteer blood donors. Journal of Viral Hepatitis 18:42-52

2010

Tee KK, Lam TT, Chan YF, Bible JM, Tong W, Kamarulzaman A, Takebe Y, Pybus OG. Evolutionary genetics of human enterovirus 71: Origin, population dynamics, natural selection and periodicity of the VP1 gene. Journal of Virology 84:3339-50

Bhatt S, Katzourakis A, Pybus OG. Detecting natural selection in RNA virus populations using sequence summary statistics. Infection, Genetics & Evolution 10:421-30

Hué S, Gray ER, Gall A, Katzourakis A, Tan CP, Houldcroft C, McLaren S, Pillay D, Futreal A, Garson J, Pybus OG, Kellam P, Towers GJ. Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology 7:111

Auguste AJ, Lemey P, Pybus OG, Suchard MA, Salas RA, Adesiyun AA, Barrett AD, Tesh RB, Weaver SC, Carrington CVF. Yellow fever virus maintenance in Trinidad and its dispersal throughout the Americas. Journal of Virology 84:9967-77

Pépin J, Lavoie M, Pybus OG, Pouillot R, Foupouapouognigni Y, Rousset D, Labbé AC, Njouom R. Risk factors for hepatitis C virus transmission in colonial Cameroon. Clinical Infectious Diseases 51:768-76

Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Muñoz-Jordan JL, Pybus OG, Holmes EC, Gubler DJ. Epidemic dynamics revealed in dengue evolution. Molecular Biology & Evolution 27:811-8

Sharp CP, LeBreton M, Kantola K, Nana A, et al. Widespread infection with homologues of human parvoviruses B19, PARV4, and human bocavirus of chimpanzees and gorillas in the wild. Journal of Virology 84:10289-96

Huang KH, Bonsall D, Katzourakis A, Thomson EC, et al. B cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection. Nature Communications 1:102

Sharp CP, Vermeulen M, Nébié Y, Djoko CK, et al. Epidemiology of human parvovirus 4 infection in sub-Saharan Africa. Emerging Infectious Diseases 16:1605-07

Sahin GO, Bowles EJ, Parker J, Uchtenhagen H et al. Generation of neutralizing antibodies and divergence of SIVmac239 in Cynomolgus macaques following short-term early antiretroviral therapy. PLoS Pathogens 6:e1001084

Jones R, Brown D, Nelson M, Low E, Bhagani S, Atkins M, Danta M, Dusheiko G, Pybus O, Asboe D. Re-emergent hepatitis C viremia after apparent clearance in HIV-positive men who have sex with men: reinfection or late recurrence? Journal of Acquired Immune Deficiency Syndromes 53:547-50

Li Y, Uenishi R, Hase S, Liao H, Li XJ, Takayo T, Tee KK, Pybus OG, Takebe Y. Explosive HIV-1 subtype B' epidemics in Asia driven by geographic and risk group founder events. Virology 402:223-7

Fu Y, Xia W, Wang Y, Tian L, Pybus OG, Lu L, Nelson K. The seroprevalence of hepatitis C virus among 559,890 first-time volunteer blood donors in China reflects regional heterogeneity in HCV prevalence and changes in blood donor recruitment models Transfusion 50:1505-11

Li Y, Tee KK, Liao H, Hase S, Uenishi R, Li XJ, Tsuchiura T, Yang R, Govindasamy S, Yong YK, Tan HY, Pybus OG, Kamarulzaman A, Takebe Y. Identification of a novel second-generation circulating recombinant form (CRF48_01B) in Malaysia: a descendant of the previously identified CRF33_01B. Journal of Acquired Immune Deficiency Syndromes 54:129-36

Takebe Y, Liao H, Hase S, Uenishi R, Li Y, Li XJ, Han X, Shang H, Kamarulzaman A, Yamamoto N, Pybus OG, Tee KK. Reconstructing the epidemic history of HIV-1 circulating recombinant forms CRF07_BC and CRF08_BC in East Asia: the relevance of genetic diversity and phylodynamics for vaccine strategies. Vaccine 28:B39-44

2009

Katzourakis A, Gifford RJ, Tristem M, Gilbert MTP, Pybus OG. The macroevolution of complex retroviruses. Science 325:1512

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD et al. Pandemic potential of a novel strain of influenza A (H1N1): early findings. Science 324:1557-61

Smith GJD*, Vijaykrishna D*, Bahl J*, Lycett SJ*, Worobey M*, Pybus OG*, Ma SK, Cheung CM, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-5 (pdf)

Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M et al. Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458:641-5

Penman BS, Pybus OG, Weatherall DJ, Gupta S. Epistatic interactions between genetic disorders of hemoglobin can explain why the sickle cell gene in uncommon in the Mediterranean. Proceedings of the National Academy of Sciences USA 106:21242-6

Pybus OG*, Barnes E*, Taggart R, Lemey P, Markov PV, Rasachak B, Syhavong B, Rattanaphone P, Sheridan I, Humphreys IS, Lu L, Newton P, Klenerman P. The genetic history of the hepatitis C virus in East Asia. Journal of Virology 83:1071-82

Pybus OG, Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease. Nature Reviews Genetics 10:540-50

Pybus OG & Shapiro B. Natural selection and adaptation of molecular sequences. In The Phylogenetic Handbook, 2nd Edition (P. Lemey, M. Salemi, A. Vandamme, editors) pp.407-418. Cambridge University Press

Markov PV, Pepin J, Frost E, Deslandes S, Labbé AC, Pybus OG. The phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa. Journal of General Virology 90:2086-96

Tee KK*, Pybus OG*, Parker J, Ng KP, Kamarulzaman A, Takebe Y. Estimating the date of origin of an HIV-1 circulating recombinant form. Virology 387:229-34

Humphreys I, Fleming V, Fabris P, Parker J, et al. Full-length characterisation of the hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection. Journal of Virology 83:11456-66

Magiorkinis G, Magiorkinis E, Paraskevis D, Ho S, Shapiro B, Pybus OG, Allain JP, Hatzakis A. 2009. The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Medicine 6:e1000198

Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing AMJ, van de Vijver DA, et al. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology 6:49

Liao H, Tee KK, Hase S, Uenishi R, Li XJ, Kusagawa S, Thang PH, Hien NT, Pybus OG, Takebe Y. Phylodynamic analysis of the dissemination of HIV-1 CRF01_AE in Vietnam. Virology 391:51-6

Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvão-Castro B, Vandamme AM, de Oliveira T. A standardized framework for accurate high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Research 37:W634-42

Takebe Y, Liao H, Hase S, Uenishi R, Li Y, Li XJ, Han X, Shang H, Kamarulzaman A, Yamamoto N, Pybus OG, Tee KK. Reconstructing the epidemic history of HIV-1 circulating recombinant forms CRF07_BC and CRF08_BC in East Asia: the relevance of genetic diversity and phylodynamics for vaccine strategies. Vaccine In press

van de Laar T, Pybus O, Bruisten S, Brown D, Nelson M et al. Evidence of a large international HCV transmission network in HIV-positive men who have sex with men (MSM). Gastroenterology 136:1609-17

Matthews PC, Leslie A, Katzourakis A, Pfafferott K, Power K, Kelleher AD, Carlson J, Heckerman D, Walker BD, Allen TM, Pybus OG, Goulder PJR. HLA footprints in HIV-1 gag are associated with phylogenetic clustering and clade-specific amino acid polymorphism. Journal of Virology 83:4605-15

Auguste AJ, Pybus OG, Carrington CVF. Evolution and dispersal of St. Louis encephalitis virus in the Americas. Infection, Genetics & Evolution 9:709-15

2008

Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature 453:615-9

Gifford, RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of the National Academy of Sciences USA 105:20362-7

Belshaw R, Gardner A, Rambaut A, Pybus OG. Pacing a small cage: mutation and RNA viruses. Trends in Ecology & Evolution 23:188-93

Parker P, Rambaut A, Pybus OG. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics and Evolution 8:239-46

Xia X, Zhao W, Tee KK, Feng Y, Takebe Y, Li Q, Pybus OG, Lu L. Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u. Journal of Medical Virology 80:1740-6

Tee KK, Pybus OG, Li XJ, Han X, Shang H, Kamarulzaman A, Takebe Y. Temporal and spatial dynamics of the HIV-1 circulating recombinant forms 08_BC and 07_BC in Asia. Journal of Virology 82:9206-15

Lam TT, Hon CC, Pybus OG, Kosakovsky Pond SL, Wong R, Yip C, Zeng F, Leung FC. Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathogens 4:e1000130

Pouillot R, Lachenal G, Pybus OG, Rousset D, Njouom R. Variable epidemic histories of hepatitis C virus genotype 2 infection in West Africa and Cameroon. Infection, Genetics & Evolution 8:676-81

Ndong-Atome GR, Makuwa M, Ouwe-Missi-Oukem-Boyer O, Pybus OG, Branger M et al. High prevalence of hepatitis C virus infection and predominance of genotype 4 in rural Gabon. Journal of Medical Virology 80:1581-7

Neumann-Haefelin C, Frick DN, Wang JJ, Pybus OG, Salloum S et al. Analysis of the evolutionary forces in an immunodominant CD8 epitope in the hepatitis C virus at a population level. Journal of Virology 82:3438-51

Danta M, Semmo N, Fabris P, Brown D, Pybus OG, Sabin CA, Bhagani S, Emery VC, Dusheiko GM, Klenerman P. Impact of HIV on host-viral interactions during early hepatitis C virus infection. Journal of Infectious Diseases 197:1558-66

Tee KK, Pybus OG, Kamarulzaman A, Lia X-J, Takebe Y. Chronology of the HIV-1 CRF07_BC expansion in Taiwan. AIDS 22:156-8

Kelly, CK, Bowler, MG, Pybus O, Harvey PH. Phylogeny, niches and relative abundance in natural communities. Ecology 89:962-70

2007

Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, Holmes EC. Phylogenetic estimation of deleterious mutation load in RNA viruses and its contribution to viral evolution. Molecular Biology & Evolution 24:845-52

Pybus OG, Markov P, Wu A, Tatem AJ. Investigating the endemic transmission of the hepatitis C Virus. International Journal of Parasitology 37:839-49

Recker M*, Pybus OG*, Nee S, Gupta S. The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types. Proceedings of the National Academy of Sciences USA 104:7711-6

Katzourakis A, Tristem M, Pybus OG, Gifford RJ. Discovery and analysis of the first endogenous lentivirus. Proceedings of the National Academy of Sciences USA 104:6261-5

Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme A-M, Kellam P, Pillay D. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of HIV-1. Journal of Virology 81:13050-6

Belshaw R, Pybus OG, Rambaut A. The evolution of genome compression and genomic novelty in RNA viruses. Genome Biology 17:1496-504

Paraskevis D, Magiorkinis E, Magiorkinis G, Sypsa V, Paparizos V et al. Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin. Journal of Infectious Diseases 196:1167-76

Lu L, Li C, Fu Y, Thaikruea L, Thongswat S, Maneekarn N et al. Complete genomes for Hepatitis C Virus subtypes 6f, 6i, 6j, and 6m: viral genetic diversity among Thai blood donors and infected spouses. Journal of General Virology 88:1505-18

Lu L, Li C, Fu Y, Gao F, Pybus OG, Abe K et al. 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. Journal of General Virology 88:1519-25

Danta M, Brown D, Bhagani S, Pybus OG, Sabin CA et al. Recent epidemic of acute hepatitis C virus in HIV-positive men who have sex with men linked to high-risk sexual behaviours. AIDS 21:983-91

Lemey P, Kosakovsky Pond S, Drummond AJ, Pybus OG, Shapiro B, Taveira N, Rambaut A. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Computational Biology 3:282-92

Saarma U, Ho SYW, Pybus OG, Kaljuste M, Tumanov IL, Kojola I et al. Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages. Molecular Ecology 16:401-413

2006

de Oliveira T*, Pybus OG*, Rambaut A*, Salemi M, Cassol S et al. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 444:836-7

Pybus OG. Model selection and the molecular clock. PLoS Biology 4:686-8

Nakano T, Lu L, He Y, Fu Y, Robertson BH, Pybus OG. Population genetic history of hepatitis C virus 1b infection in China. Journal of General Virology 87:73-82

Lemey P, Rambaut A, Pybus OG. HIV evolutionary dynamics within and among hosts. AIDS Reviews 8:125-40

Shackelton LA, Rambaut A, Pybus OG, Holmes EC. JC virus evolution and its association with human populations. Journal of Virology 80:9928-33

Edwards CTT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ. Evolution of the human immunodeficiency virus envelope gene evolution is dominated by purifying selection. Genetics 174:1441-53

Shapiro B, Rambaut A, Pybus OG, Holmes EC. A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Molecular Biology & Evolution 23:1724-30

Verbeeck J, Maes P, Lemey P, Pybus OG, Wollants E, Song E, Nevens F, Fevery J, Delport W, Van der Merwe S, Van Ranst M. Investigating the origin and spread of hepatitis C virus genotype 5a. Journal of Virology 80:4220-6

Alcantara LC, de Oliveira  T, Gordon M, Pybus O, Mascarenhas RE, Seixas MO, Goncalves M, Hlela C, Cassol S, Galvao-Castro B. Tracing the origins of Brazilian HTLV-I as determined by analysis of host and viral genes. AIDS 20:780-2

Neumann-Haefelin C, McKiernan S, Ward S, Viazov S, Spangenberg HC et al. Dominant influence of an HLA-B27 restricted virus-specific CD8+ T cell response mediating HCV clearance and evolution. Hepatology 43:563-72

Komatsu H, Lauer G, Pybus OG, Ouchi K, Wong D, Ward S, Walker B, Klenerman P. Do antiviral CD8+ T cells select hepatitis C virus escape mutants? Analysis in diverse epitopes targeted by human intrahepatic CD8+ T lymphocytes. Journal of Viral Hepatitis 13:121-30

2005

Hué S, Pillay D, Clewley J, Pybus OG. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proceedings of the National Academy of Sciences USA 102:4425-9

Pybus OG*, Cochrane A*, Holmes EC, Simmonds P. The hepatitis C virus epidemic among injecting drug users. Infection, Genetics & Evolution 5:131-9

Katzourakis A, Rambaut A, Pybus OG. The evolutionary dynamics of endogenous retroviruses. Trends in Microbiology 13:463-8

Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology & Evolution 22:1185-92

Carrington CV, Foster JE, Pybus OG, Bennett SN, Holmes EC. Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. Journal of Virology 79:14680-7

Mu J, Joy DA, Duan J, Huang Y, Carlton J et al. Host switch leads to emergence of Plasmodium vivax malaria in humans. Molecular Biology & Evolution 22:1686-93

Walker PR, Pybus OG, Rambaut A, Holmes EC. Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. Infection, Genetics & Evolution 5:199-208

Salemi M, de Oliveira T, Soares MA, Pybus O, Dumans AT, Vandamme AM, Tanuri A, Cassol S, Fitch WM. Different epidemic potentials of the HIV-1 B and C subtypes. Journal of Molecular Evolution 60:598-605

Lemey P, Pybus OG, Van Dooren S, Vandamme AM. A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates. Infection, Genetics & Evolution 5:291-8

2004

Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303:327-32

Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I et al. Rise and fall of the Beringian steppe bison. Science 306:1561-5

Nakano T, Lu L, Liu P, Pybus OG. Viral gene sequences reveal the variable history of hepatitis C virus infection among countries. Journal of Infectious Disease 190:1098-108

Flanagan NS, Tobler A, Davidson A, Pybus OG, Kapan DD, Planas S, Linares M, Heckel D, McMillan WO. Historical demography of Müllerian mimicry in the neotropical Heliconius butterflies. Proceedings of the National Academy of Sciences USA 101:9704-9

Lemey P, Pybus OG, Rambaut A, Drummond AJ, Roques P, Worobey M, Vandamme AM. The molecular population genetics of HIV-1 group O. Genetics 167:1059-68

Sheridan I, Pybus OG, Holmes EC, Klenerman P. High resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression. Journal of Virology 78:3447-54

Van Dooren S, Pybus OG, Salemi M, Liu HF, Goubau P et al. The low evolutionary rate of human T-cell lymphotropic virus type-1 confirmed by analysis of vertical transmission chains. Molecular Biology & Evolution 21:603-11

Le Goff-Vitry MC, Pybus OG, Rogers AD. Genetic structure of the deep-sea coral Lophelia pertusa in the northeast Atlantic revealed by microsatellites and internal transcribed spacer sequences. Molecular Ecology 13:537-49

2003

Walker P, Worobey M, Rambaut A, Holmes EC, Pybus OG. Sexual transmission of HIV in Africa. Nature 422:679

Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A. The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Molecular Biology & Evolution 20:381-7

Lemey P, Pybus OG, Wang B, Saksena NK, Salemi M, Vandamme AM. Tracing the origin and history of the HIV-2 epidemic. Proceedings of the National Academy of Sciences USA 100:6588-92

Drummond AJ, Pybus OG, Rambaut A. Inference of viral evolutionary rates from molecular sequences. Advances in Parasitology 54:331-58

Ndjomou J, Pybus OG, Matz, B. Phylogenetic analysis of hepatitis C virus (HCV) isolates indicates a unique pattern of endemic infection in Cameroon. Journal of General Virology 84:2333-41

Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo A. Measurably evolving populations. Trends in Ecology & Evolution 18:481-8

Twiddy SS, Pybus OG, Holmes EC. Comparative population dynamics of the mosquito-borne flaviviruses. Infection, Genetics & Evolution 3:87-95

Robbins KE, Lemey P, Pybus OG, Jaffe HW, Youngpairoj AS, Brown TM, Salemi M, Vandamme AM, Kalish ML. U.S. human immunodeficiency virus type 1 epidemic: date of origin, population history, & characterization of early strains. Journal of Virology 77:6359-66

2002

Pybus OG, Rambaut A, Holmes EC, Harvey PH. New inferences from tree shape: numbers of missing taxa and population growth rates. Systematic Biology 51:881-8

Pybus OG, Rambaut. A. GENIE: Estimating demographic history from molecular phylogenies. Bioinformatics 18:1404-5

Worobey M, Rambaut A, Pybus OG, Robertson DL. Questioning the evidence for genetic recombination in the 1918 “Spanish Flu” virus. Science 296:211a

Stumpf MPH, Pybus OG. Genetic diversity and models of viral evolution for the hepatitis C virus. FEMS Microbiology Letters 214:143-52

Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. Journal of Molecular Evolution 54:152-61

Woelk CH, Pybus OG, Jin L, Brown DWG, Holmes EC. Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections. Journal of General Virology 83:1419-30

2001

Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH. The epidemic behaviour of the hepatitis C virus. Science 292:2323-5

Rambaut A, Robertson DL, Pybus OG, Peeters M, Holmes EC. Phylogeny and the origin of HIV-1. Nature 410:1047-8

Strimmer K, Pybus OG. Exploring the demographic history of DNA sequences using the generalised skyline plot. Molecular Biology & Evolution 18:2298-305

Yusim K, Peeters M, Pybus OG, Bhattacharya T, Delaporte E et al. Using HIV-1 sequences to infer historical features of the AIDS epidemic and HIV evolution. Philosophical Transactions of the Royal Society Series B 356:855-66

2000

Pybus OG, Rambaut A, Harvey PH. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155:1429-37

Pybus OG, Harvey PH. Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society Series B 267:2267-72

Beerli P, Grassly N, Kuhner MK, Nickle D, Pybus OG, Rain M, Rambaut A, Rodrigo AG, Wang Y. Population genetics of HIV: parameter estimation using genealogy-based methods. In Computational & Evolutionary Analysis of HIV Molecular Sequences (AG Rodrigo & GH Learn, editors) pp. 217-52. Kluwer Academic Publishers

1999

Pybus OG, Holmes EC, Harvey PH. The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history. Molecular Biology & Evolution 16:953-9

Holmes EC, Pybus OG, Harvey PH. The molecular population dynamics of HIV-1. In The Evolution of HIV (KA Crandall, editor) pp. 177-207. John Hopkins University Press