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Volumn 7, Issue 3, 2011, Pages

A bayesian approach to analyse genetic variation within RNA viral populations

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NETWORKS; DISEASES; DNA; GENES; MOLECULAR BIOLOGY; POLYMERASE CHAIN REACTION; VIRUSES;

EID: 79953664745     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002027     Document Type: Article
Times cited : (7)

References (27)
  • 1
    • 0346373759 scopus 로고    scopus 로고
    • Unifying the ecological and evolutionary dynamics of pathogens
    • Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly J, et al. (2004) Unifying the ecological and evolutionary dynamics of pathogens. Science 303: 327-332.
    • (2004) Science , vol.303 , pp. 327-332
    • Grenfell, B.T.1    Pybus, O.G.2    Gog, J.R.3    Wood, J.L.4    Daly, J.5
  • 2
    • 70449510163 scopus 로고    scopus 로고
    • Dengue 1 Diversity and Microevolution, French Polynesia 2001-2006: Connection with Epidemiology and Clinics
    • Descloux E, Cao-Lormeau V, Roche C, Lamballerie XD, (2009) Dengue 1 Diversity and Microevolution, French Polynesia 2001-2006: Connection with Epidemiology and Clinics. PLoS Negl Trop Dis 3: e493.
    • (2009) PLoS Negl Trop Dis , vol.3
    • Descloux, E.1    Cao-Lormeau, V.2    Roche, C.3    Lamballerie, X.D.4
  • 3
    • 77951432232 scopus 로고    scopus 로고
    • Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs
    • Hoelzer K, Murcia PR, Baillie GJ, Wood JL, Metzger SM, et al. (2010) Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs. J Virol 84: 5329-5335.
    • (2010) J Virol , vol.84 , pp. 5329-5335
    • Hoelzer, K.1    Murcia, P.R.2    Baillie, G.J.3    Wood, J.L.4    Metzger, S.M.5
  • 4
    • 0141565071 scopus 로고    scopus 로고
    • Patterns of intra- and interhost nonsynonomous variation reveal strong purifying selection in dengue virus
    • Holmes EC, (2003) Patterns of intra- and interhost nonsynonomous variation reveal strong purifying selection in dengue virus. J Virol 77: 11296-11298.
    • (2003) J Virol , vol.77 , pp. 11296-11298
    • Holmes, E.C.1
  • 6
    • 77953755568 scopus 로고    scopus 로고
    • Intra- and inter-host evolutionary dynamics of equine influenza virus
    • Murcia PR, Baillie GJ, Daly J, Elton D, Jervis C, et al. (2010) Intra- and inter-host evolutionary dynamics of equine influenza virus. J Virol 84: 6943-6954.
    • (2010) J Virol , vol.84 , pp. 6943-6954
    • Murcia, P.R.1    Baillie, G.J.2    Daly, J.3    Elton, D.4    Jervis, C.5
  • 7
    • 44649102135 scopus 로고    scopus 로고
    • Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
    • Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, et al. (2008) Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 105: 7552-7557.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 7552-7557
    • Keele, B.F.1    Giorgi, E.E.2    Salazar-Gonzalez, J.F.3    Decker, J.M.4    Pham, K.T.5
  • 8
    • 77953292836 scopus 로고    scopus 로고
    • Dynamics and timing of in vivo mutations at Gag residue 242 during primary HIV-1 subtype C infection
    • Novitsky V, Wang R, Margolin L, Baca J, Moyo S, et al. (2010) Dynamics and timing of in vivo mutations at Gag residue 242 during primary HIV-1 subtype C infection. Virology 403: 37-46.
    • (2010) Virology , vol.403 , pp. 37-46
    • Novitsky, V.1    Wang, R.2    Margolin, L.3    Baca, J.4    Moyo, S.5
  • 9
    • 12144289425 scopus 로고    scopus 로고
    • Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission
    • Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, et al. (2004) Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303: 2019-2022.
    • (2004) Science , vol.303 , pp. 2019-2022
    • Derdeyn, C.A.1    Decker, J.M.2    Bibollet-Ruche, F.3    Mokili, J.L.4    Muldoon, M.5
  • 10
    • 77956827156 scopus 로고    scopus 로고
    • Intrapatient variation of the respiratory syncytial virus attachment protein gene
    • Agoti CN, Mbisa JL, Bett A, Medley GF, Nokes DJ, et al. (2010) Intrapatient variation of the respiratory syncytial virus attachment protein gene. J Virol 84: 10425-10428.
    • (2010) J Virol , vol.84 , pp. 10425-10428
    • Agoti, C.N.1    Mbisa, J.L.2    Bett, A.3    Medley, G.F.4    Nokes, D.J.5
  • 11
    • 79953663928 scopus 로고    scopus 로고
    • Wide variation in the multiplicity of HIV-1 infection among injection drug users
    • Bar KJ, Li H, Chamberland A, Tremblay C, Routy JP, et al. (2010) Wide variation in the multiplicity of HIV-1 infection among injection drug users. J Virol 83: 3556-3567.
    • (2010) J Virol , vol.83 , pp. 3556-3567
    • Bar, K.J.1    Li, H.2    Chamberland, A.3    Tremblay, C.4    Routy, J.P.5
  • 12
    • 77954051000 scopus 로고    scopus 로고
    • High multiplicity infection by HIV-1 in men who have sex with men
    • Li H, Bar KJ, Wang S, Decker JM, Chen Y, et al. (2010) High multiplicity infection by HIV-1 in men who have sex with men. PLoS Pathog 6: e1000890.
    • (2010) PLoS Pathog , vol.6
    • Li, H.1    Bar, K.J.2    Wang, S.3    Decker, J.M.4    Chen, Y.5
  • 13
    • 77951898043 scopus 로고    scopus 로고
    • A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia
    • Masharsky AE, Dukhovlinova EN, Verevochkin SV, Toussova OV, Skochilov RV, et al. (2010) A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia. J Infect Dis 201: 1697-1702.
    • (2010) J Infect Dis , vol.201 , pp. 1697-1702
    • Masharsky, A.E.1    Dukhovlinova, E.N.2    Verevochkin, S.V.3    Toussova, O.V.4    Skochilov, R.V.5
  • 14
    • 41949124934 scopus 로고    scopus 로고
    • Deciphering Human Immunodeficiency Virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
    • Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, et al. (2008) Deciphering Human Immunodeficiency Virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 82: 3952-3970.
    • (2008) J Virol , vol.82 , pp. 3952-3970
    • Salazar-Gonzalez, J.F.1    Bailes, E.2    Pham, K.T.3    Salazar, M.G.4    Guffey, M.B.5
  • 15
    • 77649195668 scopus 로고    scopus 로고
    • Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection
    • Schnell G, Price RW, Swanstrom R, Spudich S, (2010) Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection. J Virol 84: 2395-2407.
    • (2010) J Virol , vol.84 , pp. 2395-2407
    • Schnell, G.1    Price, R.W.2    Swanstrom, R.3    Spudich, S.4
  • 16
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    • Kosakovsky Pond SL, Frost SD, (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21: 2531-2533.
    • (2005) Bioinformatics , vol.21 , pp. 2531-2533
    • Kosakovsky Pond, S.L.1    Frost, S.D.2
  • 17
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • In: Munro N, editors, Academic Press, New York
    • Jukes T, Cantor C, (1969) Evolution of protein molecules. In: Munro N, editors. Mammalian protein metabolism pp. 21-123 Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-123
    • Jukes, T.1    Cantor, C.2
  • 18
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J, (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17: 368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 19
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M, (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 21
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57: 289-300.
    • (1995) J R Stat Soc Series B Stat Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 24
    • 70349303959 scopus 로고    scopus 로고
    • Bayesian statistical methods for genetic association studies
    • Stephens M, Balding DJ, (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10: 681-690.
    • (2009) Nat Rev Genet , vol.10 , pp. 681-690
    • Stephens, M.1    Balding, D.J.2
  • 25
    • 70149113077 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Core Development Team, Vienna, Austria. Available:
    • R Core Development Team (2009) R: A Language and Environment for Statistical Computing. Vienna, Austria. Available: http://www.R-project.org.
    • (2009)
  • 26
    • 84950945692 scopus 로고
    • Model selection and accounting for model uncertainty in graphical models using Occam's Window
    • Madigan D, Raftery AE, (1994) Model selection and accounting for model uncertainty in graphical models using Occam's Window. J Am Stat Assoc 89: 1535-1546.
    • (1994) J Am Stat Assoc , vol.89 , pp. 1535-1546
    • Madigan, D.1    Raftery, A.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.