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Volumn 8, Issue 5, 2013, Pages

Real Time Classification of Viruses in 12 Dimensions

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANTIGENICITY; ARTICLE; INTERMETHOD COMPARISON; JAPANESE ENCEPHALITIS; NONHUMAN; PHYLOGENY; PREDICTION; TAXONOMIC IDENTIFICATION; VALIDATION PROCESS; VIRUS CLASSIFICATION; VIRUS GENOME; WEST NILE FLAVIVIRUS;

EID: 84878082337     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064328     Document Type: Article
Times cited : (60)

References (39)
  • 1
    • 76549096678 scopus 로고    scopus 로고
    • The comparative genomics of viral emergence
    • Holmes EC, (2009) The comparative genomics of viral emergence. Proc Natl Acad Sci U S A 107: 1742-1746.
    • (2009) Proc Natl Acad Sci U S A , vol.107 , pp. 1742-1746
    • Holmes, E.C.1
  • 2
    • 56349152646 scopus 로고    scopus 로고
    • The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups
    • Koonin EV, Wolf YI, Nagasaki K, Dolja VV, (2008) The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 6: 925-939.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 925-939
    • Koonin, E.V.1    Wolf, Y.I.2    Nagasaki, K.3    Dolja, V.V.4
  • 3
    • 79956105255 scopus 로고    scopus 로고
    • What does virus evolution tell us about virus origins?
    • Holmes EC, (2011) What does virus evolution tell us about virus origins? J Virology 86 (11) (): 5247-5251.
    • (2011) J Virology , vol.86 , Issue.11 , pp. 5247-5251
    • Holmes, E.C.1
  • 4
    • 0037342499 scopus 로고    scopus 로고
    • Alignment-free sequence comparison-a review
    • VINGA S, Almeida J, (2003) Alignment-free sequence comparison-a review. Bioinformatics 19 (4) (): 513-523.
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 513-523
    • Vinga, S.1    Almeida, J.2
  • 5
    • 34547844142 scopus 로고    scopus 로고
    • A statistical method for alignment-free comparison of regulatory sequences
    • Kantorovitz RM, Robinson EG Sinha S, (2007) A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23: i249-i255.
    • (2007) Bioinformatics , vol.23
    • Kantorovitz, R.M.1    Robinson, E.G.2    Sinha, S.3
  • 6
    • 53749097779 scopus 로고    scopus 로고
    • Markov model plus k-word distributions: a synergy that produces novel statistical measure for sequence comparison
    • Dai Q, Yang Y, Wang T, (2008) Markov model plus k-word distributions: a synergy that produces novel statistical measure for sequence comparison. Bioinformatics 24 (20) (): 2296-2302.
    • (2008) Bioinformatics , vol.24 , Issue.20 , pp. 2296-2302
    • Dai, Q.1    Yang, Y.2    Wang, T.3
  • 7
    • 62449130191 scopus 로고    scopus 로고
    • Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
    • Sims EG, Jun S, Wu AG, Kim S, (2008) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. PNAS 106 (8) (): 2677-2682.
    • (2008) PNAS , vol.106 , Issue.8 , pp. 2677-2682
    • Sims, E.G.1    Jun, S.2    Wu, A.G.3    Kim, S.4
  • 8
    • 84857867828 scopus 로고    scopus 로고
    • Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
    • Goke J, Schulz HM, Lasserre J, Vingron M, (2012) Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics 28 (5) (): 656-663.
    • (2012) Bioinformatics , vol.28 , Issue.5 , pp. 656-663
    • Goke, J.1    Schulz, H.M.2    Lasserre, J.3    Vingron, M.4
  • 9
    • 77955944760 scopus 로고    scopus 로고
    • A novel construction of genome space with biological geometry
    • Yu C, Liang Q, Yin C, He RL, Yau SS-T, (2010) A novel construction of genome space with biological geometry. DNA Res 17 (3) (): 155-168.
    • (2010) DNA Res , vol.17 , Issue.3 , pp. 155-168
    • Yu, C.1    Liang, Q.2    Yin, C.3    He, R.L.4    Yau, S.S.-T.5
  • 10
    • 79952303267 scopus 로고    scopus 로고
    • A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications
    • Deng M, Yu C, Liang Q, He RL, Yau SS-T, (2011) A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications. PLoS ONE 6 (3) (): e17293.
    • (2011) PLoS ONE , vol.6 , Issue.3
    • Deng, M.1    Yu, C.2    Liang, Q.3    He, R.L.4    Yau, S.S.-T.5
  • 11
    • 0015114139 scopus 로고
    • Expression of animal virus genomes
    • Baltimore D, (1971) Expression of animal virus genomes. Bacteriol Rev 35 (3) (): 235-241.
    • (1971) Bacteriol Rev , vol.35 , Issue.3 , pp. 235-241
    • Baltimore, D.1
  • 12
    • 84878084215 scopus 로고    scopus 로고
    • Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses. (2012) Ed: King, AMQ, Adams, MJ, Carstens, EB and Lefkowitz, EJ, San Diego, Elsevier
    • Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses. (2012) Ed: King, AMQ, Adams, MJ, Carstens, EB and Lefkowitz, EJ, San Diego, Elsevier.
  • 13
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal R, Michener C, (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 38: 1409-1438.
    • (1958) University of Kansas Science Bulletin , vol.38 , pp. 1409-1438
    • Sokal, R.1    Michener, C.2
  • 14
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch WM, Margoliash E, (1967) Construction of phylogenetic trees. Science 155: 279-284.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 15
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 (4) (): 406-425.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 16
    • 0001925593 scopus 로고
    • A note on metric properties of trees
    • Buneman P, (1974) A note on metric properties of trees. J Combin. Theory Ser B 17: 48-50.
    • (1974) J Combin. Theory Ser B , vol.17 , pp. 48-50
    • Buneman, P.1
  • 17
    • 0030028277 scopus 로고    scopus 로고
    • Multiple UPGMA and Neighbor-joining Trees and the Performance of Some Computer Packages
    • Backeljau T, De Bruyn L, De Wolf H, Jordaens K, Van Dongen S, et al. (1996) Multiple UPGMA and Neighbor-joining Trees and the Performance of Some Computer Packages. Mol Biol Evol 13 (2) (): 309-313.
    • (1996) Mol Biol Evol , vol.13 , Issue.2 , pp. 309-313
    • Backeljau, T.1    De Bruyn, L.2    De Wolf, H.3    Jordaens, K.4    Van Dongen, S.5
  • 18
    • 13944282885 scopus 로고    scopus 로고
    • Identification and Characterization of Avihepadnaviruses Isolated from Exotic Anseriformes Maintained in Captivity
    • Guo H, Mason WS, Aldrich CE, Saputelli JR, Miller DS, et al. (2005) Identification and Characterization of Avihepadnaviruses Isolated from Exotic Anseriformes Maintained in Captivity. J Virol 79 (5) (): 2729-2742.
    • (2005) J Virol , vol.79 , Issue.5 , pp. 2729-2742
    • Guo, H.1    Mason, W.S.2    Aldrich, C.E.3    Saputelli, J.R.4    Miller, D.S.5
  • 19
    • 0033568298 scopus 로고    scopus 로고
    • A new avian hepadnavirus infecting snow geese (Anser caerulescens) produces a significant fraction of virions containing single-stranded DNA
    • Chang SF, Netter HJ, Bruns M, Schneider R, Frölich K, et al. (1999) A new avian hepadnavirus infecting snow geese (Anser caerulescens) produces a significant fraction of virions containing single-stranded DNA. Virology 262 (1) (): 39-54.
    • (1999) Virology , vol.262 , Issue.1 , pp. 39-54
    • Chang, S.F.1    Netter, H.J.2    Bruns, M.3    Schneider, R.4    Frölich, K.5
  • 21
    • 84891631250 scopus 로고    scopus 로고
    • Molecular identification of badnavirus in Dracaena sanderiana from Hubei of China
    • Chen X, Ruan X-L, Zhao Q, Li H-P, (2009) Molecular identification of badnavirus in Dracaena sanderiana from Hubei of China. Scientia Agricultura Sinica 42 (6) (): 2002-2009.
    • (2009) Scientia Agricultura Sinica , vol.42 , Issue.6 , pp. 2002-2009
    • Chen, X.1    Ruan, X.-L.2    Zhao, Q.3    Li, H.-P.4
  • 22
    • 77954539543 scopus 로고    scopus 로고
    • Plant-feeding insects harbor double-stranded RNA viruses encoding a novel proline-alanine rich protein and a polymerase distantly related to that of fungal viruses
    • Spear A, Sisterson MS, Yokomi R, Stenger DC, (2010) Plant-feeding insects harbor double-stranded RNA viruses encoding a novel proline-alanine rich protein and a polymerase distantly related to that of fungal viruses. Virology 404: 304-311.
    • (2010) Virology , vol.404 , pp. 304-311
    • Spear, A.1    Sisterson, M.S.2    Yokomi, R.3    Stenger, D.C.4
  • 23
    • 80255135552 scopus 로고    scopus 로고
    • Incidence of Phlebiopsis gigantea large virus-1 in a collection of Phlebiopsis gigantea isolates
    • Lim JM, Jamal A, Phoon X, Korhonen K, Coutts RHA, (2011) Incidence of Phlebiopsis gigantea large virus-1 in a collection of Phlebiopsis gigantea isolates. Arch Virol 156: 2091-2094.
    • (2011) Arch Virol , vol.156 , pp. 2091-2094
    • Lim, J.M.1    Jamal, A.2    Phoon, X.3    Korhonen, K.4    Coutts, R.H.A.5
  • 24
    • 70349311588 scopus 로고    scopus 로고
    • Drosophila A virus is an unusual RNA virus with a T = 3 icosahedral core and permuted RNA-dependent RNA polymerase
    • Ambrose RL, Lander GC, Maaty WS, Bothner B, Johnson JE, et al. (2009) Drosophila A virus is an unusual RNA virus with a T = 3 icosahedral core and permuted RNA-dependent RNA polymerase. J Gen Virol 90: 2191-2200.
    • (2009) J Gen Virol , vol.90 , pp. 2191-2200
    • Ambrose, R.L.1    Lander, G.C.2    Maaty, W.S.3    Bothner, B.4    Johnson, J.E.5
  • 25
    • 39149129662 scopus 로고    scopus 로고
    • Complete nucleotide sequence of a new double-stranded RNA virus from the rice blast fungus, Magnaporthe oryzae
    • Maejima K, Himeno M, Komatsu K, Kakizawa S, Yamaji Y, et al. (2008) Complete nucleotide sequence of a new double-stranded RNA virus from the rice blast fungus, Magnaporthe oryzae. Arch Virol 153 (2) (): 389-391.
    • (2008) Arch Virol , vol.153 , Issue.2 , pp. 389-391
    • Maejima, K.1    Himeno, M.2    Komatsu, K.3    Kakizawa, S.4    Yamaji, Y.5
  • 27
    • 60749128006 scopus 로고    scopus 로고
    • Southern tomato virus: The link between the families Totiviridae and Partitiviridae
    • Sabanadzovic S, Valverde RA, Brown JK, Martin RR, Tzanetakis IE, (2009) Southern tomato virus: The link between the families Totiviridae and Partitiviridae. Virus Res 140 (1-2) (): 130-137.
    • (2009) Virus Res , vol.140 , Issue.1-2 , pp. 130-137
    • Sabanadzovic, S.1    Valverde, R.A.2    Brown, J.K.3    Martin, R.R.4    Tzanetakis, I.E.5
  • 28
    • 70349332795 scopus 로고    scopus 로고
    • A novel putative virus of Gremmeniella abietina type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities
    • Tuomivirta TT, Kaitera J, Hantula J, (2009) A novel putative virus of Gremmeniella abietina type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities. J Gen Virol 90: 2299-2305.
    • (2009) J Gen Virol , vol.90 , pp. 2299-2305
    • Tuomivirta, T.T.1    Kaitera, J.2    Hantula, J.3
  • 29
    • 32844466037 scopus 로고    scopus 로고
    • Beilong virus, a novel paramyxovirus with the largest genome of non-segmented negative-stranded RNA viruses
    • Li Z, Yu M, Zhang H, Magoffin DE, Jack PJ, et al. (2006) Beilong virus, a novel paramyxovirus with the largest genome of non-segmented negative-stranded RNA viruses. Virology 346 (1) (): 219-228.
    • (2006) Virology , vol.346 , Issue.1 , pp. 219-228
    • Li, Z.1    Yu, M.2    Zhang, H.3    Magoffin, D.E.4    Jack, P.J.5
  • 31
    • 0842325992 scopus 로고    scopus 로고
    • Complete genome sequence of Fer-de-Lance virus reveals a novel gene in reptilian paramyxoviruses
    • Kurath G, Batts WN, Ahne W, Winton JR, (2004) Complete genome sequence of Fer-de-Lance virus reveals a novel gene in reptilian paramyxoviruses. J Virol 78 (4) (): 2045-2056.
    • (2004) J Virol , vol.78 , Issue.4 , pp. 2045-2056
    • Kurath, G.1    Batts, W.N.2    Ahne, W.3    Winton, J.R.4
  • 32
    • 65349195509 scopus 로고    scopus 로고
    • Nyamanini and Midway viruses define a novel taxon of RNA viruses in the Order Mononegavirales
    • Mihindukulasuriya KA, Nguyen NL, Wu G, Huang HV, da Rosa AP, et al. (2009) Nyamanini and Midway viruses define a novel taxon of RNA viruses in the Order Mononegavirales. J Virol 83 (10) (): 5109-5116.
    • (2009) J Virol , vol.83 , Issue.10 , pp. 5109-5116
    • Mihindukulasuriya, K.A.1    Nguyen, N.L.2    Wu, G.3    Huang, H.V.4    da Rosa, A.P.5
  • 33
    • 43749102897 scopus 로고    scopus 로고
    • Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae
    • Gubala AJ, Proll DF, Barnard RT, Cowled CJ, Crameri SG, et al. (2008) Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae. Virology 376: 13-23.
    • (2008) Virology , vol.376 , pp. 13-23
    • Gubala, A.J.1    Proll, D.F.2    Barnard, R.T.3    Cowled, C.J.4    Crameri, S.G.5
  • 35
    • 0030780974 scopus 로고    scopus 로고
    • Isolation of an avirulent mutant of Sendai virus with two amino acid mutations from a highly virulent field strain through adaptation to LLC-MK2 cells
    • Itoh M, Isegawa Y, Hotta H, Homma M, (1997) Isolation of an avirulent mutant of Sendai virus with two amino acid mutations from a highly virulent field strain through adaptation to LLC-MK2 cells. J Gen Virol 78: 3207-3015.
    • (1997) J Gen Virol , vol.78 , pp. 3015-3207
    • Itoh, M.1    Isegawa, Y.2    Hotta, H.3    Homma, M.4
  • 36
    • 0842325992 scopus 로고    scopus 로고
    • Complete genome sequence of Fer-de-Lance virus reveals a novel gene in reptilian paramyxoviruses
    • Kurath G, Batts WN, Ahne W, Winton JR, (2004) Complete genome sequence of Fer-de-Lance virus reveals a novel gene in reptilian paramyxoviruses. J Virol 78 (4) (): 2045-2056.
    • (2004) J Virol , vol.78 , Issue.4 , pp. 2045-2056
    • Kurath, G.1    Batts, W.N.2    Ahne, W.3    Winton, J.R.4
  • 37
    • 84878090177 scopus 로고    scopus 로고
    • Retrieved 30 August 2012 from
    • Retrieved 30 August 2012 from http://www.cdc.gov/ncidod/dvbid/westnile/index.htm.
  • 39
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Bio Evol 28: 2731-2739.
    • (2011) Mol Bio Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5


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