메뉴 건너뛰기




Volumn 11, Issue 8, 2011, Pages 2026-2033

An entropy-based approach for the identification of phylogenetically informative genomic regions of Papillomavirus

Author keywords

Entropy; Genomic diversity; Papillomavirus; Phylogeny

Indexed keywords

ARTICLE; CONTROLLED STUDY; ENTROPY; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; NONHUMAN; PAPILLOMA VIRUS; PHYLOGENETIC TREE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; VIRAL GENETICS; VIRUS GENE; VIRUS GENOME;

EID: 82655187470     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.09.013     Document Type: Article
Times cited : (23)

References (70)
  • 1
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: selection of best-fit models of protein evolution
    • Abascal F., Zardoya R., Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21:2104-2105.
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 2
    • 0000501656 scopus 로고
    • Information theory and an extension of the maximum likelihood principle
    • Akademiai Kiado, Budapest.
    • Akaike, H., 1973. Information theory and an extension of the maximum likelihood principle, In: Proceedings of the Second International Symposium on Information Theory, Akademiai Kiado, Budapest, pp. 267-281.
    • (1973) Proceedings of the Second International Symposium on Information Theory. , pp. 267-281
    • Akaike, H.1
  • 4
    • 0023144684 scopus 로고
    • Structural and transcriptional analysis of human papillomavirus type 16 sequences in cervical carcinoma cell lines
    • Baker C.C., Phelps W.C., Lindgren V., Braun M.J., Gonda M.A., Howley P.M. Structural and transcriptional analysis of human papillomavirus type 16 sequences in cervical carcinoma cell lines. J. Virol. 1987, 61:962-967.
    • (1987) J. Virol. , vol.61 , pp. 962-967
    • Baker, C.C.1    Phelps, W.C.2    Lindgren, V.3    Braun, M.J.4    Gonda, M.A.5    Howley, P.M.6
  • 5
    • 14744297766 scopus 로고    scopus 로고
    • The clinical importance of the nomenclature, evolution and taxonomy of human papillomaviruses
    • Bernard H.U. The clinical importance of the nomenclature, evolution and taxonomy of human papillomaviruses. J. Clin. Virol. 2005, 32:1-6.
    • (2005) J. Clin. Virol. , vol.32 , pp. 1-6
    • Bernard, H.U.1
  • 6
    • 77950938389 scopus 로고    scopus 로고
    • Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments
    • Bernard H.U., Burk R.D., Chen Z., van Doorslaer K., Hausen H., de Villiers E.M. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010, 401:70-79.
    • (2010) Virology , vol.401 , pp. 70-79
    • Bernard, H.U.1    Burk, R.D.2    Chen, Z.3    van Doorslaer, K.4    Hausen, H.5    de Villiers, E.M.6
  • 7
    • 18744365783 scopus 로고    scopus 로고
    • Interaction of tSNARE syntaxin 18 with the papillomavirus minor capsid protein mediates infection
    • Bossis I., Roden R.B.S., Gambhira R., Yang R., Tagaya M., Howley P.M., Meneses P.I. Interaction of tSNARE syntaxin 18 with the papillomavirus minor capsid protein mediates infection. J. Virol. 2005, 79:6723-6731.
    • (2005) J. Virol. , vol.79 , pp. 6723-6731
    • Bossis, I.1    Roden, R.B.S.2    Gambhira, R.3    Yang, R.4    Tagaya, M.5    Howley, P.M.6    Meneses, P.I.7
  • 8
    • 0037231932 scopus 로고    scopus 로고
    • Positively charged sequence of human papillomavirus type 16 capsid proteins are sufficient to mediate gene transfer into target cells via the heparan sulphate receptor
    • Bousarghin L., Touze A., Combita-Rojas A., Coursaget P. Positively charged sequence of human papillomavirus type 16 capsid proteins are sufficient to mediate gene transfer into target cells via the heparan sulphate receptor. J. Gen. Virol. 2003, 84:157-164.
    • (2003) J. Gen. Virol. , vol.84 , pp. 157-164
    • Bousarghin, L.1    Touze, A.2    Combita-Rojas, A.3    Coursaget, P.4
  • 9
    • 33947535104 scopus 로고    scopus 로고
    • Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins
    • Bravo I.G., Alonso A. Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins. Virus Genes 2007, 34:249-262.
    • (2007) Virus Genes , vol.34 , pp. 249-262
    • Bravo, I.G.1    Alonso, A.2
  • 10
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • Caffrey D.R., Somaroo S., Hughes J.D., Mintseris J., Huang E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?. Protein Sci. 2004, 13:190-202.
    • (2004) Protein Sci. , vol.13 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5
  • 11
    • 0034628480 scopus 로고    scopus 로고
    • Human papillomavirus E7 proteins stimulate proliferation independently of their ability to associate with retinoblastoma protein
    • Caldeira S., de Villiers E.M., Tommasino M. Human papillomavirus E7 proteins stimulate proliferation independently of their ability to associate with retinoblastoma protein. Oncogene 2000, 19:821-826.
    • (2000) Oncogene , vol.19 , pp. 821-826
    • Caldeira, S.1    de Villiers, E.M.2    Tommasino, M.3
  • 12
    • 0036849716 scopus 로고    scopus 로고
    • Animal models of papillomavirus pathogenesis
    • Campo M.S. Animal models of papillomavirus pathogenesis. Virus Res. 2002, 89:249-261.
    • (2002) Virus Res. , vol.89 , pp. 249-261
    • Campo, M.S.1
  • 14
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 15
    • 0026757412 scopus 로고
    • Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses
    • Chan S.Y., Bernard H.U., Ong C.K., Chan S.P., Hoffman B., Delius H. Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses. J. Virol. 1992, 66:5714-5725.
    • (1992) J. Virol. , vol.66 , pp. 5714-5725
    • Chan, S.Y.1    Bernard, H.U.2    Ong, C.K.3    Chan, S.P.4    Hoffman, B.5    Delius, H.6
  • 16
    • 0028926716 scopus 로고
    • Analysis of genomic sequences of 95 papillomavirus types: uniting typing, phylogeny, and taxonomy
    • Chan S.Y., Delius H., Halpern A.L., Bernard H.U. Analysis of genomic sequences of 95 papillomavirus types: uniting typing, phylogeny, and taxonomy. J. Virol. 1995, 69:3074-3083.
    • (1995) J. Virol. , vol.69 , pp. 3074-3083
    • Chan, S.Y.1    Delius, H.2    Halpern, A.L.3    Bernard, H.U.4
  • 17
    • 47249144103 scopus 로고    scopus 로고
    • Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection
    • Chapman E.G., Piontkivska H., Walker J.M., Stewart D.T., Curole J.P., Hoeh W.R. Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection. BMC Evol. Biol. 2008, 8:165-180.
    • (2008) BMC Evol. Biol. , vol.8 , pp. 165-180
    • Chapman, E.G.1    Piontkivska, H.2    Walker, J.M.3    Stewart, D.T.4    Curole, J.P.5    Hoeh, W.R.6
  • 18
    • 48449106792 scopus 로고    scopus 로고
    • The Jpred 3 secondary structure prediction server
    • Cole C., Barber J.D., Barton G.J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 2008, 36:197-201.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 197-201
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 19
    • 77954403053 scopus 로고    scopus 로고
    • BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
    • Criscuolo A., Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 2010, 10:210.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 210
    • Criscuolo, A.1    Gribaldo, S.2
  • 20
    • 77950658657 scopus 로고    scopus 로고
    • FLU, an amino acid substitution model for influenza proteins
    • Dang C.C., Le Q.S., Gascuel O., Le V.S. FLU, an amino acid substitution model for influenza proteins. BMC Evol. Biol. 2010, 10:99.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 99
    • Dang, C.C.1    Le, Q.S.2    Gascuel, O.3    Le, V.S.4
  • 22
    • 0036017382 scopus 로고    scopus 로고
    • RtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
    • Dimmic M.W., Rest J.S., Mindell D.P., Goldstein R.A. RtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol. 2002, 55:65-73.
    • (2002) J. Mol. Evol. , vol.55 , pp. 65-73
    • Dimmic, M.W.1    Rest, J.S.2    Mindell, D.P.3    Goldstein, R.A.4
  • 23
    • 0037384987 scopus 로고    scopus 로고
    • Interactions between papillomavirus L1 and L2 capsid proteins
    • Finnen R.L., Erikson K.D., Chen X.S., Garcea R.L. Interactions between papillomavirus L1 and L2 capsid proteins. J. Virol. 2003, 77:4818-4826.
    • (2003) J. Virol. , vol.77 , pp. 4818-4826
    • Finnen, R.L.1    Erikson, K.D.2    Chen, X.S.3    Garcea, R.L.4
  • 24
  • 25
    • 27144493802 scopus 로고    scopus 로고
    • Papillomaviruses: different genes have different histories
    • García-Vallvé S., Alonso á., Bravo I.G. Papillomaviruses: different genes have different histories. Trends Microbiol. 2005, 13:514-521.
    • (2005) Trends Microbiol. , vol.13 , pp. 514-521
    • García-Vallvé, S.1    Alonso, Á.2    Bravo, I.G.3
  • 26
    • 33751009382 scopus 로고    scopus 로고
    • Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data
    • Gottschling M., Köhler A., Stockfleth E., Nindl I. Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data. Mol. Phylogenet. Evol. 2007, 42:213-222.
    • (2007) Mol. Phylogenet. Evol. , vol.42 , pp. 213-222
    • Gottschling, M.1    Köhler, A.2    Stockfleth, E.3    Nindl, I.4
  • 29
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 30
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
    • (1999) Nucleic Acids Symp. Ser. , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 31
    • 70349119250 scopus 로고
    • Regression and time series model selection in small samples
    • Hurvich C.M., Tsai C.-L. Regression and time series model selection in small samples. Biometrika 1989, 76:297-307.
    • (1989) Biometrika , vol.76 , pp. 297-307
    • Hurvich, C.M.1    Tsai, C.-L.2
  • 32
    • 77955510363 scopus 로고    scopus 로고
    • Relative von Neumann entropy for evaluating amino acid conservation
    • Johansson F., Toh H. Relative von Neumann entropy for evaluating amino acid conservation. J. Bioinf. Comput. Biol. 2010, 8:809-823.
    • (2010) J. Bioinf. Comput. Biol. , vol.8 , pp. 809-823
    • Johansson, F.1    Toh, H.2
  • 33
    • 30344481121 scopus 로고    scopus 로고
    • A membrane-destabilizing peptide in capsid protein L2 is required for egress of papillomavirus genomes from endosomes
    • Kämper N., Day P.M., Nowak T., Selinka H.C., Florin L., Bolscher J., Hilbig L., Schiller J.T., Sapp M. A membrane-destabilizing peptide in capsid protein L2 is required for egress of papillomavirus genomes from endosomes. J. Virol. 2006, 80:759-768.
    • (2006) J. Virol. , vol.80 , pp. 759-768
    • Kämper, N.1    Day, P.M.2    Nowak, T.3    Selinka, H.C.4    Florin, L.5    Bolscher, J.6    Hilbig, L.7    Schiller, J.T.8    Sapp, M.9
  • 34
    • 0037458324 scopus 로고    scopus 로고
    • Bioinformatic principles underlying the information content of transcription factor binding sites
    • Kim J.T., Martinetz T., Polani D. Bioinformatic principles underlying the information content of transcription factor binding sites. J. Theor. Biol. 2003, 220:529-544.
    • (2003) J. Theor. Biol. , vol.220 , pp. 529-544
    • Kim, J.T.1    Martinetz, T.2    Polani, D.3
  • 35
    • 1542268964 scopus 로고    scopus 로고
    • Karmeshu Study of DNA binding sites using the Rényi parametric entropy measure
    • Krishnamachari A., moy Mandal V., Karmeshu Study of DNA binding sites using the Rényi parametric entropy measure. J. Theor. Biol. 2004, 227:429-436.
    • (2004) J. Theor. Biol. , vol.227 , pp. 429-436
    • Krishnamachari, A.1    moy Mandal, V.2
  • 36
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 37
    • 17644407653 scopus 로고    scopus 로고
    • Protein sequence entropy is closely related to packing density and hydrophobicity
    • Liao H., Yeh W., Chiang D., Jernigan R.L., Lustig B. Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Eng. Des. Sel. 2005, 18:59-64.
    • (2005) Protein Eng. Des. Sel. , vol.18 , pp. 59-64
    • Liao, H.1    Yeh, W.2    Chiang, D.3    Jernigan, R.L.4    Lustig, B.5
  • 38
    • 65649117685 scopus 로고    scopus 로고
    • DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    • Librado P., Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 39
    • 0034922289 scopus 로고    scopus 로고
    • Modeling amino acid replacement
    • Muller T., Vingron M. Modeling amino acid replacement. J. Comput. Biol. 2000, 7:761-776.
    • (2000) J. Comput. Biol. , vol.7 , pp. 761-776
    • Muller, T.1    Vingron, M.2
  • 40
    • 0035576691 scopus 로고    scopus 로고
    • Entropic approach to information coding in DNA molecules
    • Mutihac R., Cicuttin A., Mutihac R.C. Entropic approach to information coding in DNA molecules. Mater. Sci. Eng. 2001, 18:51-60.
    • (2001) Mater. Sci. Eng. , vol.18 , pp. 51-60
    • Mutihac, R.1    Cicuttin, A.2    Mutihac, R.C.3
  • 41
    • 0032900495 scopus 로고    scopus 로고
    • The variable and conserved interfaces of modeled olfactory receptor proteins
    • Pilpel Y., Lancet D. The variable and conserved interfaces of modeled olfactory receptor proteins. Protein Sci. 1999, 8:969-977.
    • (1999) Protein Sci. , vol.8 , pp. 969-977
    • Pilpel, Y.1    Lancet, D.2
  • 42
    • 2442713484 scopus 로고    scopus 로고
    • * to select a model of nucleotide substitution
    • John Wiley & Sons, Inc. A.D. Baxevanis, D.B. Davison, R.D.M. Page, G.A. Petsko, L.D. Stein, G.D. Stormo (Eds.)
    • * to select a model of nucleotide substitution. Current Protocols in Bioinformatics 2003, 651-654. John Wiley & Sons, Inc. A.D. Baxevanis, D.B. Davison, R.D.M. Page, G.A. Petsko, L.D. Stein, G.D. Stormo (Eds.).
    • (2003) Current Protocols in Bioinformatics , pp. 651-654
    • Posada, D.1
  • 43
    • 9644301241 scopus 로고    scopus 로고
    • Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio test
    • Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio test. Syst. Biol. 2004, 53:793-808.
    • (2004) Syst. Biol. , vol.53 , pp. 793-808
    • Posada, D.1    Buckley, T.R.2
  • 44
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: testing the model of DNA substitution
    • Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 46
    • 31944439998 scopus 로고    scopus 로고
    • Cleavage of the papillomavirus minor capsid protein, L2, at a furin consensus site is necessary for infection
    • Richards R.M., Lowy D., Schiller J.T., Day P.M. Cleavage of the papillomavirus minor capsid protein, L2, at a furin consensus site is necessary for infection. Proc. Natl. Acad. Sci. USA 2006, 103:1522-1527.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1522-1527
    • Richards, R.M.1    Lowy, D.2    Schiller, J.T.3    Day, P.M.4
  • 47
    • 0034630951 scopus 로고    scopus 로고
    • Minor capsid protein of human genital papillomavirus contains subdominant, cross-neutralizing epitopes
    • Roden R.B.S., Yuty W., Fallon R., Inglis S., Lowy D., Schiller J.T. Minor capsid protein of human genital papillomavirus contains subdominant, cross-neutralizing epitopes. Virology 2000, 270:254-257.
    • (2000) Virology , vol.270 , pp. 254-257
    • Roden, R.B.S.1    Yuty, W.2    Fallon, R.3    Inglis, S.4    Lowy, D.5    Schiller, J.T.6
  • 48
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck J.P. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 49
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method to reconstructing phylogenetic trees
    • Saitou N., Nei M. The neighbor-joining method: a new method to reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 50
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    von Haeseler, A.4
  • 51
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider T.D., Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990, 18:6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 52
  • 53
    • 0000882988 scopus 로고    scopus 로고
    • Papillomaviruses
    • Raven Press, New York, B.N. Fields, D.M. Knipes, P.M. Howley (Eds.)
    • Shah K.V., Howley P.M. Papillomaviruses. Virology 1996, 2077-2109. Raven Press, New York. B.N. Fields, D.M. Knipes, P.M. Howley (Eds.).
    • (1996) Virology , pp. 2077-2109
    • Shah, K.V.1    Howley, P.M.2
  • 54
    • 77952862896 scopus 로고    scopus 로고
    • Analysis of host-parasite incongruence in Papillomavirus evolution using importance sampling
    • Shah S.D., Doorbar J., Goldstein R.A. Analysis of host-parasite incongruence in Papillomavirus evolution using importance sampling. Mol. Biol. Evol. 2010, 27:1301-1314.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 1301-1314
    • Shah, S.D.1    Doorbar, J.2    Goldstein, R.A.3
  • 55
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon C.E. A mathematical theory of communication. Bell Syst. Tech. J. 1948, 27(379-423):623-656.
    • (1948) Bell Syst. Tech. J. , vol.27 , Issue.379-423 , pp. 623-656
    • Shannon, C.E.1
  • 56
    • 0031002417 scopus 로고    scopus 로고
    • Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment
    • Strimmer K., von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA 1997, 94:6815-6819.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 6815-6819
    • Strimmer, K.1    von Haeseler, A.2
  • 57
    • 0024114801 scopus 로고
    • A note on the neighbor-joining method of Saitou and Nei
    • Studier J.A., Keppler K.J. A note on the neighbor-joining method of Saitou and Nei. Mol. Biol. Evol. 1988, 4:729-731.
    • (1988) Mol. Biol. Evol. , vol.4 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2
  • 58
    • 84963178774 scopus 로고
    • Further analysis of the data by Akaike's information criterion and the finite correction
    • Sugiura N. Further analysis of the data by Akaike's information criterion and the finite correction. Comm. Statist. A-theory. meth. 1978, 7:13-26.
    • (1978) Comm. Statist. A-theory. meth. , vol.7 , pp. 13-26
    • Sugiura, N.1
  • 60
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
    • (2007) Syst. Biol. , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 61
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 62
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • American Mathematical Society, Providence, R.M. Miura (Ed.)
    • Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Some Mathematical Questions in Biology - DNA Sequence Analysis 1986, 57-86. American Mathematical Society, Providence. R.M. Miura (Ed.).
    • (1986) Some Mathematical Questions in Biology - DNA Sequence Analysis , pp. 57-86
    • Tavaré, S.1
  • 63
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 65
    • 38049016306 scopus 로고    scopus 로고
    • Human papillomavirus and vaccination in cervical cancer
    • Wang K.L. Human papillomavirus and vaccination in cervical cancer. Taiwan J. Obstet. Gynecol. 2007, 46:352-362.
    • (2007) Taiwan J. Obstet. Gynecol. , vol.46 , pp. 352-362
    • Wang, K.L.1
  • 66
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S., Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 2001, 18:691-699.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 67
    • 70349470948 scopus 로고    scopus 로고
    • Structural and functional constraints in the evolution of protein families
    • Worth C.L., Gong S., Blundell T.L. Structural and functional constraints in the evolution of protein families. Nat. Rev. Mol. Cell Biol. 2009, 10:709-720.
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 709-720
    • Worth, C.L.1    Gong, S.2    Blundell, T.L.3
  • 68
    • 0034848170 scopus 로고    scopus 로고
    • DAMBE: data analysis in molecular biology and evolution
    • Xia X., Xie Z. DAMBE: data analysis in molecular biology and evolution. J. Hered. 2001, 92:371-373.
    • (2001) J. Hered. , vol.92 , pp. 371-373
    • Xia, X.1    Xie, Z.2
  • 69
    • 0033004740 scopus 로고    scopus 로고
    • Estimation of the transition/transversion rate bias and species sampling
    • Yang Z., Yoder A. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 1999, 48:274-283.
    • (1999) J. Mol. Evol. , vol.48 , pp. 274-283
    • Yang, Z.1    Yoder, A.2
  • 70
    • 0034635349 scopus 로고    scopus 로고
    • Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure
    • Zou J., Saven J.G. Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure. J. Mol. Biol. 2000, 296:281-294.
    • (2000) J. Mol. Biol. , vol.296 , pp. 281-294
    • Zou, J.1    Saven, J.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.