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Volumn 19, Issue 10, 2012, Pages 1176-1202

A finite population model of molecular evolution: Theory and computation

Author keywords

molecular evolution; quasispecies theory

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; MOLECULAR EVOLUTION;

EID: 84866911238     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0064     Document Type: Article
Times cited : (24)

References (37)
  • 1
    • 27144440023 scopus 로고    scopus 로고
    • Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1
    • Althaus, C.L., and Bonhoeffer, S. 2005. Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1. J. Virol. 79, 13572-13578.
    • (2005) J. Virol. , vol.79 , pp. 13572-13578
    • Althaus, C.L.1    Bonhoeffer, S.2
  • 2
    • 0000286476 scopus 로고    scopus 로고
    • Error threshold in finite populations
    • Alves, D., and Fontanari, J.F. 1998. Error threshold in finite populations. Phys. Rev. E 57, 7008-7013.
    • (1998) Phys. Rev. e , vol.57 , pp. 7008-7013
    • Alves, D.1    Fontanari, J.F.2
  • 3
    • 9244238208 scopus 로고    scopus 로고
    • Viral error catastrophe by mutagenic nucleosides
    • Anderson, J.P., Daifuku, R., and Loeb, L.A. 2004. Viral error catastrophe by mutagenic nucleosides. Annu. Rev. Microbiol. 58, 183-205.
    • (2004) Annu. Rev. Microbiol. , vol.58 , pp. 183-205
    • Anderson, J.P.1    Daifuku, R.2    Loeb, L.A.3
  • 4
    • 79251574660 scopus 로고    scopus 로고
    • Taking multiple infections of cells and recombination into account leads to small within-host effective-population-size estimates of HIV-1
    • Balagam, R., Singh, V., Sagi, A.R., et al. 2011. Taking multiple infections of cells and recombination into account leads to small within-host effective-population-size estimates of HIV-1. PLoS ONE 6, e14531.
    • (2011) PLoS ONE , vol.6
    • Balagam, R.1    Singh, V.2    Sagi, A.R.3
  • 5
    • 79955043851 scopus 로고    scopus 로고
    • Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection
    • Batorsky, R., Kearney, M.F., Palmer, S. E., et al. 2011. Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc. Natl. Acad. Sci. USA 108, 5661-5666.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 5661-5666
    • Batorsky, R.1    Kearney, M.F.2    Palmer, S.E.3
  • 6
    • 0027329523 scopus 로고
    • Error thresholds on correlated fitness landscapes
    • Bonhoeffer, S., and Stadler, P.F. 1993. Error thresholds on correlated fitness landscapes. J. Theor. Biol. 164, 359-372.
    • (1993) J. Theor. Biol , vol.164 , pp. 359-372
    • Bonhoeffer, S.1    Stadler, P.F.2
  • 7
    • 9444282038 scopus 로고    scopus 로고
    • Evidence for positive epistasis in HIV-1
    • Bonhoeffer, S., Chappey, C., Parkin, N.T., et al. 2004. Evidence for positive epistasis in HIV-1. Science 306, 1547-1550.
    • (2004) Science , vol.306 , pp. 1547-1550
    • Bonhoeffer, S.1    Chappey, C.2    Parkin, N.T.3
  • 8
    • 0039756638 scopus 로고    scopus 로고
    • Stochastic model of evolving populations
    • Bonnaz, D., and Koch, A. J. 1998. Stochastic model of evolving populations. J. Phys. A Math. Gen. 31, 417.
    • (1998) J. Phys. A Math. Gen. , vol.31 , pp. 417
    • Bonnaz, D.1    Koch, A.J.2
  • 9
    • 0031359702 scopus 로고    scopus 로고
    • Path coupling: A technique for proving rapid mixing in markov chains
    • Found. Comput. Sci. (FOCS)
    • Bubley, R., and Dyer, M.E. 1997. Path coupling: a technique for proving rapid mixing in markov chains. Proc. 38th IEEE Symp. Found. Comput. Sci. (FOCS) 223-231.
    • (1997) Proc. 38th IEEE Symp , pp. 223-231
    • Bubley, R.1    Dyer, M.E.2
  • 10
    • 0039441077 scopus 로고    scopus 로고
    • Finite-size scaling of the error threshold transition in finite populations
    • Campos, P., and Fontanari, J. 1999. Finite-size scaling of the error threshold transition in finite populations. J. Phys A 32, L1-L7.
    • (1999) J. Phys A , vol.32
    • Campos, P.1    Fontanari, J.2
  • 11
    • 0035811016 scopus 로고    scopus 로고
    • RNA virus error catastrophe: Direct molecular test by using ribavirin
    • Crotty, S., Cameron, C.E., and Andino, R. 2001. RNA virus error catastrophe: direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. USA 98, 6895-6900.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 6895-6900
    • Crotty, S.1    Cameron, C.E.2    Andino, R.3
  • 13
    • 0015133749 scopus 로고
    • Selforganization of matter and the evolution of biological macromolecules
    • Eigen, M. 1971. Selforganization of matter and the evolution of biological macromolecules. Die Naturwissenschaften 58, 456-523.
    • (1971) Die Naturwissenschaften , vol.58 , pp. 456-523
    • Eigen, M.1
  • 15
    • 77956818983 scopus 로고    scopus 로고
    • Estimating frequencies of minority nevirapine-resistant strains in chronically HIV-1-infected individuals naive to nevirapine by using stochastic simulations and a mathematical model
    • Gadhamsetty, S., and Dixit, N.M. 2010. Estimating frequencies of minority nevirapine-resistant strains in chronically HIV-1-infected individuals naive to nevirapine by using stochastic simulations and a mathematical model. J. Virol. 84, 10230-10240.
    • (2010) J. Virol. , vol.84 , pp. 10230-10240
    • Gadhamsetty, S.1    Dixit, N.M.2
  • 16
    • 20044377204 scopus 로고    scopus 로고
    • The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility
    • Gonzalez, E., Kulkarni, H., Bolivar, H., et al. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307, 1434-1440.
    • (2005) Science , vol.307 , pp. 1434-1440
    • Gonzalez, E.1    Kulkarni, H.2    Bolivar, H.3
  • 17
    • 15444379112 scopus 로고    scopus 로고
    • Suppression of viral infectivity through lethal defection
    • Grande-Perez, A., Lazaro, E., Lowenstein, P., et al. 2005. Suppression of viral infectivity through lethal defection. Proc. Natl. Acad. Sci.USA 102, 4448-4452.
    • (2005) Proc. Natl. Acad. Sci.USA , vol.102 , pp. 4448-4452
    • Grande-Perez, A.1    Lazaro, E.2    Lowenstein, P.3
  • 19
    • 79955423458 scopus 로고    scopus 로고
    • A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase
    • Hinkley, T., Martins, J., Chappey, C., et al. 2011. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat. Genet. 43, 487-489.
    • (2011) Nat. Genet. , vol.43 , pp. 487-489
    • Hinkley, T.1    Martins, J.2    Chappey, C.3
  • 20
    • 84898957407 scopus 로고
    • Conductance and the rapid mixing property for markov chains: The approximation of the permanent resolved
    • Theor. Comput. (STOC 1988)
    • Jerrum, M., and Sinclair, A. 1988. Conductance and the rapid mixing property for markov chains: the approximation of the permanent resolved. Proc 20th Annu. ACM Symp. Theor. Comput. (STOC 1988) 235-243.
    • (1988) Proc 20th Annu. ACM Symp , pp. 235-243
    • Jerrum, M.1    Sinclair, A.2
  • 21
    • 33751021082 scopus 로고    scopus 로고
    • Stochastic or deterministic: What is the effective population size of HIV-1?
    • Kouyos, R.D., Althaus, C.L., and Bonhoeffer, S. 2006. Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol. 14, 507-511.
    • (2006) Trends Microbiol. , vol.14 , pp. 507-511
    • Kouyos, R.D.1    Althaus, C.L.2    Bonhoeffer, S.3
  • 22
    • 77957658175 scopus 로고    scopus 로고
    • Quasispecies theory and the behavior of RNA viruses
    • Lauring, A.S., and Andino, R. 2010. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog. 6, e1001005.
    • (2010) PLoS Pathog. , vol.6
    • Lauring, A.S.1    Andino, R.2
  • 23
    • 79251565236 scopus 로고    scopus 로고
    • Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside kp1461
    • Mullins, J.I., Heath, L., Hughes, J. P., et al. 2011. Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside kp1461. PLoS ONE 6, e15135.
    • (2011) PLoS ONE , vol.6
    • Mullins, J.I.1    Heath, L.2    Hughes, J.P.3
  • 24
    • 79151481321 scopus 로고    scopus 로고
    • A stochastic version of Eigen's model
    • Musso, F. 2011. A stochastic version of Eigen's model. Bull. Math. Biol. 73, 151-180.
    • (2011) Bull. Math. Biol. , vol.73 , pp. 151-180
    • Musso, F.1
  • 25
    • 0032564366 scopus 로고    scopus 로고
    • Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy
    • Nijhuis, M., Boucher, C. A. B., Schipper, P., et al. 1998. Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy. Proc. Nat. Acad. Sci. USA 95, 14441-14446.
    • (1998) Proc. Nat. Acad. Sci. USA , vol.95 , pp. 14441-14446
    • Nijhuis, M.1    Boucher, C.A.B.2    Schipper, P.3
  • 26
    • 0024974481 scopus 로고
    • Error thresholds of replication in finite populations-mutation frequencies and the onset of Muller's ratchet
    • Nowak, M., and Schuster, P. 1989. Error thresholds of replication in finite populations-mutation frequencies and the onset of Muller's ratchet. J. Theor. Biol. 137, 375-395.
    • (1989) J. Theor. Biol. , vol.137 , pp. 375-395
    • Nowak, M.1    Schuster, P.2
  • 27
    • 75349091080 scopus 로고    scopus 로고
    • Quasispecies theory for finite populations
    • Park, J.-M., Munoz, E., and Deem, M.W. 2010. Quasispecies theory for finite populations. Phys. Rev. E 81, 011902.
    • (2010) Phys. Rev. e , vol.81 , pp. 011902
    • Park, J.-M.1    Munoz, E.2    Deem, M.W.3
  • 28
    • 33645510409 scopus 로고    scopus 로고
    • Exact solutions of the Eigen model with general fitness functions and degradation rates
    • Saakian, D. B., and Hu, C.-K. 2006. Exact solutions of the Eigen model with general fitness functions and degradation rates. Proc. Natl. Acad. Sci. USA 103, 4935-4939.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 4935-4939
    • Saakian, D.B.1    Hu, C.-K.2
  • 29
    • 54549111432 scopus 로고    scopus 로고
    • Dynamics of the Eigen and the Crow-Kimura models for molecular evolution
    • Saakian, D.B., Rozanova, O., and Akmetzhanov, A. 2008. Dynamics of the Eigen and the Crow-Kimura models for molecular evolution. Phys. Rev. E 78, 041908.
    • (2008) Phys. Rev. E. , vol.78 , pp. 041908
    • Saakian, D.B.1    Rozanova, O.2    Akmetzhanov, A.3
  • 30
    • 0020437078 scopus 로고
    • Self-replication with errors: A model for polynucleotide replication
    • Swetina, J., and Schuster, P. 1982. Self-replication with errors: a model for polynucleotide replication. Biophys. Chem. 16, 329-345.
    • (1982) Biophys. Chem. , vol.16 , pp. 329-345
    • Swetina, J.1    Schuster, P.2
  • 31
    • 33847251630 scopus 로고    scopus 로고
    • Error-threshold exists in fitness landscapes with lethal mutants
    • Takeuchi, N., and Hogeweg, P. 2007. Error-threshold exists in fitness landscapes with lethal mutants. BMC Evol. Biol. 7, 15
    • (2007) BMC Evol. Biol. , vol.7 , pp. 15
    • Takeuchi, N.1    Hogeweg, P.2
  • 34
    • 34249318581 scopus 로고
    • What is the difference between models of error thresholds and Muller's ratchet?
    • Wagner, G.P., and Krall, P. 1993. What is the difference between models of error thresholds and Muller's ratchet? J. Math. Biol. 32, 33-44.
    • (1993) J Math. Biol. , vol.32 , pp. 33-44
    • Wagner, G.P.1    Krall, P.2
  • 35
    • 0030789022 scopus 로고    scopus 로고
    • Model dependency of error thresholds: The role of fitness functions and contrasts between the finite and infinite sites models
    • Wiehe, T. 1997. Model dependency of error thresholds: the role of fitness functions and contrasts between the finite and infinite sites models. Genet. Res. 69, 127-136.
    • (1997) Genet. Res. , vol.69 , pp. 127-136
    • Wiehe, T.1
  • 36
    • 24944485118 scopus 로고    scopus 로고
    • Quasispecies theory in the context of population genetics
    • Wilke, C. 2005. Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5, 44.
    • (2005) BMC Evol. Biol. , vol.5 , pp. 44
    • Wilke, C.1
  • 37
    • 0029913049 scopus 로고    scopus 로고
    • Population evolution on a multiplicative single-peak fitness landscape
    • Woodcock, G., and Higgs, P. 1996. Population evolution on a multiplicative single-peak fitness landscape. J. Theor. Biol. 179, 61-73.
    • (1996) J. Theor. Biol. , vol.179 , pp. 61-73
    • Woodcock, G.1    Higgs, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.