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Volumn 80, Issue 3-4, 2015, Pages 189-192

Advances in Computer Simulation of Genome Evolution: Toward More Realistic Evolutionary Genomics Analysis by Approximate Bayesian Computation

Author keywords

Approximate Bayesian computation; Computer simulations; Genome evolution; Molecular evolution; Population genetics

Indexed keywords

BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA SEQUENCE; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR EVOLUTION;

EID: 84939979471     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-015-9673-0     Document Type: Letter
Times cited : (14)

References (24)
  • 2
    • 84855717407 scopus 로고    scopus 로고
    • Genome-wide heterogeneity of nucleotide substitution model fit
    • COI: 1:CAS:528:DC%2BC3MXht12nsbrM, PID: 21824869
    • Arbiza L, Patricio M, Dopazo H, Posada D (2011) Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol 3:896–908
    • (2011) Genome Biol Evol , vol.3 , pp. 896-908
    • Arbiza, L.1    Patricio, M.2    Dopazo, H.3    Posada, D.4
  • 3
    • 84899584297 scopus 로고    scopus 로고
    • Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories
    • COI: 1:CAS:528:DC%2BC2cXmvFCisbg%3D, PID: 24557445
    • Arenas M, Posada D (2014) Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol 31(5):1295–1301
    • (2014) Mol Biol Evol , vol.31 , Issue.5 , pp. 1295-1301
    • Arenas, M.1    Posada, D.2
  • 4
    • 84926669324 scopus 로고    scopus 로고
    • CodABC: a computational framework to coestimate recombination, substitution and molecular adaptation rates by approximate Bayesian computation. Mol Biol Evol
    • Arenas M, Lopes JS, Beaumont MA, Posada D (2015) CodABC: a computational framework to coestimate recombination, substitution and molecular adaptation rates by approximate Bayesian computation. Mol Biol Evol. doi:10.1093/molbev/msu411
    • (2015) doi:10.1093/molbev/msu411
    • Arenas, M.1    Lopes, J.S.2    Beaumont, M.A.3    Posada, D.4
  • 5
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • COI: 1:CAS:528:DC%2BD1MXht1OgsrzJ, PID: 19838166
    • Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461(7268):1243–1247
    • (2009) Nature , vol.461 , Issue.7268 , pp. 1243-1247
    • Barrick, J.E.1    Yu, D.S.2    Yoon, S.H.3    Jeong, H.4    Oh, T.K.5    Schneider, D.6    Lenski, R.E.7    Kim, J.F.8
  • 6
    • 77955019593 scopus 로고    scopus 로고
    • Cassis: detection of genomic rearrangement breakpoints
    • COI: 1:CAS:528:DC%2BC3cXptV2hs74%3D, PID: 20576622
    • Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF (2010) Cassis: detection of genomic rearrangement breakpoints. Bioinformatics 26(15):1897–1898
    • (2010) Bioinformatics , vol.26 , Issue.15 , pp. 1897-1898
    • Baudet, C.1    Lemaitre, C.2    Dias, Z.3    Gautier, C.4    Tannier, E.5    Sagot, M.F.6
  • 7
    • 78149388939 scopus 로고    scopus 로고
    • Approximate Bayesian computation in evolution and ecology
    • Beaumont MA (2010) Approximate Bayesian computation in evolution and ecology. Annu Rev Ecol Evol Syst 41:379–405
    • (2010) Annu Rev Ecol Evol Syst , vol.41 , pp. 379-405
    • Beaumont, M.A.1
  • 8
    • 78049477633 scopus 로고    scopus 로고
    • The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex
    • COI: 1:CAS:528:DC%2BC3cXhsVKjs7rI, PID: 20852019
    • Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J et al (2010) The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell 22(9):2943–2955
    • (2010) Plant Cell , vol.22 , Issue.9 , pp. 2943-2955
    • Blanc, G.1    Duncan, G.2    Agarkova, I.3    Borodovsky, M.4    Gurnon, J.5    Kuo, A.6    Lindquist, E.7    Lucas, S.8    Pangilinan, J.9    Polle, J.10
  • 9
    • 84917695871 scopus 로고    scopus 로고
    • Ecological and evolutionary implications of genomic structural variations
    • PID: 25278961
    • Chain FJ, Feulner PG (2014) Ecological and evolutionary implications of genomic structural variations. Front Genet 5:326
    • (2014) Front Genet , vol.5 , pp. 326
    • Chain, F.J.1    Feulner, P.G.2
  • 10
    • 84858406580 scopus 로고    scopus 로고
    • ALF–A simulation framework for genome evolution
    • COI: 1:CAS:528:DC%2BC38Xkt1Cms74%3D, PID: 22160766
    • Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C (2012) ALF–A simulation framework for genome evolution. Mol Biol Evol 29(4):1115–1123
    • (2012) Mol Biol Evol , vol.29 , Issue.4 , pp. 1115-1123
    • Dalquen, D.A.1    Anisimova, M.2    Gonnet, G.H.3    Dessimoz, C.4
  • 11
    • 84874509525 scopus 로고    scopus 로고
    • The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study
    • COI: 1:CAS:528:DC%2BC3sXjslyks70%3D, PID: 23451112
    • Dalquen DA, Altenhoff AM, Gonnet GH, Dessimoz C (2013) The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. PLoS ONE 8(2):e56925
    • (2013) PLoS ONE , vol.8 , Issue.2 , pp. 56925
    • Dalquen, D.A.1    Altenhoff, A.M.2    Gonnet, G.H.3    Dessimoz, C.4
  • 12
    • 79951493627 scopus 로고    scopus 로고
    • On the future of genomic data
    • COI: 1:CAS:528:DC%2BC3MXhs1yrsrw%3D, PID: 21311016
    • Kahn SD (2011) On the future of genomic data. Science 331(6018):728–729
    • (2011) Science , vol.331 , Issue.6018 , pp. 728-729
    • Kahn, S.D.1
  • 13
    • 66049138940 scopus 로고    scopus 로고
    • Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
    • COI: 1:CAS:528:DC%2BD1MXlsFykurs%3D, PID: 19342477
    • Larkin DM, Pape G, Donthu R, Auvil L, Welge M, Lewin HA (2009) Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res 19(5):770–777
    • (2009) Genome Res , vol.19 , Issue.5 , pp. 770-777
    • Larkin, D.M.1    Pape, G.2    Donthu, R.3    Auvil, L.4    Welge, M.5    Lewin, H.A.6
  • 14
    • 0032855518 scopus 로고    scopus 로고
    • Gene transfer, speciation, and the evolution of bacterial genomes
    • COI: 1:CAS:528:DyaK1MXntlCku70%3D, PID: 10508729
    • Lawrence JG (1999) Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 2(5):519–523
    • (1999) Curr Opin Microbiol , vol.2 , Issue.5 , pp. 519-523
    • Lawrence, J.G.1
  • 15
    • 84894063375 scopus 로고    scopus 로고
    • Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation
    • COI: 1:STN:280:DC%2BC2c%2FovFekug%3D%3D, PID: 24149652
    • Lopes JS, Arenas M, Posada D, Beaumont MA (2014) Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation. Heredity 112(3):255–264
    • (2014) Heredity , vol.112 , Issue.3 , pp. 255-264
    • Lopes, J.S.1    Arenas, M.2    Posada, D.3    Beaumont, M.A.4
  • 16
    • 49749120556 scopus 로고    scopus 로고
    • Interacting gene clusters and the evolution of the vertebrate immune system
    • COI: 1:CAS:528:DC%2BD1cXhtV2it7rF, PID: 18573844
    • Makino T, McLysaght A (2008) Interacting gene clusters and the evolution of the vertebrate immune system. Mol Biol Evol 25(9):1855–1862
    • (2008) Mol Biol Evol , vol.25 , Issue.9 , pp. 1855-1862
    • Makino, T.1    McLysaght, A.2
  • 17
    • 33748799967 scopus 로고    scopus 로고
    • Modern computational approaches for analysing molecular genetic variation data
    • COI: 1:CAS:528:DC%2BD28Xps1ahsb0%3D, PID: 16983372
    • Marjoram P, Tavare S (2006) Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet 7(10):759–770
    • (2006) Nat Rev Genet , vol.7 , Issue.10 , pp. 759-770
    • Marjoram, P.1    Tavare, S.2
  • 18
    • 0346734143 scopus 로고    scopus 로고
    • Markov chain Monte Carlo without likelihoods
    • COI: 1:CAS:528:DC%2BD2cXhtVektw%3D%3D, PID: 14663152
    • Marjoram P, Molitor J, Plagnol V, Tavare S (2003) Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 100(26):15324–15328
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.26 , pp. 15324-15328
    • Marjoram, P.1    Molitor, J.2    Plagnol, V.3    Tavare, S.4
  • 19
    • 84882448684 scopus 로고    scopus 로고
    • A sequential coalescent algorithm for chromosomal inversions
    • COI: 1:STN:280:DC%2BC3srps1yhsQ%3D%3D, PID: 23632894
    • Peischl S, Koch E, Guerrero RF, Kirkpatrick M (2013) A sequential coalescent algorithm for chromosomal inversions. Heredity 111(3):200–209
    • (2013) Heredity , vol.111 , Issue.3 , pp. 200-209
    • Peischl, S.1    Koch, E.2    Guerrero, R.F.3    Kirkpatrick, M.4
  • 20
    • 80051563593 scopus 로고    scopus 로고
    • Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
    • COI: 1:CAS:528:DC%2BC3MXpvFeqsLs%3D, PID: 21555365
    • Skovgaard O, Bak M, Lobner-Olesen A, Tommerup N (2011) Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing. Genome Res 21(8):1388–1393
    • (2011) Genome Res , vol.21 , Issue.8 , pp. 1388-1393
    • Skovgaard, O.1    Bak, M.2    Lobner-Olesen, A.3    Tommerup, N.4
  • 21
    • 84883508065 scopus 로고    scopus 로고
    • Death of the genome paper
    • PID: 23653633
    • Smith DR (2013) Death of the genome paper. Front Genet 4:72
    • (2013) Front Genet , vol.4 , pp. 72
    • Smith, D.R.1
  • 23
    • 70350136774 scopus 로고    scopus 로고
    • Efficient approximate bayesian computation coupled with markov chain monte carlo without likelihood
    • PID: 19506307
    • Wegmann D, Leuenberger C, Excoffier L (2009) Efficient approximate bayesian computation coupled with markov chain monte carlo without likelihood. Genetics 182(4):1207–1218
    • (2009) Genetics , vol.182 , Issue.4 , pp. 1207-1218
    • Wegmann, D.1    Leuenberger, C.2    Excoffier, L.3
  • 24
    • 84872506987 scopus 로고    scopus 로고
    • Phenotypic impact of genomic structural variation: insights from and for human disease
    • COI: 1:CAS:528:DC%2BC3sXptlOgsw%3D%3D, PID: 23329113
    • Weischenfeldt J, Symmons O, Spitz F, Korbel JO (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 14(2):125–138
    • (2013) Nat Rev Genet , vol.14 , Issue.2 , pp. 125-138
    • Weischenfeldt, J.1    Symmons, O.2    Spitz, F.3    Korbel, J.O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.