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Volumn 29, Issue 7, 2012, Pages 1769-1780

Inferring divergence of context-dependent substitution rates in drosophila genomes with applications to comparative genomics

Author keywords

Con2; conservation score; context dependent evolution; Drosophila genomes; transcription factor binding site evolution

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 84863574768     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss056     Document Type: Article
Times cited : (7)

References (37)
  • 1
    • 0242659321 scopus 로고    scopus 로고
    • DNA sequence evolution with neighbor-dependent mutation
    • DOI 10.1089/10665270360688039
    • Arndt PF, Burge CB, Hwa T. 2003. DNA sequence evolution with neighbor-dependent mutation. J Comput Biol. 10:313-322. (Pubitemid 37372151)
    • (2003) Journal of Computational Biology , vol.10 , Issue.3-4 , pp. 313-322
    • Arndt, P.F.1    Burge, C.B.2    Hwa, T.3
  • 2
    • 19544383635 scopus 로고    scopus 로고
    • Identification and measurement of neighbor-dependent nucleotide substitution processes
    • DOI 10.1093/bioinformatics/bti376
    • Arndt PF, Hwa T. 2005. Identification and measurement of neighbordependent nucleotide substitution processes. Bioinformatics 21:2322-2328. (Pubitemid 40731586)
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2322-2328
    • Arndt, P.F.1    Hwa, T.2
  • 3
    • 53849128927 scopus 로고    scopus 로고
    • A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences
    • Baele G, Van de Peer Y, Vansteelandt S. 2008. A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. Syst Biol. 57:675-692.
    • (2008) Syst Biol , vol.57 , pp. 675-692
    • Baele, G.1    Van De Peer, Y.2    Vansteelandt, S.3
  • 4
    • 77955013629 scopus 로고    scopus 로고
    • Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences
    • Baele G, Van de Peer Y, Vansteelandt S. 2010a. Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. BMC Evol Biol. 10:244.
    • (2010) BMC Evol Biol , vol.10 , pp. 244
    • Baele, G.1    Van De Peer, Y.2    Vansteelandt, S.3
  • 5
    • 77955013327 scopus 로고    scopus 로고
    • Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences
    • Baele G, Van de Peer Y, Vansteelandt S. 2010b. Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J Mol Evol. 71:34-50.
    • (2010) J Mol Evol , vol.71 , pp. 34-50
    • Baele, G.1    Van De Peer, Y.2    Vansteelandt, S.3
  • 6
    • 28744439583 scopus 로고    scopus 로고
    • Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates
    • DOI 10.1089/cmb.2005.12.1166
    • Christensen OF, Hobolth A, Jensen JL. 2005. Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates. J Comput Biol. 12:1166-1182. (Pubitemid 41759888)
    • (2005) Journal of Computational Biology , vol.12 , Issue.9 , pp. 1166-1182
    • Christensen, O.F.1    Hobolth, A.2    Jensen, J.L.3
  • 8
    • 79957577720 scopus 로고    scopus 로고
    • Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection
    • Cohen NM, Kenigsberg E, Tanay A. 2011. Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell 145:773-786.
    • (2011) Cell , vol.145 , pp. 773-786
    • Cohen, N.M.1    Kenigsberg, E.2    Tanay, A.3
  • 9
    • 78649420561 scopus 로고    scopus 로고
    • Mean field variational approximation for continuous-time Bayesian networks
    • Cohn I, El-Hay T, Friedman N, Kupferman R. 2010. Mean field variational approximation for continuous-time Bayesian networks. J Mach Learn Res. 11:2745-2783.
    • (2010) J Mach Learn Res , vol.11 , pp. 2745-2783
    • Cohn, I.1    El-Hay, T.2    Friedman, N.3    Kupferman, R.4
  • 10
    • 0038360789 scopus 로고    scopus 로고
    • TGF-β1-induced Smad 3 binding to the Smad 7 gene: Knockout of Smad 7 gene transcription by sense phosphorothioate oligos, autoregulation, and effect on TGF-β1 secretion: Bleomycin acts through TGF-β1
    • DOI 10.1002/jcb.10528
    • Cutroneo KR, Phan SH. 2003. TGF-beta1-induced Smad 3 binding to the Smad 7 gene:knockout of Smad 7 gene transcription by sense phosphorothioate oligos, autoregulation, and effect on TGF-beta1 secretion:bleomycin acts through TGF-beta1. J Cell Biochem. 89:474-483. (Pubitemid 36648769)
    • (2003) Journal of Cellular Biochemistry , vol.89 , Issue.3 , pp. 474-483
    • Cutroneo, K.R.1    Phan, S.H.2
  • 11
    • 3142756502 scopus 로고    scopus 로고
    • Open source clustering software
    • DOI 10.1093/bioinformatics/bth078
    • de Hoon MJ, Imoto S, Nolan J, Miyano S. 2004. Open source clustering software. Bioinformatics 20:1453-1454. (Pubitemid 38931415)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1453-1454
    • De Hoon, M.J.L.1    Imoto, S.2    Nolan, J.3    Miyano, S.4
  • 12
    • 74549220350 scopus 로고    scopus 로고
    • Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories
    • de Koning AP, Gu W, Pollock DD. 2010. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol Biol Evol. 27:249-265.
    • (2010) Mol Biol Evol , vol.27 , pp. 249-265
    • De Koning, A.P.1    Gu, W.2    Pollock, D.D.3
  • 13
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • DOI 10.1007/BF01734359
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol. 17:368-376. (Pubitemid 11016207)
    • (1981) Journal of Molecular Evolution , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 14
    • 78651320424 scopus 로고    scopus 로고
    • The UCSC Genome Browser database:update 2011
    • Fujita PA, Rhead B, Zweig AS, et al. (27 co-authors). 2010. The UCSC Genome Browser database:update 2011. Nucleic Acids Res. 39:D876-D882.
    • (2010) Nucleic Acids Res , vol.39
    • Fujita, P.A.1    Rhead, B.2    Zweig, A.S.3
  • 16
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • DOI 10.1073/pnas.0404142101
    • Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A. 101:13994-14001. (Pubitemid 39305018)
    • (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.39 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 17
    • 24744445362 scopus 로고    scopus 로고
    • Efficient approximations for learning phylogenetic HMM models from data
    • DOI 10.1093/bioinformatics/bth917
    • Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. 2004. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics 20(SUPPL. 1):i161-i168. (Pubitemid 41296685)
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Jojic, V.1    Jojic, N.2    Meek, C.3    Geiger, D.4    Siepel, A.5    Haussler, D.6    Heckerman, D.7
  • 18
    • 0033225865 scopus 로고    scopus 로고
    • Introduction to variational methods for graphical models
    • DOI 10.1023/A:1007665907178
    • Jordan MI, Ghahramani Z, Jaakkola TS, Saul LK. 1999. An introduction to variational methods for graphical models. Mach Learn. 37:183-233. (Pubitemid 30544678)
    • (1999) Machine Learning , vol.37 , Issue.2 , pp. 183-233
    • Jordan, M.I.1    Ghahramani, Z.2    Jaakkola, T.S.3    Saul, L.K.4
  • 19
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • DOI 10.1007/BF01731581
    • 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. (Pubitemid 11166431)
    • (1980) Journal of Molecular Evolution , vol.16 , Issue.2 , pp. 111-120
    • Kimura, M.1
  • 21
    • 13244276706 scopus 로고    scopus 로고
    • A nucleotide substitution model with nearest-neighbour interactions
    • DOI 10.1093/bioinformatics/bth901
    • Lunter G, Hein J. 2004. A nucleotide substitution model with nearestneighbour interactions. Bioinformatics 20(SUPPL. 1):i216-i223. (Pubitemid 41296692)
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Lunter, G.1    Hein, J.2
  • 23
    • 0036804625 scopus 로고    scopus 로고
    • Mapping mutations on phylogenies
    • DOI 10.1080/10635150290102393
    • Nielsen R. 2002. Mapping mutations on phylogenies. Syst Biol. 51:729-739. (Pubitemid 35294805)
    • (2002) Systematic Biology , vol.51 , Issue.5 , pp. 729-739
    • Nielsen, R.1
  • 26
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
    • DOI 10.1016/j.cell.2008.05.023, PII S009286740800682X
    • Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. 2008. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133:1277-1289. (Pubitemid 351852912)
    • (2008) Cell , vol.133 , Issue.7 , pp. 1277-1289
    • Noyes, M.B.1    Christensen, R.G.2    Wakabayashi, A.3    Stormo, G.D.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 27
    • 0035035443 scopus 로고    scopus 로고
    • A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames
    • Pedersen AM, Jensen JL. 2001. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol Biol Evol. 18:763-776. (Pubitemid 32372947)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 763-776
    • Pedersen, A.-M.K.1    Jensen, J.L.2
  • 29
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • DOI 10.1093/bioinformatics/btg180
    • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3:Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 32
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    • DOI 10.1093/molbev/msh039
    • Siepel A, Haussler D. 2004. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol Biol Evol. 21:468-488. (Pubitemid 38339664)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.3 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 33
    • 67649376350 scopus 로고    scopus 로고
    • Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila
    • Singh ND, Arndt PF, Clark AG, Aquadro CF. 2009. Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila. Mol Biol Evol. 26:1591-1605.
    • (2009) Mol Biol Evol , vol.26 , pp. 1591-1605
    • Singh, N.D.1    Arndt, P.F.2    Clark, A.G.3    Aquadro, C.F.4
  • 36
    • 43549095247 scopus 로고    scopus 로고
    • Sequence context affects the rate of short insertions and deletions in flies and primates
    • Tanay A, Siggia ED. 2008. Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol. 9:R37.
    • (2008) Genome Biol , vol.9
    • Tanay, A.1    Siggia, E.D.2


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