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Volumn 13, Issue 7, 2006, Pages 1369-1383

Segmenting eukaryotic genomes with the generalized Gibbs sampler

Author keywords

Bayesian modelling; Eukaryotic genomes; Functional non coding RNA; GC content; Generalized Gibbs sampler; Genome segmentation; Markov chain Monte Carlo

Indexed keywords

GENOMIC DNA; UNTRANSLATED RNA;

EID: 33846221985     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.1369     Document Type: Article
Times cited : (29)

References (26)
  • 1
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano, G., Pheasant, M., Makunin, I., et al. 2004. Ultraconserved elements in the human genome. Science 304, 1321-1325.
    • (2004) Science , vol.304 , pp. 1321-1325
    • Bejerano, G.1    Pheasant, M.2    Makunin, I.3
  • 2
    • 4444274988 scopus 로고    scopus 로고
    • A Bayesian approach to DNA sequence segmentation
    • Boys, R.J., and Henderson, D.A. 2004. A Bayesian approach to DNA sequence segmentation. Biometrics 60, 573-588.
    • (2004) Biometrics , vol.60 , pp. 573-588
    • Boys, R.J.1    Henderson, D.A.2
  • 3
    • 0036455552 scopus 로고    scopus 로고
    • On determining the order of Markov dependence of an observed process governed by a hidden Markov model
    • Boys, R.J., and Henderson, D.A. 2002. On determining the order of Markov dependence of an observed process governed by a hidden Markov model. Sci. Prog. 10, 241-251.
    • (2002) Sci. Prog , vol.10 , pp. 241-251
    • Boys, R.J.1    Henderson, D.A.2
  • 4
    • 0034360451 scopus 로고    scopus 로고
    • Detecting homogenous segments in DNA sequences by using hidden Markov models
    • Boys, R.J., Henderson, D.A., and Wilkinson, D.J. 2000. Detecting homogenous segments in DNA sequences by using hidden Markov models. Appl. Statist. 49, 269-285.
    • (2000) Appl. Statist , vol.49 , pp. 269-285
    • Boys, R.J.1    Henderson, D.A.2    Wilkinson, D.J.3
  • 5
    • 0347503105 scopus 로고    scopus 로고
    • Statistical methods for DNA sequence segmentation
    • Braun, J.V., and Muller, H.-G. 1998. Statistical methods for DNA sequence segmentation. Statist. Sci. 13, 142-162.
    • (1998) Statist. Sci , vol.13 , pp. 142-162
    • Braun, J.V.1    Muller, H.-G.2
  • 6
    • 0001652129 scopus 로고    scopus 로고
    • Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation
    • Braun, J.F., Braun, R.K., and Muller, H.-G. 2000. Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation. Biometrika 87, 301-314.
    • (2000) Biometrika , vol.87 , pp. 301-314
    • Braun, J.F.1    Braun, R.K.2    Muller, H.-G.3
  • 7
    • 84950453304 scopus 로고
    • Sampling-based approaches to calculating marginal densities
    • Gelfand, A.E., and Smith, A.F.M. 1990. Sampling-based approaches to calculating marginal densities. J. Am. Statist. Assoc. 85, 398-409.
    • (1990) J. Am. Statist. Assoc , vol.85 , pp. 398-409
    • Gelfand, A.E.1    Smith, A.F.M.2
  • 8
    • 0021518209 scopus 로고
    • Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images
    • Geman, S., and Geman, D. 1984. Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans. Pattern Analysis 6, 721-741.
    • (1984) IEEE Trans. Pattern Analysis , vol.6 , pp. 721-741
    • Geman, S.1    Geman, D.2
  • 9
    • 0002082662 scopus 로고    scopus 로고
    • Full conditional distributions
    • Gilks, W.R, Richardson, S, and Spiegehalter, D.J, eds, Chapman and Hall, London
    • Gilks, W.R. 1996. Full conditional distributions. In Gilks, W.R., Richardson, S., and Spiegehalter, D.J., eds. Markov Chain Monte Carlo in Practice. Chapman and Hall, London, 75-88.
    • (1996) Markov Chain Monte Carlo in Practice , pp. 75-88
    • Gilks, W.R.1
  • 11
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 12
    • 0037250168 scopus 로고    scopus 로고
    • The UCSC genome browser database
    • Available at:, Accessed July 1, 2006
    • Karolchik, D., Baertsch, R., Diekhans, M., et al. 2003. The UCSC genome browser database. Nucleic Acids Res. 31, 51-54. Available at: http://genome.ucsc.edu/. Accessed July 1, 2006.
    • (2003) Nucleic Acids Res , vol.31 , pp. 51-54
    • Karolchik, D.1    Baertsch, R.2    Diekhans, M.3
  • 13
    • 0036855578 scopus 로고    scopus 로고
    • A simulated annealing algorithm for finding consensus sequences
    • Keith, J.M., Adams, P., Bryant, D., et al. 2002. A simulated annealing algorithm for finding consensus sequences. Bioinformatics 18, 1494-1499.
    • (2002) Bioinformatics , vol.18 , pp. 1494-1499
    • Keith, J.M.1    Adams, P.2    Bryant, D.3
  • 14
    • 7244250963 scopus 로고    scopus 로고
    • Inferring an original sequence from erroneous copies: A Bayesian approach
    • Keith, J.M., Adams, P., Bryant, D., et al. 2003. Inferring an original sequence from erroneous copies: a Bayesian approach. Proc. 1st Asia-Pacific Bioinform. Conf. 19, 23-28.
    • (2003) Proc. 1st Asia-Pacific Bioinform. Conf , vol.19 , pp. 23-28
    • Keith, J.M.1    Adams, P.2    Bryant, D.3
  • 16
    • 15244341643 scopus 로고    scopus 로고
    • Sampling phylogenetic tree space with the generalized Gibbs sampler
    • Keith, J.M., Adams, P., Ragan, M.A., et al. 2005. Sampling phylogenetic tree space with the generalized Gibbs sampler. Mol. Phylogenet. Evol. 34, 459-468.
    • (2005) Mol. Phylogenet. Evol , vol.34 , pp. 459-468
    • Keith, J.M.1    Adams, P.2    Ragan, M.A.3
  • 18
    • 0033059370 scopus 로고    scopus 로고
    • Bayesian inference on biopolymer models
    • Liu, J.S., and Lawrence, C.E. 1999. Bayesian inference on biopolymer models. Bioinformatics 15, 38-52.
    • (1999) Bioinformatics , vol.15 , pp. 38-52
    • Liu, J.S.1    Lawrence, C.E.2
  • 19
    • 0035195942 scopus 로고    scopus 로고
    • Non-coding RNAs: The architects of eukaryotic complexity
    • 2, 986-991
    • Mattick, J.S. 2001. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2, 986-991.
    • (2001) EMBO Rep
    • Mattick, J.S.1
  • 20
    • 0141867857 scopus 로고    scopus 로고
    • Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms
    • Mattick, J.S. 2003. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25, 930-939.
    • (2003) Bioessays , vol.25 , pp. 930-939
    • Mattick, J.S.1
  • 21
    • 17644429619 scopus 로고    scopus 로고
    • SEGMENT: Identifying compositional domains in DNA sequences
    • Oliver, J.L., Roman-Roldan, R., Perez, J., et al. 1999. SEGMENT: identifying compositional domains in DNA sequences. Bioinformatics 15, 974-979.
    • (1999) Bioinformatics , vol.15 , pp. 974-979
    • Oliver, J.L.1    Roman-Roldan, R.2    Perez, J.3
  • 22
    • 0035802388 scopus 로고    scopus 로고
    • Isochore chromosome maps of eukaryotic genomes
    • Oliver, J.L., Bernaola-Galvan, P., Carpena, P., et al. 2001. Isochore chromosome maps of eukaryotic genomes. Gene 276, 47-56.
    • (2001) Gene , vol.276 , pp. 47-56
    • Oliver, J.L.1    Bernaola-Galvan, P.2    Carpena, P.3
  • 23
    • 18744381824 scopus 로고    scopus 로고
    • Isochore chromosome maps of the human genome
    • Oliver, J.L., Carpena, P., Roman-Roldan, R., et al. 2002. Isochore chromosome maps of the human genome. Gene 300, 117-127.
    • (2002) Gene , vol.300 , pp. 117-127
    • Oliver, J.L.1    Carpena, P.2    Roman-Roldan, R.3
  • 24
    • 23044446529 scopus 로고    scopus 로고
    • Genome segmentation using piecewise constant intensity models and reversible jump MCMC
    • Salmenkivi, M., Kere, J., and Mannila, H. 2002. Genome segmentation using piecewise constant intensity models and reversible jump MCMC. Bioinformatics 18, S211-S218.
    • (2002) Bioinformatics , vol.18
    • Salmenkivi, M.1    Kere, J.2    Mannila, H.3
  • 25
    • 0344721480 scopus 로고    scopus 로고
    • Complete sequence and gene map of a human major histocompatibility complex
    • MHC Sequencing Consortium
    • MHC Sequencing Consortium. 1999. Complete sequence and gene map of a human major histocompatibility complex. Nature 401, 921-923.
    • (1999) Nature , vol.401 , pp. 921-923
  • 26
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston, R.H., Lindblad-Toh, K., Birney, E., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1    Lindblad-Toh, K.2    Birney, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.