메뉴 건너뛰기




Volumn 12, Issue 3, 2011, Pages 462-477

A continuous-index Bayesian hidden Markov model for prediction of nucleosome positioning in genomic DNA

Author keywords

Chromatin structure; Data augmentation; FAIRE; Tiling arrays

Indexed keywords

FUNGAL DNA;

EID: 79959469318     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxq077     Document Type: Article
Times cited : (3)

References (27)
  • 1
    • 0000353178 scopus 로고
    • Amaximizationtechniqueoccurringinthe statistical analysis ofprobabilistic functions ofmarkov chains
    • BAUM,L. E., PETRIE, T., SOULES, G. AND WEISS,N. (1970). Amaximizationtechniqueoccurringinthe statistical analysis ofprobabilistic functions ofmarkov chains. The Annals of Mathematical Statistics 41, 164-170.
    • (1970) The Annals of Mathematical Statistics , vol.41 , pp. 164-170
    • Bauml, E.1    Petrie, T.2    Soules, G.3    Weiss, N.4
  • 2
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • DOI 10.1016/j.ygeno.2003.11.004
    • BUCK, M. J. AND LIEB, J. D. (2004). Ch IP-chip: considerations for the design, analysis, and application ofgenome-wide chromatin immunoprecipitation experiments. Genomics 83, 349-360. (Pubitemid 38220840)
    • (2004) Genomics , vol.83 , Issue.3 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 3
    • 0003107701 scopus 로고    scopus 로고
    • Calculating posterior distributions and modal estimates in Markov mixture models
    • DOI 10.1016/0304-4076(95)01770-4
    • CHIB, S. (1996). Calculating posterior distributions and modal estimates in Markov mixture models. Journal of Econometrics 75, 79-97. (Pubitemid 126372907)
    • (1996) Journal of Econometrics , vol.75 , Issue.1 , pp. 79-97
    • Chib, S.1
  • 6
    • 34548396434 scopus 로고    scopus 로고
    • Generalized hierarchical Markov models for the discovery of length-constrained sequence features from genome tiling arrays
    • DOI 10.1111/j.1541-0420.2007.00760.x
    • GUPTA, M. (2007). Generalized hierarchical Markov models for the discovery of length-constrained sequence features from genome tiling arrays. Biometrics 63, 797-805. (Pubitemid 47352838)
    • (2007) Biometrics , vol.63 , Issue.3 , pp. 797-805
    • Gupta, M.1
  • 7
    • 35348825777 scopus 로고    scopus 로고
    • Variable selection in regression mixture modeling for the discovery ofgene regulatory networks
    • GUPTA, M. AND IBRAHIM, J. G. (2007). Variable selection in regression mixture modeling for the discovery ofgene regulatory networks. Journal of the American Statistical Association 102, 867-880.
    • (2007) Journal of the American Statistical Association , vol.102 , pp. 867-880
    • Gupta, M.1    Ibrahim, J.G.2
  • 8
    • 0037361669 scopus 로고    scopus 로고
    • Discovery ofconserved sequence patterns using a stochastic dictionary model
    • GUPTA, M. AND LIU, J. S. (2003). Discovery ofconserved sequence patterns using a stochastic dictionary model. Journal of the American Statistical Association 98, 55-56.
    • (2003) Journal of the American Statistical Association , vol.98 , pp. 55-56
    • Gupta, M.1    Liu, J.S.2
  • 9
    • 33749406106 scopus 로고    scopus 로고
    • Cell cycle-specifed fuctuation of nucleosome occupancy at gene promoters
    • HOGAN, G. J., LEE, C.-K. AND LIEB, J. D. (2006). Cell cycle-specifed fuctuation of nucleosome occupancy at gene promoters. PLoS Genetics 2,e158.
    • (2006) PLoS Genetics , vol.2
    • Hogan, G.J.1    Lee, C.-K.2    Lieb, J.D.3
  • 10
    • 77955041719 scopus 로고    scopus 로고
    • Doubly-stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays
    • JOHNSON, W., LIU, X. AND LIU, J. S. (2009). Doubly-stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays. Annals of Applied Statistics 3, 1183-1203.
    • (2009) Annals of Applied Statistics , vol.3 , pp. 1183-1203
    • Johnson, W.1    Liu, X.2    Liu, J.S.3
  • 12
    • 34748826166 scopus 로고    scopus 로고
    • A high-resolution atlas of nucleosome occupancy in yeast
    • DOI 10.1038/ng2117, PII NG2117
    • LEE, W., TILLO, D., BRAY, N., MORSE, R. H., DAVIS, R. W., HUGHES, T. R. AND NISLOW, C. (2007). A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics 39, 1235-1244. (Pubitemid 47482684)
    • (2007) Nature Genetics , vol.39 , Issue.10 , pp. 1235-1244
    • Lee, W.1    Tillo, D.2    Bray, N.3    Morse, R.H.4    Davis, R.W.5    Hughes, T.R.6    Nislow, C.7
  • 13
    • 84950424966 scopus 로고
    • Bayesian models formultiplelocal sequence alignment and Gibbs sampling strategies
    • LIU, J. S.,NEUWALD,A. F. ANDLAWRENCE, C. E. (1995). Bayesian models formultiplelocal sequence alignment and Gibbs sampling strategies. Journal of the American Statistical Association 90, 1156-1170. (Pubitemid 126093131)
    • (1995) Journal of the American Statistical Association , vol.90 , Issue.432 , pp. 1156-1170
    • Liu, J.S.1    Neuwald, A.F.2    Lawrence, C.E.3
  • 14
    • 36949023082 scopus 로고    scopus 로고
    • A nucleosome-guided map of transcription factor binding sites in yeast
    • NARLIKAR, L., GORDAN, R. AND HARTEMINK, A. J. (2007). A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Computational Biology 3,e215.
    • (2007) PLoS Computational Biology , vol.3
    • Narlikar, L.1    Gordan, R.2    Hartemink, A.J.3
  • 15
    • 70349312354 scopus 로고    scopus 로고
    • Ch IP-seq: Advantages and challenges of a maturing technology
    • PARK, P. J. (2009). Ch IP-seq: advantages and challenges of a maturing technology. Nature Reviews Genetics 10, 669-680.
    • (2009) Nature Reviews Genetics , vol.10 , pp. 669-680
    • Park, P.J.1
  • 17
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • RABINER, L. R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77,257-286.
    • (1989) Proceedings of the IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 18
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • DOI 10.1038/nature01595
    • RICHMOND, T. J. AND DAVEY, C. A. (2003). The structure of DNA in the nucleosome core. Nature 423, 145-150. (Pubitemid 36569532)
    • (2003) Nature , vol.423 , Issue.6936 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 22
    • 20444403749 scopus 로고    scopus 로고
    • Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
    • DOI 10.1016/j.molcel.2005.05.003, PII S1097276505013092
    • SEKINGER, E. A., MOQTADERI, Z. AND STRUHL, K. (2005). Intrinsic histone-DNA interactions and low nu-cleosome density are important for preferential accessibility of promoter regions in yeast. Molecular Cell 18, 735-748. (Pubitemid 40804808)
    • (2005) Molecular Cell , vol.18 , Issue.6 , pp. 735-748
    • Sekinger, E.A.1    Moqtaderi, Z.2    Struhl, K.3
  • 23
    • 34249681894 scopus 로고    scopus 로고
    • Continuous-index hidden Markov modelling of array CGH copy number data
    • DOI 10.1093/bioinformatics/btm059
    • STJERNQVIST, S., RYDEN, T., SKOLD, M. AND STAAF, J. (2007). Continuous-index hidden Markov modelling of array CGH copy number data. Bioinformatics 23, 1006-1014. (Pubitemid 47050588)
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 1006-1014
    • Stjernqvist, S.1    Ryden, T.2    Skold, M.3    Staaf, J.4
  • 24
    • 0000069552 scopus 로고
    • Identifability ofmixtures ofproduct measures
    • TEICHER, H. (1967). Identifability ofmixtures ofproduct measures. The Annals of Mathematical Statistics 38, 1300-1302.
    • (1967) The Annals of Mathematical Statistics , vol.38 , pp. 1300-1302
    • Teicher, H.1
  • 25
    • 0026517738 scopus 로고
    • A relationship between the helical twist of DNA and the ordered positioning ofnucleosomes in all eukaryotic cells
    • WIDOM, J. (1992). A relationship between the helical twist of DNA and the ordered positioning ofnucleosomes in all eukaryotic cells. Proceedings of the National Academy of Sciences of the United States of America 89, 1095-1099.
    • (1992) Proceedings of the National Academy of Sciences of the United States of America , vol.89 , pp. 1095-1099
    • Widom, J.1
  • 26
    • 38949204996 scopus 로고    scopus 로고
    • Genomic sequence is highly predictive oflocal nucleosome depletion
    • YUAN, G. C. AND LIU, J. S. (2008). Genomic sequence is highly predictive oflocal nucleosome depletion. PLoS Computational Biology 4, e13.
    • (2008) PLoS Computational Biology , vol.4
    • Yuan, G.C.1    Liu, J.S.2
  • 27
    • 22744432660 scopus 로고    scopus 로고
    • Molecular biology: Genome-scale identification of nucleosome positions in S. cerevisiae
    • DOI 10.1126/science.1112178
    • YUAN, G. C., LIU, Y. J., DION, M. F., SLACK, M. D., WU, L. F., ALTSCHULER, S. J. AND RANDO, O. J. (2005). Genome-scale identifcation of nucleosome positions in S. cerevisiae. Science 309, 626-630. (Pubitemid 41033649)
    • (2005) Science , vol.309 , Issue.5734 , pp. 626-630
    • Yuan, G.-C.1    Liu, Y.-J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5    Altschuler, S.J.6    Rando, O.J.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.