메뉴 건너뛰기




Volumn 14, Issue SUPPL.5, 2013, Pages

Discovering and mapping chromatin states using a tree hidden Markov model

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL TECHNIQUES; DISEASE PROGRESSION; EPIGENETIC MODIFICATION; HIGH-THROUGHPUT SEQUENCING; HISTONE MODIFICATION; MULTIPLE CELL TYPES; TECHNOLOGICAL ADVANCES; VARIATIONAL APPROXIMATION;

EID: 84876128377     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S5-S4     Document Type: Article
Times cited : (35)

References (33)
  • 1
    • 79952534189 scopus 로고    scopus 로고
    • Regulation of chromatin by histone modifications
    • 10.1038/cr.2011.22, 3193420, 21321607
    • Bannister A, Kouzarides T. Regulation of chromatin by histone modifications. Cell research 2011, 21(3):381-395. 10.1038/cr.2011.22, 3193420, 21321607.
    • (2011) Cell research , vol.21 , Issue.3 , pp. 381-395
    • Bannister, A.1    Kouzarides, T.2
  • 2
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • 10.1038/47412, 10638745
    • Strahl BD, Allis CD. The language of covalent histone modifications. Nature 2000, 403(6765):41-5. 10.1038/47412, 10638745.
    • (2000) Nature , vol.403 , Issue.6765 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 3
    • 0037074010 scopus 로고    scopus 로고
    • Signaling network model of chromatin
    • 10.1016/S0092-8674(02)01196-0, 12526804
    • Schreiber SL, Bernstein BE. Signaling network model of chromatin. Cell 2002, 111(6):771-8. 10.1016/S0092-8674(02)01196-0, 12526804.
    • (2002) Cell , vol.111 , Issue.6 , pp. 771-778
    • Schreiber, S.L.1    Bernstein, B.E.2
  • 4
    • 85015069067 scopus 로고    scopus 로고
    • Controlling the double helix
    • 10.1038/nature01411, 12540921
    • Felsenfeld G, Groudine M. Controlling the double helix. Nature 2003, 421(6921):448-453. 10.1038/nature01411, 12540921.
    • (2003) Nature , vol.421 , Issue.6921 , pp. 448-453
    • Felsenfeld, G.1    Groudine, M.2
  • 5
    • 77954766475 scopus 로고    scopus 로고
    • Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression
    • 2928206, 20653935
    • Xu X, Hoang S, Mayo MW, Bekiranov S. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. BMC bioinformatics 2010, 11:396. 2928206, 20653935.
    • (2010) BMC bioinformatics , vol.11 , pp. 396
    • Xu, X.1    Hoang, S.2    Mayo, M.W.3    Bekiranov, S.4
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An Integrated Encyclopedia of DNA Elements in the Human Genome
    • 10.1038/nature11247, 3439153, 22955616
    • Khatun J. An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature 2012, 489:57-74. 10.1038/nature11247, 3439153, 22955616.
    • (2012) Nature , vol.489 , pp. 57-74
    • Khatun, J.1
  • 9
    • 78249266271 scopus 로고    scopus 로고
    • Epigenetic control of recombination in the immune system
    • 10.1016/j.smim.2010.07.003, 2981633, 20832333
    • Bergman Y, Cedar H. Epigenetic control of recombination in the immune system. Seminars in immunology 2010, 22(6):323-9. 10.1016/j.smim.2010.07.003, 2981633, 20832333.
    • (2010) Seminars in immunology , vol.22 , Issue.6 , pp. 323-329
    • Bergman, Y.1    Cedar, H.2
  • 10
    • 68049107038 scopus 로고    scopus 로고
    • Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution
    • 10.1086/598822, 19606595
    • Jablonka E, Raz G. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. The Quarterly review of biology 2009, 84(2):131-176. 10.1086/598822, 19606595.
    • (2009) The Quarterly review of biology , vol.84 , Issue.2 , pp. 131-176
    • Jablonka, E.1    Raz, G.2
  • 11
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: advantages and challenges of a maturing technology
    • 10.1038/nrg2641, 3191340, 19736561
    • Park P. ChIP-seq: advantages and challenges of a maturing technology. Nature Reviews Genetics 2009, 10(10):669-680. 10.1038/nrg2641, 3191340, 19736561.
    • (2009) Nature Reviews Genetics , vol.10 , Issue.10 , pp. 669-680
    • Park, P.1
  • 12
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nature methods 2009, 6(11 Suppl):S22-32.
    • (2009) Nature methods , vol.6 , Issue.11 SUPPL
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 13
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • 10.1038/ng1966, 17277777
    • Heintzman N, Stuart R, Hon G, Fu Y, Ching C, Hawkins R, Barrera L, Van Calcar S, Qu C, Ching K, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature genetics 2007, 39(3):311-318. 10.1038/ng1966, 17277777.
    • (2007) Nature genetics , vol.39 , Issue.3 , pp. 311-318
    • Heintzman, N.1    Stuart, R.2    Hon, G.3    Fu, Y.4    Ching, C.5    Hawkins, R.6    Barrera, L.7    Van Calcar, S.8    Qu, C.9    Ching, K.10
  • 14
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • 10.1038/nature07672, 2754849, 19182780
    • Mitchell Guttman I, Garber M, French C, Lin M, Feldser D, Huarte M, Zuk O, Carey B, Cassady J, Cabili M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458(7235):223-227. 10.1038/nature07672, 2754849, 19182780.
    • (2009) Nature , vol.458 , Issue.7235 , pp. 223-227
    • Mitchell Guttman, I.1    Garber, M.2    French, C.3    Lin, M.4    Feldser, D.5    Huarte, M.6    Zuk, O.7    Carey, B.8    Cassady, J.9    Cabili, M.10
  • 15
    • 73449092184 scopus 로고    scopus 로고
    • Discovery and annotation of functional chromatin signatures in the human genome
    • 10.1371/journal.pcbi.1000566, 2775352, 19918365
    • Hon G, Wang W, Ren B. Discovery and annotation of functional chromatin signatures in the human genome. PLoS computational biology 2009, 5(11):e1000566. 10.1371/journal.pcbi.1000566, 2775352, 19918365.
    • (2009) PLoS computational biology , vol.5 , Issue.11
    • Hon, G.1    Wang, W.2    Ren, B.3
  • 16
    • 79961186157 scopus 로고    scopus 로고
    • Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering
    • 10.1093/nar/gkr016, 3105409, 21266477
    • Ucar D, Hu Q, Tan K. Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic acids research 2011, 39(10):4063-75. 10.1093/nar/gkr016, 3105409, 21266477.
    • (2011) Nucleic acids research , vol.39 , Issue.10 , pp. 4063-4075
    • Ucar, D.1    Hu, Q.2    Tan, K.3
  • 17
    • 67650330565 scopus 로고    scopus 로고
    • Spatial clustering of multivariate genomic and epigenomic information
    • Springer
    • Jaschek R, Tanay A. Spatial clustering of multivariate genomic and epigenomic information. Research in Computational Molecular Biology 2009, 170-183. Springer.
    • (2009) Research in Computational Molecular Biology , pp. 170-183
    • Jaschek, R.1    Tanay, A.2
  • 18
    • 84862785201 scopus 로고    scopus 로고
    • Unsupervised pattern discovery in human chromatin structure through genomic segmentation
    • 10.1038/nmeth.1937, 3340533, 22426492
    • Hoffman M, Buske O, Wang J, Weng Z, Bilmes J, Noble W. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature methods 2012, 9(5):473-476. 10.1038/nmeth.1937, 3340533, 22426492.
    • (2012) Nature methods , vol.9 , Issue.5 , pp. 473-476
    • Hoffman, M.1    Buske, O.2    Wang, J.3    Weng, Z.4    Bilmes, J.5    Noble, W.6
  • 19
    • 53749092745 scopus 로고    scopus 로고
    • An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
    • 10.1093/bioinformatics/btn402, 18667444
    • Xu H, Wei C, Lin F, Sung W. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 2008, 24(20):2344-2349. 10.1093/bioinformatics/btn402, 18667444.
    • (2008) Bioinformatics , vol.24 , Issue.20 , pp. 2344-2349
    • Xu, H.1    Wei, C.2    Lin, F.3    Sung, W.4
  • 20
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • 10.1038/nbt.1662, 2919626, 20657582
    • Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature biotechnology 2010, 28(8):817-25. 10.1038/nbt.1662, 2919626, 20657582.
    • (2010) Nature biotechnology , vol.28 , Issue.8 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 24
    • 65749118363 scopus 로고    scopus 로고
    • Graphical models, exponential families, and variational inference
    • 3553421, 23355817
    • Wainwright M, Jordan M. Graphical models, exponential families, and variational inference. Foundations and Trends® in Machine Learning 2008, 1(1-2):1-305. 3553421, 23355817.
    • (2008) Foundations and Trends® in Machine Learning , vol.1 , Issue.1-2 , pp. 1-305
    • Wainwright, M.1    Jordan, M.2
  • 29
    • 84876109759 scopus 로고    scopus 로고
    • ENCODE
    • ENCODE 2012, ENCODE., http://genome.ucsc.edu/ENCODE/
    • (2012)
  • 32
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • 10.1038/nature08514, 2857523, 19829295
    • Lister R, Pelizzola M, Dowen R, Hawkins R, Hon G, Tonti-Filippini J, Nery J, Lee L, Ye Z, Ngo Q, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462(7271):315-322. 10.1038/nature08514, 2857523, 19829295.
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.3    Hawkins, R.4    Hon, G.5    Tonti-Filippini, J.6    Nery, J.7    Lee, L.8    Ye, Z.9    Ngo, Q.10
  • 33
    • 61349098460 scopus 로고    scopus 로고
    • Differential chromatin marking of introns and expressed exons by H3K36me3
    • 10.1038/ng.322, 2648722, 19182803
    • Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu X, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature genetics 2009, 41(3):376-381. 10.1038/ng.322, 2648722, 19182803.
    • (2009) Nature genetics , vol.41 , Issue.3 , pp. 376-381
    • Kolasinska-Zwierz, P.1    Down, T.2    Latorre, I.3    Liu, T.4    Liu, X.5    Ahringer, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.