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Volumn 11, Issue , 2010, Pages

Multivariate Hawkes process models of the occurrence of regulatory elements

Author keywords

[No Author keywords available]

Indexed keywords

HIGH-THROUGHPUT DATA; MULTIVARIATE DISTRIBUTIONS; PRE-PROCESSING STEP; PROCESS MODEL; QUANTITATIVE RESULT; REGULATORY ELEMENTS; REGULATORY REGIONS; TRANSCRIPTIONAL REGULATION;

EID: 77956489081     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-456     Document Type: Article
Times cited : (48)

References (31)
  • 1
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • 10.1038/nrg1315, 15131651
    • Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5(4):276-287. 10.1038/nrg1315, 15131651.
    • (2004) Nat Rev Genet , vol.5 , Issue.4 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 2
    • 0034819935 scopus 로고    scopus 로고
    • A predictive model for regulatory sequences directing liver-specific transcription
    • 10.1101/gr.180601, 311083, 11544200
    • Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11:1559-1566. 10.1101/gr.180601, 311083, 11544200.
    • (2001) Genome Res , vol.11 , pp. 1559-1566
    • Krivan, W.1    Wasserman, W.W.2
  • 3
    • 0032562789 scopus 로고    scopus 로고
    • Identification of regulatory regions which confer muscle-specific gene expression
    • 10.1006/jmbi.1998.1700, 9571041
    • Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278:167-181. 10.1006/jmbi.1998.1700, 9571041.
    • (1998) J Mol Biol , vol.278 , pp. 167-181
    • Wasserman, W.W.1    Fickett, J.W.2
  • 4
    • 3242879521 scopus 로고    scopus 로고
    • CREME: Cis-Regulatory Module Explorer for the human genome
    • 10.1093/nar/gkh385, 441523, 15215390
    • Sharan R, Ben-Hur A, Loots GG, Ovcharenko I. CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res 2004, 32:W253-256. 10.1093/nar/gkh385, 441523, 15215390.
    • (2004) Nucleic Acids Res , vol.32
    • Sharan, R.1    Ben-Hur, A.2    Loots, G.G.3    Ovcharenko, I.4
  • 5
    • 48249097859 scopus 로고    scopus 로고
    • Modeling promoter grammars with evolving hidden Markov models
    • 10.1093/bioinformatics/btn254, 18535083
    • Won KJ, Sandelin A, Marstrand TT, Krogh A. Modeling promoter grammars with evolving hidden Markov models. Bioinformatics 2008, 24:1669-1675. 10.1093/bioinformatics/btn254, 18535083.
    • (2008) Bioinformatics , vol.24 , pp. 1669-1675
    • Won, K.J.1    Sandelin, A.2    Marstrand, T.T.3    Krogh, A.4
  • 6
    • 34250896139 scopus 로고    scopus 로고
    • Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    • 10.1093/nar/gkm201, 1904283, 17452354
    • Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res 2007, 35:3203-3213. 10.1093/nar/gkm201, 1904283, 17452354.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3203-3213
    • Vardhanabhuti, S.1    Wang, J.2    Hannenhalli, S.3
  • 7
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: advantages and challenges of a maturing technology
    • 10.1038/nrg2641, 19736561
    • Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10(10):669-680. 10.1038/nrg2641, 19736561.
    • (2009) Nat Rev Genet , vol.10 , Issue.10 , pp. 669-680
    • Park, P.J.1
  • 8
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • 10.1016/j.ygeno.2003.11.004, 14986705
    • Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
    • (2004) Genomics , vol.83 , Issue.3 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 9
    • 37849044185 scopus 로고    scopus 로고
    • Graphical models for marked point processes based on local independence
    • Didelez V. Graphical models for marked point processes based on local independence. Journal of the Royal Statistical Society 2008, 70:245-264.
    • (2008) Journal of the Royal Statistical Society , vol.70 , pp. 245-264
    • Didelez, V.1
  • 11
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) Project
    • 10.1126/science.1105136, 15499007, The ENCODE Project Consortium
    • The ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640. 10.1126/science.1105136, 15499007, The ENCODE Project Consortium.
    • (2004) Science , vol.306 , pp. 636-640
  • 13
    • 34250366235 scopus 로고    scopus 로고
    • Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    • 10.1101/gr.5573107, 1891338, 17567997
    • Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res 2007, 17:787-797. 10.1101/gr.5573107, 1891338, 17567997.
    • (2007) Genome Res , vol.17 , pp. 787-797
    • Zhang, Z.D.1    Paccanaro, A.2    Fu, Y.3    Weissman, S.4    Weng, Z.5    Chang, J.6    Snyder, M.7    Gerstein, M.B.8
  • 15
    • 34249098071 scopus 로고    scopus 로고
    • Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    • 10.1038/nrg2026, 17486122
    • Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume D. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 2007, 8:424-436. 10.1038/nrg2026, 17486122.
    • (2007) Nat Rev Genet , vol.8 , pp. 424-436
    • Sandelin, A.1    Carninci, P.2    Lenhard, B.3    Ponjavic, J.4    Hayashizaki, Y.5    Hume, D.6
  • 17
    • 24944525791 scopus 로고    scopus 로고
    • FADO: a statistical method to detect favored or avoided distances between motif occurrences using the Hawkes' model
    • Gusto G, Schbath S. FADO: a statistical method to detect favored or avoided distances between motif occurrences using the Hawkes' model. Statistical Applications in Genetics and Molecular Biology 2005, 4(1):24.
    • (2005) Statistical Applications in Genetics and Molecular Biology , vol.4 , Issue.1 , pp. 24
    • Gusto, G.1    Schbath, S.2
  • 18
    • 0037398319 scopus 로고    scopus 로고
    • Homotypic regulatory clusters in Drosophila
    • 10.1101/gr.668403, 430164, 12670999
    • Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA. Homotypic regulatory clusters in Drosophila. Genome Res 2003, 13:579-588. 10.1101/gr.668403, 430164, 12670999.
    • (2003) Genome Res , vol.13 , pp. 579-588
    • Lifanov, A.P.1    Makeev, V.J.2    Nazina, A.G.3    Papatsenko, D.A.4
  • 19
    • 77951874066 scopus 로고    scopus 로고
    • Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
    • 10.1101/gr.104471.109, 2860159, 20363979
    • Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 2010, 20:565-577. 10.1101/gr.104471.109, 2860159, 20363979.
    • (2010) Genome Res , vol.20 , pp. 565-577
    • Gotea, V.1    Visel, A.2    Westlund, J.M.3    Nobrega, M.A.4    Pennacchio, L.A.5    Ovcharenko, I.6
  • 20
    • 0037732643 scopus 로고    scopus 로고
    • Active repression by unliganded retinoid receptors in development: less is sometimes more
    • 10.1083/jcb.200211117, 2172895, 12719467
    • Weston AD, Blumberg B, Underhill TM. Active repression by unliganded retinoid receptors in development: less is sometimes more. J Cell Biol 2003, 161:223-228. 10.1083/jcb.200211117, 2172895, 12719467.
    • (2003) J Cell Biol , vol.161 , pp. 223-228
    • Weston, A.D.1    Blumberg, B.2    Underhill, T.M.3
  • 21
    • 33644943043 scopus 로고    scopus 로고
    • Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
    • 10.1007/s10577-006-1036-7, 16544193
    • Nishida H, Suzuki T, Kondo S, Miura H, Fujimura Y, Hayashizaki Y. Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Res 2006, 14:203-211. 10.1007/s10577-006-1036-7, 16544193.
    • (2006) Chromosome Res , vol.14 , pp. 203-211
    • Nishida, H.1    Suzuki, T.2    Kondo, S.3    Miura, H.4    Fujimura, Y.5    Hayashizaki, Y.6
  • 22
    • 59949085939 scopus 로고    scopus 로고
    • H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
    • 10.1101/gr.080861.108, 2652204, 19047520
    • Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, Sommer A, Aszodi A, Jenuwein T, Barlow DP. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 2009, 19:221-233. 10.1101/gr.080861.108, 2652204, 19047520.
    • (2009) Genome Res , vol.19 , pp. 221-233
    • Pauler, F.M.1    Sloane, M.A.2    Huang, R.3    Regha, K.4    Koerner, M.V.5    Tamir, I.6    Sommer, A.7    Aszodi, A.8    Jenuwein, T.9    Barlow, D.P.10
  • 23
    • 77649325496 scopus 로고    scopus 로고
    • Causal inference in statistics: an overview
    • Pearl J. Causal inference in statistics: an overview. Stat Surv 2009, 3:96-146.
    • (2009) Stat Surv , vol.3 , pp. 96-146
    • Pearl, J.1
  • 27
    • 0030352915 scopus 로고    scopus 로고
    • Stability of nonlinear Hawkes processes
    • Brémaud P, Massoulié L. Stability of nonlinear Hawkes processes. Ann Probab 1996, 24(3):1563-1588.
    • (1996) Ann Probab , vol.24 , Issue.3 , pp. 1563-1588
    • Brémaud, P.1    Massoulié, L.2
  • 31
    • 84944178665 scopus 로고
    • Hierarchical Grouping to Optimize an Objective Function
    • Ward JHJ. Hierarchical Grouping to Optimize an Objective Function. Journal of the American Statistical Association 1963, 58(301):236-244.
    • (1963) Journal of the American Statistical Association , vol.58 , Issue.301 , pp. 236-244
    • Ward, J.H.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.