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Volumn 31, Issue 7, 2013, Pages 615-622

Uniform, optimal signal processing of mapped deep-sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ESTIMATION ALGORITHM; FUNCTIONAL ANNOTATION; HIGH-THROUGHPUT SEQUENCING; HISTONE MODIFICATION; INTEGRATIVE ANALYSIS; MATHEMATICAL FORMALISM; OPTIMAL SIGNAL PROCESSING; SIGNAL PROCESSING THEORY;

EID: 84880310432     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2596     Document Type: Article
Times cited : (129)

References (53)
  • 1
    • 77953808473 scopus 로고    scopus 로고
    • Next-generation genomics: An integrative approach
    • Hawkins, R.D., Hon, G.C. & Ren, B. Next-generation genomics: an integrative approach. Nat. Rev. Genet. 11, 476-486 (2010).
    • (2010) Nat. Rev. Genet , vol.11 , pp. 476-486
    • Hawkins, R.D.1    Hon, G.C.2    Ren, B.3
  • 2
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010).
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1
  • 3
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Song, L. et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21, 1757-1767 (2011).
    • (2011) Genome Res , vol.21 , pp. 1757-1767
    • Song, L.1
  • 4
    • 50849090969 scopus 로고    scopus 로고
    • Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
    • Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5, 829-834 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 829-834
    • Valouev, A.1
  • 5
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol , vol.9
    • Zhang, Y.1
  • 6
    • 54949147307 scopus 로고    scopus 로고
    • F-Seq: A feature density estimator for high-throughput sequence tags
    • Boyle, A.P., Guinney, J., Crawford, G.E. & Furey, T.S. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24, 2537-2538 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 2537-2538
    • Boyle, A.P.1    Guinney, J.2    Crawford, G.E.3    Furey, T.S.4
  • 7
    • 79960614727 scopus 로고    scopus 로고
    • ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
    • Rashid, N.U., Giresi, P.G., Ibrahim, J.G., Sun, W. & Lieb, J.D. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol. 12, R67 (2011).
    • (2011) Genome Biol , vol.12
    • Rashid, N.U.1    Giresi, P.G.2    Ibrahim, J.G.3    Sun, W.4    Lieb, J.D.5
  • 8
    • 76249091269 scopus 로고    scopus 로고
    • A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
    • Lun, D.S., Sherrid, A., Weiner, B., Sherman, D.R. & Galagan, J.E. A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol. 10, R142 (2009).
    • (2009) Genome Biol , vol.10
    • Lun, D.S.1    Sherrid, A.2    Weiner, B.3    Sherman, D.R.4    Galagan, J.E.5
  • 9
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in ChIP-seq peak detection
    • Wilbanks, E.G. & Facciotti, M.T. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS ONE 5, e11471 (2010).
    • (2010) PLoS ONE , vol.5
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 10
    • 84875960191 scopus 로고    scopus 로고
    • A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
    • Han, Z. et al. A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data. BMC Bioinformatics 13 (suppl. 2), S2 (2012).
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL. 2
    • Han, Z.1
  • 11
    • 0001038967 scopus 로고
    • The generalization of student's ratio
    • Hotelling, H. The generalization of student's ratio. Ann. Math. Stat. 2, 360-378 (1931).
    • (1931) Ann. Math. Stat , vol.2 , pp. 360-378
    • Hotelling, H.1
  • 12
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1
  • 13
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 14
    • 48249140621 scopus 로고    scopus 로고
    • FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    • Fejes, A.P. et al. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24, 1729-1730 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 1729-1730
    • Fejes, A.P.1
  • 15
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952-1958 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1
  • 16
    • 77249117360 scopus 로고    scopus 로고
    • Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
    • Chepelev, I., Wei, G., Tang, Q. & Zhao, K. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res. 37, e106 (2009).
    • (2009) Nucleic Acids Res , vol.37
    • Chepelev, I.1    Wei, G.2    Tang, Q.3    Zhao, K.4
  • 17
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1
  • 18
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1
  • 19
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 21
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 22
    • 79952696158 scopus 로고    scopus 로고
    • A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
    • Cheng, C. et al. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol. 12, R15 (2011).
    • (2011) Genome Biol , vol.12
    • Cheng, C.1
  • 23
    • 84865761246 scopus 로고    scopus 로고
    • Modeling gene expression using chromatin features in various cellular contexts
    • Dong, X. et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 13, R53 (2012).
    • (2012) Genome Biol , vol.13
    • Dong, X.1
  • 24
    • 84865712383 scopus 로고    scopus 로고
    • Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    • Cheng, C. et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 22, 1658-1667 (2012).
    • (2012) Genome Res , vol.22 , pp. 1658-1667
    • Cheng, C.1
  • 25
    • 84864929478 scopus 로고    scopus 로고
    • Computational inference of mRNA stability from histone modification and transcriptome profiles
    • Wang, C. et al. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res. 40, 6414-6423 (2012).
    • (2012) Nucleic Acids Res , vol.40 , pp. 6414-6423
    • Wang, C.1
  • 26
    • 20044388557 scopus 로고    scopus 로고
    • From signatures to models: Understanding cancer using microarrays
    • Segal, E., Friedman, N., Kaminski, N., Regev, A. & Koller, D. From signatures to models: understanding cancer using microarrays. Nat. Genet. 37, S38-S45 (2005).
    • (2005) Nat. Genet , vol.37
    • Segal, E.1    Friedman, N.2    Kaminski, N.3    Regev, A.4    Koller, D.5
  • 27
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • Wingender, E., Dietze, P., Karas, H. & Knuppel, R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 24, 238-241 (1996).
    • (1996) Nucleic Acids Res , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 28
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. & Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94 (2004).
    • (2004) Nucleic Acids Res , vol.32
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 29
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 30
    • 0035118134 scopus 로고    scopus 로고
    • Nestin-EGFP transgenic mice: Visualization of the self-renewal and multipotency of CNS stem cells
    • Kawaguchi, A. et al. Nestin-EGFP transgenic mice: visualization of the self-renewal and multipotency of CNS stem cells. Mol. Cell Neurosci. 17, 259-273 (2001).
    • (2001) Mol. Cell Neurosci , vol.17 , pp. 259-273
    • Kawaguchi, A.1
  • 31
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    • Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
    • (2007) Nature , vol.448 , pp. 553-560
    • Mikkelsen, T.S.1
  • 32
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008).
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1
  • 33
    • 79959349283 scopus 로고    scopus 로고
    • Genome-wide remodeling of the epigenetic landscape during myogenic differentiation
    • Asp, P. et al. Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc. Natl. Acad. Sci. USA 108, E149-E158 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108
    • Asp, P.1
  • 34
    • 34247092473 scopus 로고    scopus 로고
    • A locus on 2p12 containing the co-regulated MRPL19 and C2ORF3 genes is associated to dyslexia
    • Anthoni, H. et al. A locus on 2p12 containing the co-regulated MRPL19 and C2ORF3 genes is associated to dyslexia. Hum. Mol. Genet. 16, 667-677 (2007).
    • (2007) Hum. Mol. Genet , vol.16 , pp. 667-677
    • Anthoni, H.1
  • 35
    • 70449353513 scopus 로고    scopus 로고
    • A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB
    • Need, A.C. et al. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. Hum. Mol. Genet. 18, 4650-4661 (2009).
    • (2009) Hum. Mol. Genet , vol.18 , pp. 4650-4661
    • Need, A.C.1
  • 36
    • 77955866537 scopus 로고    scopus 로고
    • PTIP promotes chromatin changes critical for immunoglobulin class switch recombination
    • Daniel, J.A. et al. PTIP promotes chromatin changes critical for immunoglobulin class switch recombination. Science 329, 917-923 (2010).
    • (2010) Science , vol.329 , pp. 917-923
    • Daniel, J.A.1
  • 37
    • 77957220857 scopus 로고    scopus 로고
    • Comparative epigenomic analysis of murine and human adipogenesis
    • Mikkelsen, T.S. et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 143, 156-169 (2010).
    • (2010) Cell , vol.143 , pp. 156-169
    • Mikkelsen, T.S.1
  • 38
    • 80052569569 scopus 로고    scopus 로고
    • Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells
    • Wang, H. et al. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc. Natl. Acad. Sci. USA 108, 14908-14913 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 14908-14913
    • Wang, H.1
  • 39
    • 0142184265 scopus 로고    scopus 로고
    • Neural crest specification: Migrating into genomics
    • Gammill, L.S. & Bronner-Fraser, M. Neural crest specification: migrating into genomics. Nat. Rev. Neurosci. 4, 795-805 (2003).
    • (2003) Nat. Rev. Neurosci , vol.4 , pp. 795-805
    • Gammill, L.S.1    Bronner-Fraser, M.2
  • 40
    • 77952214662 scopus 로고    scopus 로고
    • GREAT improves functional interpretation of cis-regulatory regions
    • McLean, C.Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495-501 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 495-501
    • McLean, C.Y.1
  • 41
    • 4444220683 scopus 로고    scopus 로고
    • Activation of REST/NRSF target genes in neural stem cells is sufficient to cause neuronal differentiation
    • Su, X., Kameoka, S., Lentz, S. & Majumder, S. Activation of REST/NRSF target genes in neural stem cells is sufficient to cause neuronal differentiation. Mol. Cell Biol. 24, 8018-8025 (2004).
    • (2004) Mol. Cell Biol , vol.24 , pp. 8018-8025
    • Su, X.1    Kameoka, S.2    Lentz, S.3    Majumder, S.4
  • 42
    • 76549105557 scopus 로고    scopus 로고
    • Cell-context specific role of the E2F/Rb pathway in development and disease
    • Swiss, V.A. & Casaccia, P. Cell-context specific role of the E2F/Rb pathway in development and disease. Glia 58, 377-390 (2010).
    • (2010) Glia , vol.58 , pp. 377-390
    • Swiss, V.A.1    Casaccia, P.2
  • 43
    • 70949100121 scopus 로고    scopus 로고
    • Telomere shortening in neural stem cells disrupts neuronal differentiation and neuritogenesis
    • Ferron, S.R. et al. Telomere shortening in neural stem cells disrupts neuronal differentiation and neuritogenesis. J. Neurosci. 29, 14394-14407 (2009).
    • (2009) J. Neurosci , vol.29 , pp. 14394-14407
    • Ferron, S.R.1
  • 44
    • 0036205049 scopus 로고    scopus 로고
    • Notch pathway molecules are essential for the maintenance, but not the generation, of mammalian neural stem cells
    • Hitoshi, S. et al. Notch pathway molecules are essential for the maintenance, but not the generation, of mammalian neural stem cells. Genes Dev. 16, 846-858 (2002).
    • (2002) Genes Dev , vol.16 , pp. 846-858
    • Hitoshi, S.1
  • 45
    • 70349267600 scopus 로고    scopus 로고
    • Mapping accessible chromatin regions using Sono-Seq
    • Auerbach, R.K. et al. Mapping accessible chromatin regions using Sono-Seq. Proc. Natl. Acad. Sci. USA 106, 14926-14931 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 14926-14931
    • Auerbach, R.K.1
  • 46
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    • Rhee, H.S. & Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419 (2011).
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 47
    • 33644858608 scopus 로고    scopus 로고
    • Developmental mechanisms and cis-regulatory codes
    • Ochoa-Espinosa, A. & Small, S. Developmental mechanisms and cis-regulatory codes. Curr. Opin. Genet. Dev. 16, 165-170 (2006).
    • (2006) Curr. Opin. Genet. Dev , vol.16 , pp. 165-170
    • Ochoa-Espinosa, A.1    Small, S.2
  • 48
    • 67649268137 scopus 로고    scopus 로고
    • Spatio-temporal Hotelling observer for signal detection from image sequences
    • Caucci, L., Barrett, H.H. & Rodriguez, J.J. Spatio-temporal Hotelling observer for signal detection from image sequences. Opt. Express 17, 10946-10958 (2009).
    • (2009) Opt. Express , vol.17 , pp. 10946-10958
    • Caucci, L.1    Barrett, H.H.2    Rodriguez, J.J.3
  • 49
    • 0018015137 scopus 로고
    • Modeling by shortest data description
    • Rissanen, J. Modeling by shortest data description. Automatica 14, 465-471 (1978).
    • (1978) Automatica , vol.14 , pp. 465-471
    • Rissanen, J.1
  • 50
    • 46149133538 scopus 로고
    • On detection of the number of signals in presence of white noise
    • Zhao, L.C., Krishnaiah, P.R. & Bai, Z.D. On detection of the number of signals in presence of white noise. J. Multivariate Anal. 20, 1-25 (1986).
    • (1986) J. Multivariate Anal , vol.20 , pp. 1-25
    • Zhao, L.C.1    Krishnaiah, P.R.2    Bai, Z.D.3
  • 51
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1
  • 52
    • 75949117507 scopus 로고    scopus 로고
    • MOODS: Fast search for position weight matrix matches in DNA sequences
    • Korhonen, J., Martinmaki, P., Pizzi, C., Rastas, P. & Ukkonen, E. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 25, 3181-3182 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 3181-3182
    • Korhonen, J.1    Martinmaki, P.2    Pizzi, C.3    Rastas, P.4    Ukkonen, E.5


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