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Volumn 31, Issue 19, 2015, Pages 3085-3091

FourCSeq: Analysis of 4C sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; CONFORMATION; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; PROCEDURES; STATISTICS;

EID: 84943388333     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv335     Document Type: Article
Times cited : (67)

References (20)
  • 1
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106
    • (2010) Genome Biol , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate-a practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker, J. et al. (2002) Capturing chromosome conformation. Science, 295, 1306-1311
    • (2002) Science , vol.295 , pp. 1306-1311
    • Dekker, J.1
  • 4
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R. et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1
  • 5
    • 84905593782 scopus 로고    scopus 로고
    • Enhancer loops appear stable during development and are associated with paused polymerase
    • Ghavi-Helm, Y. et al. (2014) Enhancer loops appear stable during development and are associated with paused polymerase. Nature, 512, 96-100
    • (2014) Nature , vol.512 , pp. 96-100
    • Ghavi-Helm, Y.1
  • 6
    • 84866997011 scopus 로고    scopus 로고
    • Iterative correction of Hi-C data reveals hallmarks of chromosome organization
    • Imakaev, M. et al. (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods, 9, 999-1003
    • (2012) Nat. Methods , vol.9 , pp. 999-1003
    • Imakaev, M.1
  • 7
    • 80455179726 scopus 로고    scopus 로고
    • ICLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution
    • König, J. et al. (2011) iCLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J. Vis. Exp. JoVE, 50, 2638
    • (2011) J. Vis. Exp. JoVE , vol.50 , pp. 2638
    • König, J.1
  • 8
    • 84883368195 scopus 로고    scopus 로고
    • Software for computing and annotating genomic ranges
    • Lawrence, M. et al. (2013) Software for computing and annotating genomic ranges. PLoS Comput. Biol., 9, e1003118
    • (2013) PLoS Comput. Biol , vol.9 , pp. e1003118
    • Lawrence, M.1
  • 9
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
    • Love, M.I. et al. (2014) Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol., 15, 550
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1
  • 10
    • 85023624227 scopus 로고    scopus 로고
    • Neural lineage induction reveals multi-scale dynamics of 3d chromatin organization
    • Pekowska, A. et al. (2014) Neural lineage induction reveals multi-scale dynamics of 3d chromatin organization. bioRxiv
    • (2014) Bio. Rxiv
    • Pekowska, A.1
  • 11
    • 84943406648 scopus 로고    scopus 로고
    • fda: FunctionalData Analysis. R Package Version 2.4.3
    • Ramsay, J.O. et al. (2014) fda: FunctionalData Analysis. R Package Version 2.4.3
    • (2014)
    • Ramsay, J.O.1
  • 12
    • 84856008906 scopus 로고    scopus 로고
    • Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
    • Ross-Innes, C.S. et al. (2012) Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 481, 389-393
    • (2012) Nature , vol.481 , pp. 389-393
    • Ross-Innes, C.S.1
  • 13
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C
    • Simonis, M. et al. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet., 38, 1348-1354
    • (2006) Nat. Genet , vol.38 , pp. 1348-1354
    • Simonis, M.1
  • 14
    • 84870310006 scopus 로고    scopus 로고
    • Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation
    • Splinter, E. et al. (2012) Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods, 58, 221-230
    • (2012) Methods , vol.58 , pp. 221-230
    • Splinter, E.1
  • 15
    • 84875143934 scopus 로고    scopus 로고
    • Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions
    • Stadhouders, R. et al. (2013) Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nat. Protoc., 8, 509-524
    • (2013) Nat. Protoc , vol.8 , pp. 509-524
    • Stadhouders, R.1
  • 16
    • 79955760882 scopus 로고    scopus 로고
    • Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
    • Thomas, S. et al. (2011) Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol., 12, R43
    • (2011) Genome Biol , vol.12 , pp. R43
    • Thomas, S.1
  • 17
    • 84880531963 scopus 로고    scopus 로고
    • R3Cseq: An R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data
    • Thongjuea, S. et al. (2013) r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res., 41, e132
    • (2013) Nucleic Acids Res , vol.41 , pp. e132
    • Thongjuea, S.1
  • 18
    • 84924366664 scopus 로고    scopus 로고
    • A discrete transition zone organizes the topological and regulatory autonomy of the adjacent Tfap2c and Bmp7 genes
    • Tsujimura, T. et al. (2015) A discrete transition zone organizes the topological and regulatory autonomy of the adjacent Tfap2c and Bmp7 genes. PLoS Genet., 11, e1004897
    • (2015) PLoS Genet , vol.11 , pp. e1004897
    • Tsujimura, T.1
  • 19
    • 84867003195 scopus 로고    scopus 로고
    • Robust 4C-seq data analysis to screen for regulatory DNA interactions
    • Van de Werken, H.J.G. et al. (2012) Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods, 9, 969-972
    • (2012) Nat. Methods , vol.9 , pp. 969-972
    • Van De Werken, H.J.G.1
  • 20
    • 80054984337 scopus 로고    scopus 로고
    • Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
    • Yaffe, E. and Tanay, A. (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet., 43, 1059-1065
    • (2011) Nat. Genet , vol.43 , pp. 1059-1065
    • Yaffe, E.1    Tanay, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.