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Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.

Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE.

PLoS Genet. 2007 Aug;3(8):e136. Epub 2007 Jul 2.


Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12.


Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).

Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS.

Genome Res. 2006 Jan;16(1):123-31. Epub 2005 Dec 12.


Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.

Shu W, Chen H, Bo X, Wang S.

Nucleic Acids Res. 2011 Sep 1;39(17):7428-43. doi: 10.1093/nar/gkr443. Epub 2011 Jun 17.


Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome.

Chen H, Tian Y, Shu W, Bo X, Wang S.

PLoS One. 2012;7(7):e41374. doi: 10.1371/journal.pone.0041374. Epub 2012 Jul 19.


CTCF-dependent enhancer blockers at the upstream region of the chicken alpha-globin gene domain.

Valadez-Graham V, Razin SV, Recillas-Targa F.

Nucleic Acids Res. 2004 Feb 23;32(4):1354-62. Print 2004.


Characterization of chromatin structure and enhancer elements for murine recombination activating gene-2.

Wei XC, Kishi H, Jin ZX, Zhao WP, Kondo S, Matsuda T, Saito S, Muraguchi A.

J Immunol. 2002 Jul 15;169(2):873-81.


Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region.

Jin Y, Oomah K, Cattini PA.

DNA Cell Biol. 2011 Dec;30(12):995-1005. doi: 10.1089/dna.2011.1268. Epub 2011 Jun 28.


Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries.

Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA.

Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4537-42. Epub 2004 Mar 19.


Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.

Follows GA, Dhami P, Göttgens B, Bruce AW, Campbell PJ, Dillon SC, Smith AM, Koch C, Donaldson IJ, Scott MA, Dunham I, Janes ME, Vetrie D, Green AR.

Genome Res. 2006 Oct;16(10):1310-9. Epub 2006 Sep 8.


Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

Shibata Y, Crawford GE.

Methods Mol Biol. 2009;556:177-90. doi: 10.1007/978-1-60327-192-9_13.


High-resolution mapping and characterization of open chromatin across the genome.

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE.

Cell. 2008 Jan 25;132(2):311-22. doi: 10.1016/j.cell.2007.12.014.


An open chromatin structure in a liver-specific enhancer that confers high level expression to human apolipoprotein b transgenes in mice.

Levy-Wilson B, Paulweber B, Antes TJ, Goodart SA, Lee SY.

Mol Cell Biol Res Commun. 2000 Oct;4(4):206-11.


Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.

Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K.

Genome Res. 2009 Jan;19(1):24-32. doi: 10.1101/gr.082800.108. Epub 2008 Dec 3.


Chromatin profiling across the human tumour necrosis factor gene locus reveals a complex, cell type-specific landscape with novel regulatory elements.

Taylor JM, Wicks K, Vandiedonck C, Knight JC.

Nucleic Acids Res. 2008 Sep;36(15):4845-62. doi: 10.1093/nar/gkn444. Epub 2008 Jul 24.


Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS.

Genome Res. 2013 May;23(5):777-88. doi: 10.1101/gr.152140.112. Epub 2013 Mar 12.


Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

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