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Items: 1 to 20 of 99

1.

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome.

Yang CC, Buck MJ, Chen MH, Chen YF, Lan HC, Chen JJ, Cheng C, Liu CC.

BMC Genomics. 2013 May 8;14:310. doi: 10.1186/1471-2164-14-310.

2.

Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma.

Buck MJ, Raaijmakers LM, Ramakrishnan S, Wang D, Valiyaparambil S, Liu S, Nowak NJ, Pili R.

Oncogene. 2014 Oct 9;33(41):4961-5. doi: 10.1038/onc.2013.455. Epub 2013 Nov 4.

PMID:
24186201
3.

Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq).

Bianco S, Rodrigue S, Murphy BD, Gévry N.

Methods Mol Biol. 2015;1334:261-72. doi: 10.1007/978-1-4939-2877-4_17.

PMID:
26404156
4.

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti.

Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M.

BMC Genomics. 2016 May 10;17:341. doi: 10.1186/s12864-016-2468-x.

5.

A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana.

Omidbakhshfard MA, Winck FV, Arvidsson S, Riaño-Pachón DM, Mueller-Roeber B.

J Integr Plant Biol. 2014 Jun;56(6):527-38. doi: 10.1111/jipb.12151. Epub 2014 Mar 16.

PMID:
24373132
6.
7.

Sequence and chromatin determinants of cell-type-specific transcription factor binding.

Arvey A, Agius P, Noble WS, Leslie C.

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.

8.

Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells.

Hong CP, Choe MK, Roh TY.

Genomics Inform. 2012 Sep;10(3):145-52. doi: 10.5808/GI.2012.10.3.145. Epub 2012 Sep 28.

9.

Mapping open chromatin with formaldehyde-assisted isolation of regulatory elements.

Nammo T, Rodríguez-Seguí SA, Ferrer J.

Methods Mol Biol. 2011;791:287-96. doi: 10.1007/978-1-61779-316-5_21.

PMID:
21913087
10.

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.

11.

Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast.

Kent NA, Eibert SM, Mellor J.

J Biol Chem. 2004 Jun 25;279(26):27116-23. Epub 2004 Apr 24.

12.

Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis.

Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J.

BMC Genomics. 2013 Apr 5;14:226. doi: 10.1186/1471-2164-14-226.

13.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

14.

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

Todt TJ, Wels M, Bongers RS, Siezen RS, van Hijum SA, Kleerebezem M.

PLoS One. 2012;7(9):e45097. doi: 10.1371/journal.pone.0045097. Epub 2012 Sep 20.

15.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

16.

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.

Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M.

Genome Res. 2013 May;23(5):800-11. doi: 10.1101/gr.144899.112. Epub 2013 Mar 19.

17.

Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.

Baek S, Sung MH.

Methods Mol Biol. 2016;1418:225-40. doi: 10.1007/978-1-4939-3578-9_12.

18.

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

Giresi PG, Lieb JD.

Methods. 2009 Jul;48(3):233-9. doi: 10.1016/j.ymeth.2009.03.003. Epub 2009 Mar 18.

19.

Systematic identification of conserved motif modules in the human genome.

Cai X, Hou L, Su N, Hu H, Deng M, Li X.

BMC Genomics. 2010 Oct 14;11:567. doi: 10.1186/1471-2164-11-567.

20.

Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells.

Wong KC, Li Y, Peng C.

Bioinformatics. 2016 Feb 1;32(3):321-4. doi: 10.1093/bioinformatics/btv555. Epub 2015 Sep 26.

PMID:
26411866

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