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Items: 1 to 20 of 76

1.

Insights from genomic profiling of transcription factors.

Farnham PJ.

Nat Rev Genet. 2009 Sep;10(9):605-16. doi: 10.1038/nrg2636. Epub 2009 Aug 11. Review.

2.

Genomic location analysis by ChIP-Seq.

Barski A, Zhao K.

J Cell Biochem. 2009 May 1;107(1):11-8. doi: 10.1002/jcb.22077. Review.

3.

Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.

Wei G, Hu G, Cui K, Zhao K.

Methods Enzymol. 2012;513:297-313. doi: 10.1016/B978-0-12-391938-0.00013-6.

PMID:
22929775
4.

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V.

Genome Res. 2011 Feb;21(2):245-54. doi: 10.1101/gr.114587.110. Epub 2010 Dec 22.

5.

Identification of transcription factor target genes by ChIP display.

Barski A, Pregizer S, Frenkel B.

Methods Mol Biol. 2008;455:177-90. doi: 10.1007/978-1-59745-104-8_14.

PMID:
18463820
6.

Computational discovery of transcriptional regulatory rules.

Pham TH, Clemente JC, Satou K, Ho TB.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii101-7.

PMID:
16204087
7.

Genomic characterization of perturbation sensitivity.

Ohn JH, Kim J, Kim JH.

Bioinformatics. 2007 Jul 1;23(13):i354-8.

PMID:
17646317
8.

The comprehensive transcriptional analysis in Caenorhabditis elegans by integrating ChIP-seq and gene expression data.

He K, Shao J, Zhao Z, Liu D.

Genet Res (Camb). 2014;96:e005. doi: 10.1017/S0016672314000081.

PMID:
25023089
9.

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.

Gilchrist DA, Fargo DC, Adelman K.

Methods. 2009 Aug;48(4):398-408. doi: 10.1016/j.ymeth.2009.02.024. Epub 2009 Mar 9. Review.

10.

DamID: a methylation-based chromatin profiling approach.

Orian A, Abed M, Kenyagin-Karsenti D, Boico O.

Methods Mol Biol. 2009;567:155-69. doi: 10.1007/978-1-60327-414-2_11. Review.

PMID:
19588092
11.

Nuclear Factor I genomic binding associates with chromatin boundaries.

Pjanic M, Schmid CD, Gaussin A, Ambrosini G, Adamcik J, Pjanic P, Plasari G, Kerschgens J, Dietler G, Bucher P, Mermod N.

BMC Genomics. 2013 Feb 12;14:99. doi: 10.1186/1471-2164-14-99.

12.

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P.

Nat Biotechnol. 2002 Aug;20(8):831-5. Epub 2002 Jul 8.

PMID:
12101405
13.

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways.

Pfenning AR, Kim TK, Spotts JM, Hemberg M, Su D, West AE.

PLoS One. 2010 May 27;5(5):e10870. doi: 10.1371/journal.pone.0010870.

14.

Genomic tools for dissecting oncogenic transcriptional networks in human leukemia.

Palomero T, Ferrando AA.

Leukemia. 2009 Jul;23(7):1236-42. doi: 10.1038/leu.2008.394. Epub 2009 Jan 22. Review.

PMID:
19158827
15.

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.

16.

Genome-wide transcription factor binding: beyond direct target regulation.

MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ.

Trends Genet. 2011 Apr;27(4):141-8. doi: 10.1016/j.tig.2011.01.001. Epub 2011 Feb 4. Review.

17.

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.

Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M.

Bioinformatics. 2006 Dec 15;22(24):3016-24. Epub 2006 Oct 12.

PMID:
17038339
18.

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.

Qian J, Lin J, Luscombe NM, Yu H, Gerstein M.

Bioinformatics. 2003 Oct 12;19(15):1917-26.

PMID:
14555624
19.

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.

Liu L, Ramsay T, Zinkgraf M, Sundell D, Street NR, Filkov V, Groover A.

Plant J. 2015 Jun;82(5):887-98. doi: 10.1111/tpj.12850.

20.

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