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Items: 18

1.

ChIP-seq: advantages and challenges of a maturing technology.

Park PJ.

Nat Rev Genet. 2009 Oct;10(10):669-80. doi: 10.1038/nrg2641. Epub 2009 Sep 8. Review.

2.

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T.

Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Review.

3.

[Processing and analysis of ChIP-seq data].

Gao S, Zhang N, Li B, Xu S, Ye YB, Ruan JS.

Yi Chuan. 2012 Jun;34(6):773-83. Review. Chinese.

PMID:
22698750
4.

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.

Furey TS.

Nat Rev Genet. 2012 Dec;13(12):840-52. doi: 10.1038/nrg3306. Epub 2012 Oct 23. Review.

5.

Defining bacterial regulons using ChIP-seq.

Myers KS, Park DM, Beauchene NA, Kiley PJ.

Methods. 2015 Sep 15;86:80-8. doi: 10.1016/j.ymeth.2015.05.022. Epub 2015 May 29. Review.

6.

Combining genomic and proteomic approaches for epigenetics research.

Han Y, Garcia BA.

Epigenomics. 2013 Aug;5(4):439-52. doi: 10.2217/epi.13.37. Review.

7.

Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.

Hoffman BG, Jones SJ.

J Endocrinol. 2009 Apr;201(1):1-13. doi: 10.1677/JOE-08-0526. Epub 2009 Jan 9. Review.

8.

Computation for ChIP-seq and RNA-seq studies.

Pepke S, Wold B, Mortazavi A.

Nat Methods. 2009 Nov;6(11 Suppl):S22-32. doi: 10.1038/nmeth.1371. Review.

9.

The state-of-the-art of chromatin immunoprecipitation.

Collas P.

Methods Mol Biol. 2009;567:1-25. doi: 10.1007/978-1-60327-414-2_1. Review.

PMID:
19588082
10.

Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation.

Collas P, Dahl JA.

Front Biosci. 2008 Jan 1;13:929-43. Review.

PMID:
17981601
11.

Application of ChIP-Seq and related techniques to the study of immune function.

Northrup DL, Zhao K.

Immunity. 2011 Jun 24;34(6):830-42. doi: 10.1016/j.immuni.2011.06.002. Review.

12.

A short survey of computational analysis methods in analysing ChIP-seq data.

Kim H, Kim J, Selby H, Gao D, Tong T, Phang TL, Tan AC.

Hum Genomics. 2011 Jan;5(2):117-23. Review.

13.

Protein-DNA binding in high-resolution.

Mahony S, Pugh BF.

Crit Rev Biochem Mol Biol. 2015;50(4):269-83. doi: 10.3109/10409238.2015.1051505. Epub 2015 Jun 3. Review.

14.

Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.

Wade JT.

Adv Exp Med Biol. 2015;883:119-34. doi: 10.1007/978-3-319-23603-2_7. Review.

PMID:
26621465
15.

Deciphering transcriptional control mechanisms in hematopoiesis:the impact of high-throughput sequencing technologies.

Wilson NK, Tijssen MR, Gƶttgens B.

Exp Hematol. 2011 Oct;39(10):961-8. doi: 10.1016/j.exphem.2011.07.005. Epub 2011 Jul 23. Review.

PMID:
21781948
16.

[Genomic analysis of DNA-protein interaction by chromatin immunoprecipitation].

Li ML, Wang W, Lu ZH.

Yi Chuan. 2010 Mar;32(3):219-28. Review. Chinese.

PMID:
20233698
17.

Sequencing depth and coverage: key considerations in genomic analyses.

Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP.

Nat Rev Genet. 2014 Feb;15(2):121-32. doi: 10.1038/nrg3642. Review.

PMID:
24434847
18.

A review of three different studies on hidden markov models for epigenetic problems: a computational perspective.

Lee KE, Park HS.

Genomics Inform. 2014 Dec;12(4):145-50. doi: 10.5808/GI.2014.12.4.145. Epub 2014 Dec 31. Review.

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