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Items: 18

1.

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649.

2.

Rules and regulation in the primary structure of chromatin.

Rando OJ, Ahmad K.

Curr Opin Cell Biol. 2007 Jun;19(3):250-6. Review.

PMID:
17466507
3.

Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution.

Korber P.

Biochem Soc Trans. 2012 Apr;40(2):377-82. doi: 10.1042/BST20110730. Review.

PMID:
22435815
4.

Taking into account nucleosomes for predicting gene expression.

Teif VB, Erdel F, Beshnova DA, Vainshtein Y, Mallm JP, Rippe K.

Methods. 2013 Jul 15;62(1):26-38. doi: 10.1016/j.ymeth.2013.03.011. Review.

PMID:
23523656
5.

Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM.

Rodriguez J, McKnight JN, Tsukiyama T.

Curr Protoc Mol Biol. 2014 Oct 1;108:21.28.1-16. doi: 10.1002/0471142727.mb2128s108. Review.

6.

Predicting nucleosome positioning in genomes: physical and bioinformatic approaches.

Scipioni A, De Santis P.

Biophys Chem. 2011 May;155(2-3):53-64. doi: 10.1016/j.bpc.2011.03.006. Review.

PMID:
21482020
7.

An overview of the computational analyses and discovery of transcription factor binding sites.

Ladunga I.

Methods Mol Biol. 2010;674:1-22. doi: 10.1007/978-1-60761-854-6_1. Review.

PMID:
20827582
8.

Functional roles of nucleosome stability and dynamics.

Chereji RV, Morozov AV.

Brief Funct Genomics. 2015 Jan;14(1):50-60. doi: 10.1093/bfgp/elu038. Review.

9.

Mechanisms by which transcription factors gain access to target sequence elements in chromatin.

Guertin MJ, Lis JT.

Curr Opin Genet Dev. 2013 Apr;23(2):116-23. doi: 10.1016/j.gde.2012.11.008. Review.

10.

Transcription Factor Binding Site Mapping Using ChIP-Seq.

Jaini S, Lyubetskaya A, Gomes A, Peterson M, Park ST, Raman S, Schoolnik G, Galagan J.

Microbiol Spectr. 2014 Apr;2(2). doi: 10.1128/microbiolspec.MGM2-0035-2013. Review.

PMID:
26105820
11.

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. Review.

12.

A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions.

Kuan PF, Huebert D, Gasch A, Keles S.

Stat Appl Genet Mol Biol. 2009;8:Article29. doi: 10.2202/1544-6115.1454. Review.

13.

Nucleosome positioning: bringing order to the eukaryotic genome.

Iyer VR.

Trends Cell Biol. 2012 May;22(5):250-6. doi: 10.1016/j.tcb.2012.02.004. Review.

14.

Pioneer transcription factors in cell reprogramming.

Iwafuchi-Doi M, Zaret KS.

Genes Dev. 2014 Dec 15;28(24):2679-92. doi: 10.1101/gad.253443.114. Review.

15.

Chromatin 'programming' by sequence--is there more to the nucleosome code than %GC?

Hughes A, Rando OJ.

J Biol. 2009;8(11):96. doi: 10.1186/jbiol207. Review.

16.

Absence of a simple code: how transcription factors read the genome.

Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R.

Trends Biochem Sci. 2014 Sep;39(9):381-99. doi: 10.1016/j.tibs.2014.07.002. Review.

17.

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.

Elnitski L, Jin VX, Farnham PJ, Jones SJ.

Genome Res. 2006 Dec;16(12):1455-64. Review.

18.

Effects of DNA supercoiling on chromatin architecture.

Corless S, Gilbert N.

Biophys Rev. 2016;8(3):245-258. Review.

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