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Results: 1 to 20 of 64

1.

Computational analysis of nucleosome positioning.

Tirosh I.

Methods Mol Biol. 2012;833:443-9. doi: 10.1007/978-1-61779-477-3_27.

PMID:
22183610
[PubMed - indexed for MEDLINE]
2.

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
[PubMed - indexed for MEDLINE]
3.

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy.

Lubliner S, Segal E.

Bioinformatics. 2009 Jun 15;25(12):i348-55. doi: 10.1093/bioinformatics/btp216.

PMID:
19478009
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
20098497
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome.

Feng J, Dai X, Xiang Q, Dai Z, Wang J, Deng Y, He C.

BMC Genomics. 2010 Jan 15;11:33. doi: 10.1186/1471-2164-11-33.

PMID:
20078849
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Epigenome sequencing comes of age in development, differentiation and disease mechanism research.

Zhao Q, Zhang Y.

Epigenomics. 2011 Apr;3(2):207-20. doi: 10.2217/epi.10.78. Review.

PMID:
22122282
[PubMed - indexed for MEDLINE]
7.

DiNuP: a systematic approach to identify regions of differential nucleosome positioning.

Fu K, Tang Q, Feng J, Liu XS, Zhang Y.

Bioinformatics. 2012 Aug 1;28(15):1965-71. doi: 10.1093/bioinformatics/bts329. Epub 2012 Jun 4.

PMID:
22668788
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.

Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W.

Genome Res. 2013 Feb;23(2):341-51. doi: 10.1101/gr.142067.112. Epub 2012 Nov 28.

PMID:
23193179
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals.

Halder K, Halder R, Chowdhury S.

Mol Biosyst. 2009 Dec;5(12):1703-12. doi: 10.1039/b905132e. Epub 2009 May 29.

PMID:
19587895
[PubMed - indexed for MEDLINE]
10.

Re-cracking the nucleosome positioning code.

Segal MR.

Stat Appl Genet Mol Biol. 2008;7(1):Article14. doi: 10.2202/1544-6115.1367. Epub 2008 Apr 21.

PMID:
18454729
[PubMed - indexed for MEDLINE]
11.

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences.

Tirosh I, Sigal N, Barkai N.

Mol Syst Biol. 2010 May 11;6:365. doi: 10.1038/msb.2010.20.

PMID:
20461072
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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. Epub 2011 Apr 9. Review.

PMID:
21482020
[PubMed - indexed for MEDLINE]
13.

G+C content dominates intrinsic nucleosome occupancy.

Tillo D, Hughes TR.

BMC Bioinformatics. 2009 Dec 22;10:442. doi: 10.1186/1471-2105-10-442.

PMID:
20028554
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Transcriptional interaction-assisted identification of dynamic nucleosome positioning.

Dai Z, Dai X, Xiang Q, Feng J, Deng Y, Wang J, He C.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S31. doi: 10.1186/1471-2105-10-S1-S31.

PMID:
19208132
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

DNA methyltransferase accessibility protocol for individual templates by deep sequencing.

Darst RP, Nabilsi NH, Pardo CE, Riva A, Kladde MP.

Methods Enzymol. 2012;513:185-204. doi: 10.1016/B978-0-12-391938-0.00008-2.

PMID:
22929770
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Prediction of nucleosome occupancy in Saccharomyces cerevisiae using position-correlation scoring function.

Xing Y, Zhao X, Cai L.

Genomics. 2011 Nov;98(5):359-66. doi: 10.1016/j.ygeno.2011.07.008. Epub 2011 Aug 2.

PMID:
21839161
[PubMed - indexed for MEDLINE]
Free Article
17.

A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome.

Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF.

Science. 2011 May 20;332(6032):977-80. doi: 10.1126/science.1200508.

PMID:
21596991
[PubMed - indexed for MEDLINE]
Free Article
18.

Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions.

Davey C, Fraser R, Smolle M, Simmen MW, Allan J.

J Mol Biol. 2003 Jan 31;325(5):873-87.

PMID:
12527297
[PubMed - indexed for MEDLINE]
19.

Biochemical screening of stable dinucleosomes using DNA fragments from a dinucleosome DNA library.

Kato M, Onishi Y, Wada-Kiyama Y, Kiyama R.

J Mol Biol. 2005 Jul 8;350(2):215-27.

PMID:
15935377
[PubMed - indexed for MEDLINE]
20.

Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast.

Dai Z, Dai X, Xiang Q.

Bioinformatics. 2011 Jul 1;27(13):1758-64. doi: 10.1093/bioinformatics/btr290. Epub 2011 May 6.

PMID:
21551148
[PubMed - indexed for MEDLINE]
Free Article

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