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Items: 1 to 20 of 146

1.

Nucleosome positioning signals in genomic DNA.

Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z.

Genome Res. 2007 Aug;17(8):1170-7. Epub 2007 Jul 9.

2.

Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning.

Wang JY, Wang J, Liu G.

Chromosome Res. 2012 Oct;20(7):889-902. doi: 10.1007/s10577-012-9328-6. Epub 2012 Dec 5.

PMID:
23247720
3.

A genomic code for nucleosome positioning.

Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang JP, Widom J.

Nature. 2006 Aug 17;442(7104):772-8. Epub 2006 Jul 19.

4.

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
5.

Genome-scale identification of nucleosome positions in S. cerevisiae.

Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ.

Science. 2005 Jul 22;309(5734):626-30. Epub 2005 Jun 16.

6.

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

Ozonov EA, van Nimwegen E.

PLoS Comput Biol. 2013;9(8):e1003181. doi: 10.1371/journal.pcbi.1003181. Epub 2013 Aug 22.

7.

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2009 Aug;16(8):847-52. doi: 10.1038/nsmb.1636. Epub 2009 Jul 20.

8.

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF.

Nature. 2007 Mar 29;446(7135):572-6.

PMID:
17392789
9.

Structural features based genome-wide characterization and prediction of nucleosome organization.

Gan Y, Guan J, Zhou S, Zhang W.

BMC Bioinformatics. 2012 Mar 26;13:49. doi: 10.1186/1471-2105-13-49.

10.

Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence.

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

BMC Genomics. 2009 Jan 10;10:15. doi: 10.1186/1471-2164-10-15.

11.

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.

12.

Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches.

De Santis P, Morosetti S, Scipioni A.

J Biomol Struct Dyn. 2010 Jun;27(6):747-64.

PMID:
20232931
13.

Nucleosome positioning on yeast plasmids is determined only by the internal signal of DNA sequence occupied by the nucleosome.

Kiryanov GI, Isaeva LV, Kinzurashvili LN, Zacharova MG.

Biochemistry (Mosc). 2003 Apr;68(4):492-6.

14.

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.

15.

Predicting nucleosome positions in yeast: using the absolute frequency.

Zhang Z, Zhang Y, Gutman I.

J Biomol Struct Dyn. 2012;29(5):1081-8.

PMID:
22292961
16.

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.

Lantermann AB, Straub T, Strålfors A, Yuan GC, Ekwall K, Korber P.

Nat Struct Mol Biol. 2010 Feb;17(2):251-7. doi: 10.1038/nsmb.1741. Epub 2010 Jan 31.

PMID:
20118936
17.

Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

Reynolds SM, Bilmes JA, Noble WS.

PLoS Comput Biol. 2010 Jul 8;6(7):e1000834. doi: 10.1371/journal.pcbi.1000834.

18.

Nucleosome positioning based on the sequence word composition.

Yi XF, He ZS, Chou KC, Kong XY.

Protein Pept Lett. 2012 Jan;19(1):79-90.

PMID:
21919856
19.

Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis.

Zhao X, Pei Z, Liu J, Qin S, Cai L.

Chromosome Res. 2010 Nov;18(7):777-85. doi: 10.1007/s10577-010-9160-9. Epub 2010 Oct 16.

PMID:
20953693
20.

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.

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