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Items: 1 to 20 of 198

1.

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast.

Deniz O, Flores O, Battistini F, Pérez A, Soler-López M, Orozco M.

BMC Genomics. 2011 Oct 7;12:489. doi: 10.1186/1471-2164-12-489.

2.

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.

3.

Insights into distinct regulatory modes of nucleosome positioning.

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

BMC Genomics. 2009 Dec 14;10:602. doi: 10.1186/1471-2164-10-602.

4.

Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe.

Lantermann A, Strålfors A, Fagerström-Billai F, Korber P, Ekwall K.

Methods. 2009 Jul;48(3):218-25. doi: 10.1016/j.ymeth.2009.02.004. Epub 2009 Feb 20.

PMID:
19233281
5.

Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites.

Möbius W, Gerland U.

PLoS Comput Biol. 2010 Aug 19;6(8). pii: e1000891. doi: 10.1371/journal.pcbi.1000891.

6.

Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.

Wu X, Liu H, Liu H, Su J, Lv J, Cui Y, Wang F, Zhang Y.

Gene. 2013 Nov 1;530(1):8-18. doi: 10.1016/j.gene.2013.08.018. Epub 2013 Aug 16.

PMID:
23958656
7.

Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast.

Swamy KB, Chu WY, Wang CY, Tsai HK, Wang D.

BMC Evol Biol. 2011 May 31;11:150. doi: 10.1186/1471-2148-11-150.

8.

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
9.

Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.

Gutiérrez G, Millán-Zambrano G, Medina DA, Jordán-Pla A, Pérez-Ortín JE, Peñate X, Chávez S.

Epigenetics Chromatin. 2017 Dec 7;10(1):58. doi: 10.1186/s13072-017-0165-x.

10.

Prediction of nucleosome positioning based on transcription factor binding sites.

Yi X, Cai YD, He Z, Cui W, Kong X.

PLoS One. 2010 Sep 1;5(9). pii: e12495. doi: 10.1371/journal.pone.0012495.

11.

DNA physical properties determine nucleosome occupancy from yeast to fly.

Miele V, Vaillant C, d'Aubenton-Carafa Y, Thermes C, Grange T.

Nucleic Acids Res. 2008 Jun;36(11):3746-56. doi: 10.1093/nar/gkn262. Epub 2008 May 17.

12.

The effect of micrococcal nuclease digestion on nucleosome positioning data.

Chung HR, Dunkel I, Heise F, Linke C, Krobitsch S, Ehrenhofer-Murray AE, Sperling SR, Vingron M.

PLoS One. 2010 Dec 29;5(12):e15754. doi: 10.1371/journal.pone.0015754.

13.
14.

The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer.

Babbitt GA, Tolstorukov MY, Kim Y.

J Biomol Struct Dyn. 2010 Jun;27(6):765-80.

PMID:
20232932
15.

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
16.

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
17.

Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.

Nishida H, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J.

Open Biol. 2012 Apr;2(4):120043. doi: 10.1098/rsob.120043. Erratum in: Open Biol. 2012 Dec;2(12):120171.

18.

Nucleosome organization in the vicinity of transcription factor binding sites in the human genome.

Nie Y, Cheng X, Chen J, Sun X.

BMC Genomics. 2014 Jun 19;15:493. doi: 10.1186/1471-2164-15-493.

19.

Fuzziness and noise in nucleosomal architecture.

Flores O, Deniz Ö, Soler-López M, Orozco M.

Nucleic Acids Res. 2014 Apr;42(8):4934-46. doi: 10.1093/nar/gku165. Epub 2014 Feb 27.

20.

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

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