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Items: 1 to 20 of 189

1.

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.

2.

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.

3.

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
4.

An analysis and prediction of nucleosome positioning based on information content.

Xing YQ, Liu GQ, Zhao XJ, Cai L.

Chromosome Res. 2013 Mar;21(1):63-74. doi: 10.1007/s10577-013-9338-z. Epub 2013 Feb 22.

PMID:
23435498
5.

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.

Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J, Wang JP.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20158-63. doi: 10.1073/pnas.1315809110. Epub 2013 Nov 25.

6.

DNA structural patterns and nucleosome positioning.

Staffelbach H, Koller T, Burks C.

J Biomol Struct Dyn. 1994 Oct;12(2):301-25.

PMID:
7702771
7.
8.

Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy.

Cui F, Chen L, LoVerso PR, Zhurkin VB.

BMC Bioinformatics. 2014 Sep 22;15:313. doi: 10.1186/1471-2105-15-313.

9.

Nucleosome positioning in yeasts: methods, maps, and mechanisms.

Lieleg C, Krietenstein N, Walker M, Korber P.

Chromosoma. 2015 Jun;124(2):131-51. doi: 10.1007/s00412-014-0501-x. Epub 2014 Dec 23. Review.

PMID:
25529773
10.

Training-free atomistic prediction of nucleosome occupancy.

Minary P, Levitt M.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6293-8. doi: 10.1073/pnas.1404475111. Epub 2014 Apr 14.

11.

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
12.

Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisiae.

Cohanim AB, Kashi Y, Trifonov EN.

J Biomol Struct Dyn. 2005 Jun;22(6):687-94.

PMID:
15842173
13.

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
14.

A deformation energy-based model for predicting nucleosome dyads and occupancy.

Liu G, Xing Y, Zhao H, Wang J, Shang Y, Cai L.

Sci Rep. 2016 Apr 7;6:24133. doi: 10.1038/srep24133.

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.

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.

17.

Experiments confirm the influence of genome long-range correlations on nucleosome positioning.

Vaillant C, Audit B, Arneodo A.

Phys Rev Lett. 2007 Nov 23;99(21):218103. Epub 2007 Nov 21.

PMID:
18233262
18.

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.

19.

Nucleosome structure and repair of N-methylpurines in the GAL1-10 genes of Saccharomyces cerevisiae.

Li S, Smerdon MJ.

J Biol Chem. 2002 Nov 22;277(47):44651-9. Epub 2002 Sep 19.

20.

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