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Items: 1 to 20 of 87

1.

Targeted recruitment of histone modifications in humans predicted by genomic sequences.

Yuan GC.

J Comput Biol. 2009 Feb;16(2):341-55. doi: 10.1089/cmb.2008.18TT.

PMID:
19193151
2.

Evidence for sequence biases associated with patterns of histone methylation.

Wang Z, Willard HF.

BMC Genomics. 2012 Aug 2;13:367. doi: 10.1186/1471-2164-13-367.

3.

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

Ashoor H, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V.

Bioinformatics. 2013 Dec 1;29(23):2979-86. doi: 10.1093/bioinformatics/btt524. Epub 2013 Sep 9.

4.

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

Hon G, Ren B, Wang W.

PLoS Comput Biol. 2008 Oct;4(10):e1000201. doi: 10.1371/journal.pcbi.1000201. Epub 2008 Oct 17.

5.

Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.

Zhang Y, Shin H, Song JS, Lei Y, Liu XS.

BMC Genomics. 2008 Nov 13;9:537. doi: 10.1186/1471-2164-9-537.

6.
7.

Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking.

Lee BM, Mahadevan LC.

J Cell Biochem. 2009 Sep 1;108(1):22-34. doi: 10.1002/jcb.22250.

PMID:
19623574
8.

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

Won KJ, Chepelev I, Ren B, Wang W.

BMC Bioinformatics. 2008 Dec 18;9:547. doi: 10.1186/1471-2105-9-547.

9.

Identifying differential histone modification sites from ChIP-seq data.

Xu H, Sung WK.

Methods Mol Biol. 2012;802:293-303. doi: 10.1007/978-1-61779-400-1_19.

PMID:
22130888
10.

Computational micromodel for epigenetic mechanisms.

Raghavan K, Ruskin HJ, Perrin D, Goasmat F, Burns J.

PLoS One. 2010 Nov 30;5(11):e14031. doi: 10.1371/journal.pone.0014031.

11.

Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression.

Xu X, Hoang S, Mayo MW, Bekiranov S.

BMC Bioinformatics. 2010 Jul 23;11:396. doi: 10.1186/1471-2105-11-396.

12.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

13.

Histone modifications for human epigenome analysis.

Kimura H.

J Hum Genet. 2013 Jul;58(7):439-45. doi: 10.1038/jhg.2013.66. Epub 2013 Jun 6. Review.

PMID:
23739122
14.

The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos.

Bogdanović O, Fernández-Miñán A, Tena JJ, de la Calle-Mustienes E, Gómez-Skarmeta JL.

Methods. 2013 Aug 15;62(3):207-15. doi: 10.1016/j.ymeth.2013.04.011. Epub 2013 Apr 23.

PMID:
23624103
15.

Computational characterization of modes of transcriptional regulation of nuclear receptor genes.

Sharma Y, Chilamakuri CS, Bakke M, Lenhard B.

PLoS One. 2014 Feb 13;9(2):e88880. doi: 10.1371/journal.pone.0088880. eCollection 2014.

16.

Interplay between different epigenetic modifications and mechanisms.

Murr R.

Adv Genet. 2010;70:101-41. doi: 10.1016/B978-0-12-380866-0.60005-8. Review.

PMID:
20920747
17.

HHMD: the human histone modification database.

Zhang Y, Lv J, Liu H, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X.

Nucleic Acids Res. 2010 Jan;38(Database issue):D149-54. doi: 10.1093/nar/gkp968. Epub 2009 Nov 5.

18.

Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes.

Lu Y, Qu W, Min B, Liu Z, Chen C, Zhang C.

IET Syst Biol. 2014 Jun;8(3):104-15. doi: 10.1049/iet-syb.2013.0042.

PMID:
25014377
19.

Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data.

Podsiadło A, Wrzesień M, Paja W, Rudnicki W, Wilczyński B.

BMC Syst Biol. 2013;7 Suppl 6:S16. doi: 10.1186/1752-0509-7-S6-S16. Epub 2013 Dec 13.

20.

Schistosoma mansoni histones: from transcription to chromatin regulation; an in silico analysis.

Anderson L, Pierce RJ, Verjovski-Almeida S.

Mol Biochem Parasitol. 2012 Jun;183(2):105-14. doi: 10.1016/j.molbiopara.2012.03.001. Epub 2012 Mar 10. Review.

PMID:
22414701

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