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Items: 1 to 20 of 97

1.

Discovery and characterization of chromatin states for systematic annotation of the human genome.

Ernst J, Kellis M.

Nat Biotechnol. 2010 Aug;28(8):817-25. doi: 10.1038/nbt.1662. Epub 2010 Jul 25.

2.

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A.

Mol Syst Biol. 2014 Dec 19;10:768. doi: 10.15252/msb.20145654.

3.

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.

4.

'Traffic light rules': Chromatin states direct miRNA-mediated network motifs running by integrating epigenome and regulatome.

Zhao H, Zhang G, Pang L, Lan Y, Wang L, Yu F, Hu J, Li F, Zhao T, Xiao Y, Li X.

Biochim Biophys Acta. 2016 Jul;1860(7):1475-88. doi: 10.1016/j.bbagen.2016.04.008. Epub 2016 Apr 14.

PMID:
27091612
5.
6.

Human genome replication proceeds through four chromatin states.

Julienne H, Zoufir A, Audit B, Arneodo A.

PLoS Comput Biol. 2013;9(10):e1003233. doi: 10.1371/journal.pcbi.1003233. Epub 2013 Oct 10.

7.

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.

8.

Discovering and mapping chromatin states using a tree hidden Markov model.

Biesinger J, Wang Y, Xie X.

BMC Bioinformatics. 2013;14 Suppl 5:S4. doi: 10.1186/1471-2105-14-S5-S4. Epub 2013 Apr 10.

9.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS.

Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12.

10.

A tiered hidden Markov model characterizes multi-scale chromatin states.

Larson JL, Huttenhower C, Quackenbush J, Yuan GC.

Genomics. 2013 Jul;102(1):1-7. doi: 10.1016/j.ygeno.2013.03.009. Epub 2013 Apr 6.

11.

Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.

Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q, Zhang Y.

Nucleic Acids Res. 2016 Jan 8;44(1):75-94. doi: 10.1093/nar/gkv1332. Epub 2015 Dec 3.

12.

Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.

Ucar D, Hu Q, Tan K.

Nucleic Acids Res. 2011 May;39(10):4063-75. doi: 10.1093/nar/gkr016. Epub 2011 Jan 25.

13.

Mapping and analysis of chromatin state dynamics in nine human cell types.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE.

Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906. Epub 2011 Mar 23.

14.

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X.

Nature. 2016 Jan 21;529(7586):418-22. doi: 10.1038/nature16496. Epub 2016 Jan 13.

15.

Chromatin and epigenetic features of long-range gene regulation.

Harmston N, Lenhard B.

Nucleic Acids Res. 2013 Aug;41(15):7185-99. doi: 10.1093/nar/gkt499. Epub 2013 Jun 13. Review.

16.

The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.

17.

Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis.

Chen C, Zhang S, Zhang XS.

Nucleic Acids Res. 2013 Nov;41(20):9230-42. doi: 10.1093/nar/gkt712. Epub 2013 Aug 14.

18.

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.

19.

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.

Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K.

Cell Res. 2012 Mar;22(3):490-503. doi: 10.1038/cr.2012.15. Epub 2012 Jan 24.

20.

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation.

Mendizabal I, Yi SV.

Hum Mol Genet. 2016 Jan 1;25(1):69-82. doi: 10.1093/hmg/ddv449. Epub 2015 Oct 28.

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