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Results: 1 to 20 of 124

1.

RFECS: a random-forest based algorithm for enhancer identification from chromatin state.

Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B.

PLoS Comput Biol. 2013;9(3):e1002968. doi: 10.1371/journal.pcbi.1002968. Epub 2013 Mar 14.

PMID:
23526891
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.

PMID:
22537144
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19094206
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Finding combinatorial histone code by semi-supervised biclustering.

Teng L, Tan K.

BMC Genomics. 2012 Jul 3;13:301. doi: 10.1186/1471-2164-13-301.

PMID:
22759587
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
18927605
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genome-wide prediction of transcription factor binding sites using an integrated model.

Won KJ, Ren B, Wang W.

Genome Biol. 2010 Jan 22;11(1):R7. doi: 10.1186/gb-2010-11-1-r7.

PMID:
20096096
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22115494
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Chromatin signatures of active enhancers.

Spicuglia S, Vanhille L.

Nucleus. 2012 Mar 1;3(2):126-31. doi: 10.4161/nucl.19232. Epub 2012 Mar 1. Review.

PMID:
22555596
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP.

Genome Res. 2012 Jun;22(6):1069-80. doi: 10.1101/gr.129817.111. Epub 2012 Mar 15.

PMID:
22421546
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B.

Nat Genet. 2007 Mar;39(3):311-8. Epub 2007 Feb 4.

PMID:
17277777
[PubMed - indexed for MEDLINE]
11.

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX.

Nucleic Acids Res. 2012 Sep;40(16):7690-704. Epub 2012 Jun 6.

PMID:
22675074
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Prediction of transposable element derived enhancers using chromatin modification profiles.

Huda A, Tyagi E, Mariño-Ramírez L, Bowen NJ, Jjingo D, Jordan IK.

PLoS One. 2011;6(11):e27513. doi: 10.1371/journal.pone.0027513. Epub 2011 Nov 7.

PMID:
22087331
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Predicting enhancer transcription and activity from chromatin modifications.

Zhu Y, Sun L, Chen Z, Whitaker JW, Wang T, Wang W.

Nucleic Acids Res. 2013 Dec;41(22):10032-43. doi: 10.1093/nar/gkt826. Epub 2013 Sep 12.

PMID:
24038352
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

He A, Kong SW, Ma Q, Pu WT.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5632-7. doi: 10.1073/pnas.1016959108. Epub 2011 Mar 17.

PMID:
21415370
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Chromatin signature discovery via histone modification profile alignments.

Wang J, Lunyak VV, Jordan IK.

Nucleic Acids Res. 2012 Nov;40(21):10642-56. doi: 10.1093/nar/gks848. Epub 2012 Sep 18.

PMID:
22989711
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines.

Fernández M, Miranda-Saavedra D.

Nucleic Acids Res. 2012 May;40(10):e77. doi: 10.1093/nar/gks149. Epub 2012 Feb 10.

PMID:
22328731
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Modification of enhancer chromatin: what, how, and why?

Calo E, Wysocka J.

Mol Cell. 2013 Mar 7;49(5):825-37. doi: 10.1016/j.molcel.2013.01.038. Review.

PMID:
23473601
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.

Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT.

Genome Res. 2013 Jun;23(6):917-27. doi: 10.1101/gr.149674.112. Epub 2013 Apr 1.

PMID:
23547170
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B.

Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.

PMID:
19295514
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Identification of genetic variants that affect histone modifications in human cells.

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK.

Science. 2013 Nov 8;342(6159):747-9. doi: 10.1126/science.1242429. Epub 2013 Oct 17.

PMID:
24136359
[PubMed - indexed for MEDLINE]
Free PMC Article

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