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Results: 1 to 20 of 136

1.

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets.

Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ.

Genome Biol. 2012 Mar 16;13(3):R16. doi: 10.1186/gb-2012-13-3-r16.

PMID:
22424423
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

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

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

PMID:
22863112
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

PMID:
18684996
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

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
6.

Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-Seq.

Hitchler MJ, Rice JC.

Methods Mol Biol. 2011;767:253-67. doi: 10.1007/978-1-61779-201-4_19.

PMID:
21822881
[PubMed - indexed for MEDLINE]
7.

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.

Xu H, Wei CL, Lin F, Sung WK.

Bioinformatics. 2008 Oct 15;24(20):2344-9. doi: 10.1093/bioinformatics/btn402. Epub 2008 Jul 29.

PMID:
18667444
[PubMed - indexed for MEDLINE]
Free Article
8.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keleş S.

PLoS Comput Biol. 2011 Jul;7(7):e1002111. doi: 10.1371/journal.pcbi.1002111. Epub 2011 Jul 14.

PMID:
21779159
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.

Orlov Y, Xu H, Afonnikov D, Lim B, Heng JC, Yuan P, Chen M, Yan J, Clarke N, Orlova N, Huss M, Gunbin K, Podkolodnyy N, Ng HH.

J Integr Bioinform. 2012 Sep 18;9(2):211. doi: 10.2390/biecoll-jib-2012-211.

PMID:
22987856
[PubMed - indexed for MEDLINE]
10.

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
11.

seqMINER: an integrated ChIP-seq data interpretation platform.

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L.

Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.

PMID:
21177645
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

[Genome-wide analysis of chromatin and transcription factor by ChIP-seq].

Kurata T.

Tanpakushitsu Kakusan Koso. 2009 Aug;54(10):1248-55. Review. Japanese. No abstract available.

PMID:
19663251
[PubMed - indexed for MEDLINE]
13.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

PMID:
20158869
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques.

Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M.

PLoS One. 2010 Dec 29;5(12):e15898. doi: 10.1371/journal.pone.0015898.

PMID:
21209968
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

Xing H, Mo Y, Liao W, Zhang MQ.

PLoS Comput Biol. 2012;8(7):e1002613. doi: 10.1371/journal.pcbi.1002613. Epub 2012 Jul 26.

PMID:
22844240
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genome-wide in silico prediction of gene expression.

McLeay RC, Lesluyes T, Cuellar Partida G, Bailey TL.

Bioinformatics. 2012 Nov 1;28(21):2789-96. doi: 10.1093/bioinformatics/bts529. Epub 2012 Sep 6.

PMID:
22954627
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones.

Gokhman D, Livyatan I, Sailaja BS, Melcer S, Meshorer E.

Nat Struct Mol Biol. 2013 Jan;20(1):119-26. doi: 10.1038/nsmb.2448. Epub 2012 Dec 9.

PMID:
23222641
[PubMed - indexed for MEDLINE]
18.

Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq.

Shamimuzzaman M, Vodkin L.

BMC Genomics. 2013 Jul 16;14:477. doi: 10.1186/1471-2164-14-477.

PMID:
23865409
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

PMID:
19956545
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells.

Chen G, Zhou Q.

BMC Genomics. 2011 Oct 20;12:515. doi: 10.1186/1471-2164-12-515.

PMID:
22011333
[PubMed - indexed for MEDLINE]
Free PMC Article

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