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Results: 1 to 20 of 23

1.

QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions.

Liu B, Yi J, Sv A, Lan X, Ma Y, Huang TH, Leone G, Jin VX.

BMC Genomics. 2013;14 Suppl 8:S3. doi: 10.1186/1471-2164-14-S8-S3. Epub 2013 Dec 9.

PMID:
24564479
[PubMed - in process]
Free PMC Article
2.

Binding sites analyser (BiSA): software for genomic binding sites archiving and overlap analysis.

Khushi M, Liddle C, Clarke CL, Graham JD.

PLoS One. 2014 Feb 12;9(2):e87301. doi: 10.1371/journal.pone.0087301. eCollection 2014.

PMID:
24533055
[PubMed - in process]
Free PMC Article
3.

The B-subdomain of the Xenopus laevis XFIN KRAB-AB domain is responsible for its weaker transcriptional repressor activity compared to human ZNF10/Kox1.

Born N, Thiesen HJ, Lorenz P.

PLoS One. 2014 Feb 3;9(2):e87609. doi: 10.1371/journal.pone.0087609. eCollection 2014.

PMID:
24498343
[PubMed - in process]
Free PMC Article
4.

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.

Kheradpour P, Kellis M.

Nucleic Acids Res. 2014 Mar;42(5):2976-87. doi: 10.1093/nar/gkt1249. Epub 2013 Dec 13.

PMID:
24335146
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions.

Lupo A, Cesaro E, Montano G, Zurlo D, Izzo P, Costanzo P.

Curr Genomics. 2013 Jun;14(4):268-78. doi: 10.2174/13892029113149990002.

PMID:
24294107
[PubMed]
Free PMC Article
6.

Breaking through an epigenetic wall: re-activation of Oct4 by KRAB-containing designer zinc finger transcription factors.

Juárez-Moreno K, Erices R, Beltran AS, Stolzenburg S, Cuello-Fredes M, Owen GI, Qian H, Blancafort P.

Epigenetics. 2013 Feb;8(2):164-76. doi: 10.4161/epi.23503. Epub 2013 Jan 11.

PMID:
23314702
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.

PMID:
23161675
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.

Frietze S, Wang R, Yao L, Tak YG, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX.

Genome Biol. 2012 Sep 26;13(9):R52. doi: 10.1186/gb-2012-13-9-r52.

PMID:
22951069
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The KRAB zinc finger protein RSL1 regulates sex- and tissue-specific promoter methylation and dynamic hormone-responsive chromatin configuration.

Krebs CJ, Schultz DC, Robins DM.

Mol Cell Biol. 2012 Sep;32(18):3732-42. doi: 10.1128/MCB.00615-12. Epub 2012 Jul 16.

PMID:
22801370
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments.

Kennedy BA, Lan X, Huang TH, Farnham PJ, Jin VX.

Methods Mol Biol. 2012;802:323-34. doi: 10.1007/978-1-61779-400-1_21.

PMID:
22130890
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Discriminative prediction of mammalian enhancers from DNA sequence.

Lee D, Karchin R, Beer MA.

Genome Res. 2011 Dec;21(12):2167-80. doi: 10.1101/gr.121905.111. Epub 2011 Aug 29.

PMID:
21875935
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer.

Kennedy BA, Deatherage DE, Gu F, Tang B, Chan MW, Nephew KP, Huang TH, Jin VX.

PLoS One. 2011;6(7):e22606. doi: 10.1371/journal.pone.0022606. Epub 2011 Jul 25.

PMID:
21799915
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12.

PMID:
21750106
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

ConTra v2: a tool to identify transcription factor binding sites across species, update 2011.

Broos S, Hulpiau P, Galle J, Hooghe B, Van Roy F, De Bleser P.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W74-8. doi: 10.1093/nar/gkr355. Epub 2011 May 16.

PMID:
21576231
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer.

Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH.

Cancer Res. 2011 Mar 1;71(5):1752-62. doi: 10.1158/0008-5472.CAN-10-3573. Epub 2011 Jan 7.

PMID:
21216892
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.

Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ.

PLoS One. 2010 Dec 8;5(12):e15082. doi: 10.1371/journal.pone.0015082.

PMID:
21170338
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data.

Gu F, Hsu HK, Hsu PY, Wu J, Ma Y, Parvin J, Huang TH, Jin VX.

BMC Syst Biol. 2010 Dec 17;4:170. doi: 10.1186/1752-0509-4-170.

PMID:
21167036
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.

Lan X, Bonneville R, Apostolos J, Wu W, Jin VX.

Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.

PMID:
21138948
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.

Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK.

Genome Res. 2011 Mar;21(3):447-55. doi: 10.1101/gr.112623.110. Epub 2010 Nov 24.

PMID:
21106904
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Molecular Mechanisms and Genome-Wide Aspects of PPAR Subtype Specific Transactivation.

Bugge A, Mandrup S.

PPAR Res. 2010;2010. pii: 169506. doi: 10.1155/2010/169506. Epub 2010 Aug 31.

PMID:
20862367
[PubMed]
Free PMC Article

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