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Results: 1 to 20 of 61

1.

Functional annotation of colon cancer risk SNPs.

Yao L, Tak YG, Berman BP, Farnham PJ.

Nat Commun. 2014 Sep 30;5:5114. doi: 10.1038/ncomms6114.

PMID:
25268989
[PubMed - in process]
Free PMC Article
2.

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes.

Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ.

Genome Biol. 2014 Sep 20;15(9):469. [Epub ahead of print]

PMID:
25239471
[PubMed - as supplied by publisher]
Free PMC Article
3.

Bipartite recognition of DNA by TCF/Pangolin is remarkably flexible and contributes to transcriptional responsiveness and tissue specificity of wingless signaling.

Archbold HC, Broussard C, Chang MV, Cadigan KM.

PLoS Genet. 2014 Sep 4;10(9):e1004591. doi: 10.1371/journal.pgen.1004591. eCollection 2014 Sep.

PMID:
25188465
[PubMed - in process]
Free PMC Article
4.

Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha.

Frietze S, O'Geen H, Littlepage LE, Simion C, Sweeney CA, Farnham PJ, Krig SR.

BMC Genomics. 2014 Jun 24;15:520. doi: 10.1186/1471-2164-15-520.

PMID:
24962896
[PubMed - in process]
Free PMC Article
5.

OccuPeak: ChIP-Seq peak calling based on internal background modelling.

de Boer BA, van Duijvenboden K, van den Boogaard M, Christoffels VM, Barnett P, Ruijter JM.

PLoS One. 2014 Jun 17;9(6):e99844. doi: 10.1371/journal.pone.0099844. eCollection 2014.

PMID:
24936875
[PubMed - in process]
Free PMC Article
6.

The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Picard F, Cadoret JC, Audit B, Arneodo A, Alberti A, Battail C, Duret L, Prioleau MN.

PLoS Genet. 2014 May 1;10(5):e1004282. doi: 10.1371/journal.pgen.1004282. eCollection 2014 May.

PMID:
24785686
[PubMed - in process]
Free PMC Article
7.

Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data.

Ghosh D, Qin ZS.

Genes (Basel). 2010 Sep 27;1(2):317-34. doi: 10.3390/genes1020317.

PMID:
24710049
[PubMed]
Free PMC Article
8.

Leveraging biological replicates to improve analysis in ChIP-seq experiments.

Yang Y, Fear J, Hu J, Haecker I, Zhou L, Renne R, Bloom D, McIntyre LM.

Comput Struct Biotechnol J. 2014 Jan 31;9:e201401002. doi: 10.5936/csbj.201401002. eCollection 2014.

PMID:
24688750
[PubMed]
Free PMC Article
9.

Widespread FRA1-dependent control of mesenchymal transdifferentiation programs in colorectal cancer cells.

Diesch J, Sanij E, Gilan O, Love C, Tran H, Fleming NI, Ellul J, Amalia M, Haviv I, Pearson RB, Tulchinsky E, Mariadason JM, Sieber OM, Hannan RD, Dhillon AS.

PLoS One. 2014 Mar 21;9(3):e88950. doi: 10.1371/journal.pone.0088950. eCollection 2014.

PMID:
24658684
[PubMed - in process]
Free PMC Article
10.

AnnotateGenomicRegions: a web application.

Zammataro L, DeMolfetta R, Bucci G, Ceol A, Muller H.

BMC Bioinformatics. 2014;15 Suppl 1:S8. doi: 10.1186/1471-2105-15-S1-S8. Epub 2014 Jan 10.

PMID:
24564446
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

Tran NT, Huang CH.

Biol Direct. 2014 Feb 20;9:4. doi: 10.1186/1745-6150-9-4. Review.

PMID:
24555784
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Comprehensive functional annotation of 77 prostate cancer risk loci.

Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG; Ellipse/GAME-ON consortium; Practical consortium, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA.

PLoS Genet. 2014 Jan 30;10(1):e1004102. doi: 10.1371/journal.pgen.1004102. eCollection 2014 Jan.

PMID:
24497837
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses.

Lukic S, Nicolas JC, Levine AJ.

Cell Death Differ. 2014 Mar;21(3):381-7. doi: 10.1038/cdd.2013.150. Epub 2013 Oct 25.

PMID:
24162661
[PubMed - in process]
Free PMC Article
14.

Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros.

Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST.

Nat Immunol. 2013 Oct;14(10):1073-83. doi: 10.1038/ni.2707. Epub 2013 Sep 8.

PMID:
24013668
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Past visits present: TCF/LEFs partner with ATFs for β-catenin-independent activity.

Sprowl S, Waterman ML.

PLoS Genet. 2013;9(8):e1003745. doi: 10.1371/journal.pgen.1003745. Epub 2013 Aug 15. No abstract available.

PMID:
23966883
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Integrative analysis of SF-1 transcription factor dosage impact on genome-wide binding and gene expression regulation.

Doghman M, Figueiredo BC, Volante M, Papotti M, Lalli E.

Nucleic Acids Res. 2013 Oct;41(19):8896-907. doi: 10.1093/nar/gkt658. Epub 2013 Aug 1.

PMID:
23907384
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Integrative genomics of gene and metabolic regulation by estrogen receptors α and β, and their coregulators.

Madak-Erdogan Z, Charn TH, Jiang Y, Liu ET, Katzenellenbogen JA, Katzenellenbogen BS.

Mol Syst Biol. 2013 Jun 18;9:676. doi: 10.1038/msb.2013.28.

PMID:
23774759
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data.

Bao Y, Vinciotti V, Wit E, 't Hoen PA.

BMC Bioinformatics. 2013 May 30;14:169. doi: 10.1186/1471-2105-14-169.

PMID:
23721376
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes.

Blattler A, Yao L, Wang Y, Ye Z, Jin VX, Farnham PJ.

Epigenetics Chromatin. 2013 May 21;6(1):13. doi: 10.1186/1756-8935-6-13.

PMID:
23693142
[PubMed]
Free PMC Article
20.

MeCP2 modulates gene expression pathways in astrocytes.

Yasui DH, Xu H, Dunaway KW, Lasalle JM, Jin LW, Maezawa I.

Mol Autism. 2013 Jan 25;4(1):3. doi: 10.1186/2040-2392-4-3.

PMID:
23351786
[PubMed]
Free PMC Article

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