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Results: 1 to 20 of 141

1.

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(1):520. doi: 10.1186/1471-2164-15-520.

PMID:
24962896
[PubMed - in process]
Free PMC Article
2.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

PMID:
24753594
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
4.

Cross-talk between site-specific transcription factors and DNA methylation states.

Blattler A, Farnham PJ.

J Biol Chem. 2013 Nov 29;288(48):34287-94. doi: 10.1074/jbc.R113.512517. Epub 2013 Oct 22. Review.

PMID:
24151070
[PubMed - indexed for MEDLINE]
5.

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
6.

Recombinant antibodies to histone post-translational modifications.

Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S.

Nat Methods. 2013 Oct;10(10):992-5. doi: 10.1038/nmeth.2605. Epub 2013 Aug 18.

PMID:
23955773
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data.

Wang R, Hsu HK, Blattler A, Wang Y, Lan X, Wang Y, Hsu PY, Leu YW, Huang TH, Farnham PJ, Jin VX.

PLoS One. 2013 Jun 25;8(6):e67788. doi: 10.1371/journal.pone.0067788. Print 2013.

PMID:
23825685
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.

Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T.

Genome Res. 2013 Sep;23(9):1522-40. doi: 10.1101/gr.156539.113. Epub 2013 Jun 26.

PMID:
23804400
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.

Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T.

Nat Genet. 2013 Jul;45(7):836-41. doi: 10.1038/ng.2649. Epub 2013 May 26.

PMID:
23708189
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

Spark: a navigational paradigm for genomic data exploration.

Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ.

Genome Res. 2012 Nov;22(11):2262-9. doi: 10.1101/gr.140665.112. Epub 2012 Sep 7.

PMID:
22960372
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

PMID:
22955991
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

PMID:
22955619
[PubMed - indexed for MEDLINE]
14.

Uncovering transcription factor modules using one- and three-dimensional analyses.

Lan X, Farnham PJ, Jin VX.

J Biol Chem. 2012 Sep 7;287(37):30914-21. doi: 10.1074/jbc.R111.309229. Epub 2012 Sep 5. Review.

PMID:
22952238
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

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
17.

Human ESC self-renewal promoting microRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFβ tumor suppressor signaling pathways.

Jung CJ, Iyengar S, Blahnik KR, Jiang JX, Tahimic C, Torok NJ, de vere White RW, Farnham PJ, Zern M.

Mol Cancer Res. 2012 Jul;10(7):979-91. doi: 10.1158/1541-7786.MCR-11-0421. Epub 2012 May 23.

PMID:
22622027
[PubMed - indexed for MEDLINE]
Free Article
18.

The transcription factor encyclopedia.

Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW.

Genome Biol. 2012;13(3):R24. doi: 10.1186/gb-2012-13-3-r24.

PMID:
22458515
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Thematic minireview series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome.

Farnham PJ.

J Biol Chem. 2012 Sep 7;287(37):30885-7. doi: 10.1074/jbc.R112.365940. Epub 2012 Sep 5. No abstract available.

PMID:
22451669
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation.

Jung CJ, Iyengar S, Blahnik KR, Ajuha TP, Jiang JX, Farnham PJ, Zern M.

PLoS One. 2011;6(11):e27740. doi: 10.1371/journal.pone.0027740. Epub 2011 Nov 28.

PMID:
22140464
[PubMed - indexed for MEDLINE]
Free PMC Article

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