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Results: 1 to 20 of 24

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.

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
3.

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
4.

Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development.

Bush KM, Yuen BT, Barrilleaux BL, Riggs JW, O'Geen H, Cotterman RF, Knoepfler PS.

Epigenetics Chromatin. 2013 Apr 9;6(1):7. doi: 10.1186/1756-8935-6-7.

5.

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
6.

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]
7.

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
8.

Autophagy driven by a master regulator of hematopoiesis.

Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH.

Mol Cell Biol. 2012 Jan;32(1):226-39. doi: 10.1128/MCB.06166-11. Epub 2011 Oct 24.

PMID:
22025678
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Using ChIP-seq technology to generate high-resolution profiles of histone modifications.

O'Geen H, Echipare L, Farnham PJ.

Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.

PMID:
21913086
[PubMed - indexed for MEDLINE]
10.

Genetic framework for GATA factor function in vascular biology.

Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6. doi: 10.1073/pnas.1108440108. Epub 2011 Aug 1.

PMID:
21808000
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.

Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ.

PLoS One. 2011 Feb 15;6(2):e17121. doi: 10.1371/journal.pone.0017121.

PMID:
21347206
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes.

O'Geen H, Lin YH, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA, Engel JD, Farnham PJ.

BMC Genomics. 2010 Dec 2;11:689. doi: 10.1186/1471-2164-11-689.

PMID:
21126370
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF.

Nat Biotechnol. 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682. Epub 2010 Sep 19.

PMID:
20852635
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Using ChIP-seq technology to identify targets of zinc finger transcription factors.

O'Geen H, Frietze S, Farnham PJ.

Methods Mol Biol. 2010;649:437-55. doi: 10.1007/978-1-60761-753-2_27.

PMID:
20680851
[PubMed - indexed for MEDLINE]
16.

Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy.

Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH.

Mol Cell. 2009 Nov 25;36(4):667-81. doi: 10.1016/j.molcel.2009.11.001.

PMID:
19941826
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ.

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.

PMID:
19906703
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells.

Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ.

Genome Res. 2008 Apr;18(4):521-32. doi: 10.1101/gr.074609.107. Epub 2008 Mar 17.

PMID:
18347325
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches.

Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ.

Genome Res. 2007 Jun;17(6):807-17.

PMID:
17567999
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ.

PLoS Genet. 2007 Jun;3(6):e89. Epub 2007 Apr 19.

PMID:
17542650
[PubMed - indexed for MEDLINE]
Free PMC Article

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