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Items: 1 to 20 of 30

1.

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.

Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O'Geen H, Segal DJ, Farnham PJ.

Nucleic Acids Res. 2016 May 19;44(9):4123-33. doi: 10.1093/nar/gkv1530.

2.

Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain.

Bailus BJ, Pyles B, McAlister MM, O'Geen H, Lockwood SH, Adams AN, Nguyen JT, Yu A, Berman RF, Segal DJ.

Mol Ther. 2016 Mar;24(3):548-55. doi: 10.1038/mt.2015.236.

3.

How specific is CRISPR/Cas9 really?

O'Geen H, Yu AS, Segal DJ.

Curr Opin Chem Biol. 2015 Dec;29:72-8. doi: 10.1016/j.cbpa.2015.10.001. Review.

4.

A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture.

O'Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ.

Nucleic Acids Res. 2015 Mar 31;43(6):3389-404. doi: 10.1093/nar/gkv137.

5.

Epigenetic and transcriptional determinants of the human breast.

Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M.

Nat Commun. 2015 Feb 18;6:6351. doi: 10.1038/ncomms7351.

6.

De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms.

Peng Y, Lai Z, Lane T, Nageswara-Rao M, Okada M, Jasieniuk M, O'Geen H, Kim RW, Sammons RD, Rieseberg LH, Stewart CN Jr.

Plant Physiol. 2014 Nov;166(3):1241-54. doi: 10.1104/pp.114.247668. Erratum in: Plant Physiol. 2014 Dec;166(4):2218.

7.

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.

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.

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.

10.

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.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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