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Items: 1 to 20 of 40

1.

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.

O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ.

Epigenetics Chromatin. 2019 May 3;12(1):26. doi: 10.1186/s13072-019-0275-8.

2.

In Vivo Applications of Cell-Penetrating Zinc-Finger Transcription Factors.

Ren C, Adams AN, Pyles B, Bailus BJ, O'Geen H, Segal DJ.

Methods Mol Biol. 2018;1867:239-251. doi: 10.1007/978-1-4939-8799-3_18.

3.
4.

Unexpected binding behaviors of bacterial Argonautes in human cells cast doubts on their use as targetable gene regulators.

O'Geen H, Ren C, Coggins NB, Bates SL, Segal DJ.

PLoS One. 2018 Mar 27;13(3):e0193818. doi: 10.1371/journal.pone.0193818. eCollection 2018.

5.

Purified Protein Delivery to Activate an Epigenetically Silenced Allele in Mouse Brain.

Pyles B, Bailus BJ, O'Geen H, Segal DJ.

Methods Mol Biol. 2018;1767:227-239. doi: 10.1007/978-1-4939-7774-1_12.

6.

Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance.

Coggins NB, Stultz J, O'Geen H, Carvajal-Carmona LG, Segal DJ.

Sci Rep. 2017 Nov 8;7(1):15044. doi: 10.1038/s41598-017-15407-4. Erratum in: Sci Rep. 2018 Apr 12;8(1):6140.

7.

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.

O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, Segal DJ.

Nucleic Acids Res. 2017 Sep 29;45(17):9901-9916. doi: 10.1093/nar/gkx578.

8.

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. Epub 2016 Jan 6.

9.

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. Epub 2016 Jan 4.

10.

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. Epub 2015 Oct 24. Review.

11.

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. Epub 2015 Feb 20.

12.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

13.

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.

14.

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. Epub 2014 Sep 10. Erratum in: Plant Physiol. 2014 Dec;166(4):2218.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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 JJ, 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.

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