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Items: 1 to 20 of 158

1.

4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus.

Cai M, Kim S, Wang K, Farnham PJ, Coetzee GA, Lu W.

Sci Rep. 2016 Mar 3;6:22462. doi: 10.1038/srep22462.

2.

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 Jan 6. pii: gkv1530. [Epub ahead of print]

3.

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome.

Tak YG, Farnham PJ.

Epigenetics Chromatin. 2015 Dec 30;8:57. doi: 10.1186/s13072-015-0050-4. eCollection 2015. Review.

4.

The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

5.

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.

Yao L, Berman BP, Farnham PJ.

Crit Rev Biochem Mol Biol. 2015;50(6):550-73. doi: 10.3109/10409238.2015.1087961. Epub 2015 Oct 8.

6.

Altering cancer transcriptomes using epigenomic inhibitors.

Gaddis M, Gerrard D, Frietze S, Farnham PJ.

Epigenetics Chromatin. 2015 Feb 24;8:9. doi: 10.1186/1756-8935-8-9. eCollection 2015.

7.

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

Yao L, Shen H, Laird PW, Farnham PJ, Berman BP.

Genome Biol. 2015 May 21;16:105. doi: 10.1186/s13059-015-0668-3.

8.

The role of DNA methylation in directing the functional organization of the cancer epigenome.

Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP.

Genome Res. 2015 Apr;25(4):467-77. doi: 10.1101/gr.183368.114. Epub 2015 Mar 6.

9.

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.

10.

Intermediate DNA methylation is a conserved signature of genome regulation.

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF.

Nat Commun. 2015 Feb 18;6:6363. doi: 10.1038/ncomms7363.

11.

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.

12.

Can genome engineering be used to target cancer-associated enhancers?

Grimmer MR, Farnham PJ.

Epigenomics. 2014;6(5):493-501. doi: 10.2217/epi.14.30. Review.

13.

Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.

Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB.

Nat Commun. 2014 Nov 25;5:5442. doi: 10.1038/ncomms6442.

14.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

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 J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

15.

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.

16.

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. doi: 10.1186/s13059-014-0469-0.

17.

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.

Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ.

Nucleic Acids Res. 2014;42(16):10856-68. doi: 10.1093/nar/gku708. Epub 2014 Aug 13.

18.

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.

19.

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.

20.

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.

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