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Items: 1 to 20 of 48

1.

Species-specific strategies underlying conserved functions of metabolic transcription factors.

Soccio RE, Tuteja G, Everett LJ, Li Z, Lazar MA, Kaestner KH.

Mol Endocrinol. 2011 Apr;25(4):694-706. doi: 10.1210/me.2010-0454. Epub 2011 Feb 3.

2.

Interchromosomal association and gene regulation in trans.

Williams A, Spilianakis CG, Flavell RA.

Trends Genet. 2010 Apr;26(4):188-97. doi: 10.1016/j.tig.2010.01.007. Epub 2010 Mar 16. Review.

3.

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK.

Genome Biol. 2010;11(2):R22. doi: 10.1186/gb-2010-11-2-r22. Epub 2010 Feb 25.

4.

Enhancers: the abundance and function of regulatory sequences beyond promoters.

Bulger M, Groudine M.

Dev Biol. 2010 Mar 15;339(2):250-7. doi: 10.1016/j.ydbio.2009.11.035. Epub 2009 Dec 16. Review.

5.

Stable chromatin binding prevents FoxA acetylation, preserving FoxA chromatin remodeling.

Kohler S, Cirillo LA.

J Biol Chem. 2010 Jan 1;285(1):464-72. doi: 10.1074/jbc.M109.063149. Epub 2009 Nov 5.

6.

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology.

Simonis M, Klous P, Homminga I, Galjaard RJ, Rijkers EJ, Grosveld F, Meijerink JP, de Laat W.

Nat Methods. 2009 Nov;6(11):837-42. doi: 10.1038/nmeth.1391. Epub 2009 Oct 11.

PMID:
19820713
7.

The alpha-fetoprotein enhancer region activates the albumin and alpha-fetoprotein promoters during liver development.

Jin L, Long L, Green MA, Spear BT.

Dev Biol. 2009 Dec 15;336(2):294-300. doi: 10.1016/j.ydbio.2009.09.026. Epub 2009 Sep 24.

8.

Identifying regulatory elements in eukaryotic genomes.

Narlikar L, Ovcharenko I.

Brief Funct Genomic Proteomic. 2009 Jul;8(4):215-30. doi: 10.1093/bfgp/elp014. Epub 2009 Jun 4. Review.

9.

Functional autonomy of distant-acting human enhancers.

Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA.

Genomics. 2009 Jun;93(6):509-13. doi: 10.1016/j.ygeno.2009.02.002. Epub 2009 Mar 5.

10.

ChIP-seq accurately predicts tissue-specific activity of enhancers.

Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA.

Nature. 2009 Feb 12;457(7231):854-8. doi: 10.1038/nature07730.

11.

Long-range chromosomal interactions and gene regulation.

Miele A, Dekker J.

Mol Biosyst. 2008 Nov;4(11):1046-57. doi: 10.1039/b803580f. Epub 2008 Aug 13. Review.

12.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

13.

Gene expression profiling and differentiation assessment in primary human hepatocyte cultures, established hepatoma cell lines, and human liver tissues.

Olsavsky KM, Page JL, Johnson MC, Zarbl H, Strom SC, Omiecinski CJ.

Toxicol Appl Pharmacol. 2007 Jul 1;222(1):42-56. Epub 2007 Apr 21.

14.

Promoter targeting sequence mediates enhancer interference in the Drosophila embryo.

Lin Q, Chen Q, Lin L, Smith S, Zhou J.

Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3237-42. Epub 2007 Feb 16.

15.

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B.

Nat Genet. 2007 Mar;39(3):311-8. Epub 2007 Feb 4.

PMID:
17277777
16.

Specific interactions of the wing domains of FOXA1 transcription factor with DNA.

Cirillo LA, Zaret KS.

J Mol Biol. 2007 Feb 23;366(3):720-4. Epub 2006 Dec 5.

17.
18.

In vivo enhancer analysis of human conserved non-coding sequences.

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM.

Nature. 2006 Nov 23;444(7118):499-502. Epub 2006 Nov 5.

PMID:
17086198
19.

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R.

Nat Genet. 2006 Nov;38(11):1341-7. Epub 2006 Oct 8.

PMID:
17033624
20.

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W.

Nat Genet. 2006 Nov;38(11):1348-54. Epub 2006 Oct 8.

PMID:
17033623

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