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Results: 1 to 20 of 49

1.

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.

Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H, Dumais J, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P.

Nat Methods. 2010 Jul;7(7):528-34. doi: 10.1038/nmeth.1470. Epub 2010 Jun 13.

PMID:
20543846
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns.

Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO.

BMC Genomics. 2010 Apr 21;11:257. doi: 10.1186/1471-2164-11-257.

PMID:
20409305
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Genome-wide analysis of histone modifications in human pancreatic islets.

Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, Liu C, Naji A, Kaestner KH.

Genome Res. 2010 Apr;20(4):428-33. doi: 10.1101/gr.102038.109. Epub 2010 Feb 24.

PMID:
20181961
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Histone modification levels are predictive for gene expression.

Karlić R, Chung HR, Lasserre J, Vlahovicek K, Vingron M.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2926-31. doi: 10.1073/pnas.0909344107. Epub 2010 Feb 1.

PMID:
20133639
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Human DNA methylomes at base resolution show widespread epigenomic differences.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.

PMID:
19829295
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The logic of chromatin architecture and remodelling at promoters.

Cairns BR.

Nature. 2009 Sep 10;461(7261):193-8. doi: 10.1038/nature08450. Review.

PMID:
19741699
[PubMed - indexed for MEDLINE]
7.

ChIP-seq: advantages and challenges of a maturing technology.

Park PJ.

Nat Rev Genet. 2009 Oct;10(10):669-80. doi: 10.1038/nrg2641. Epub 2009 Sep 8. Review.

PMID:
19736561
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.

Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G.

Nat Genet. 2009 Aug;41(8):941-5. doi: 10.1038/ng.409. Epub 2009 Jul 26.

PMID:
19633671
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.

Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST.

Cell. 2009 Jul 10;138(1):114-28. doi: 10.1016/j.cell.2009.04.020.

PMID:
19596239
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Epigenetics of human T cells during the G0-->G1 transition.

Smith AE, Chronis C, Christodoulakis M, Orr SJ, Lea NC, Twine NA, Bhinge A, Mufti GJ, Thomas NS.

Genome Res. 2009 Aug;19(8):1325-37. doi: 10.1101/gr.085530.108. Epub 2009 Jun 22.

PMID:
19546172
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.

Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.

PMID:
19377474
[PubMed - indexed for MEDLINE]
12.

CpG islands--'a rough guide'.

Illingworth RS, Bird AP.

FEBS Lett. 2009 Jun 5;583(11):1713-20. doi: 10.1016/j.febslet.2009.04.012. Epub 2009 Apr 18. Review.

PMID:
19376112
[PubMed - indexed for MEDLINE]
Free Article
13.

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes.

Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ.

Genome Res. 2009 Jun;19(6):967-77. doi: 10.1101/gr.084830.108. Epub 2009 Feb 26.

PMID:
19246569
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Nucleosome positioning and gene regulation: advances through genomics.

Jiang C, Pugh BF.

Nat Rev Genet. 2009 Mar;10(3):161-72. doi: 10.1038/nrg2522. Review.

PMID:
19204718
[PubMed - indexed for MEDLINE]
15.

Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.

Zhang Y, Shin H, Song JS, Lei Y, Liu XS.

BMC Genomics. 2008 Nov 13;9:537. doi: 10.1186/1471-2164-9-537.

PMID:
19014516
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Combinatorial patterns of histone acetylations and methylations in the human genome.

Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K.

Nat Genet. 2008 Jul;40(7):897-903. doi: 10.1038/ng.154. Epub 2008 Jun 15.

PMID:
18552846
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF.

Genome Res. 2008 Jul;18(7):1073-83. doi: 10.1101/gr.078261.108. Epub 2008 Jun 12.

PMID:
18550805
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Two strategies for gene regulation by promoter nucleosomes.

Tirosh I, Barkai N.

Genome Res. 2008 Jul;18(7):1084-91. doi: 10.1101/gr.076059.108. Epub 2008 Apr 30.

PMID:
18448704
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Dynamic regulation of nucleosome positioning in the human genome.

Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K.

Cell. 2008 Mar 7;132(5):887-98. doi: 10.1016/j.cell.2008.02.022.

PMID:
18329373
[PubMed - indexed for MEDLINE]
Free Article
20.

Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.

Brayer KJ, Segal DJ.

Cell Biochem Biophys. 2008;50(3):111-31. doi: 10.1007/s12013-008-9008-5. Epub 2008 Feb 6. Review.

PMID:
18253864
[PubMed - indexed for MEDLINE]

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