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Items: 1 to 20 of 52

1.

Epigenetic modifications and human disease.

Portela A, Esteller M.

Nat Biotechnol. 2010 Oct;28(10):1057-68. doi: 10.1038/nbt.1685. Review.

PMID:
20944598
2.

A unique H3K4me2 profile marks tissue-specific gene regulation.

Pekowska A, Benoukraf T, Ferrier P, Spicuglia S.

Genome Res. 2010 Nov;20(11):1493-502. doi: 10.1101/gr.109389.110. Epub 2010 Sep 14.

3.

Conserved role of intragenic DNA methylation in regulating alternative promoters.

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF.

Nature. 2010 Jul 8;466(7303):253-7. doi: 10.1038/nature09165.

4.

Genome-wide functional analysis of human 5' untranslated region introns.

Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP.

Genome Biol. 2010;11(3):R29. doi: 10.1186/gb-2010-11-3-r29. Epub 2010 Mar 11.

5.

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.

6.

Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B.

Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.

7.

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM.

Genome Res. 2009 Jun;19(6):1044-56. doi: 10.1101/gr.088773.108. Epub 2009 Mar 9.

8.

MicroRNAs: target recognition and regulatory functions.

Bartel DP.

Cell. 2009 Jan 23;136(2):215-33. doi: 10.1016/j.cell.2009.01.002. Review.

9.

Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells.

Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O'Shea JJ, Zhao K.

Immunity. 2009 Jan 16;30(1):155-67. doi: 10.1016/j.immuni.2008.12.009.

10.

Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.

Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K.

Cell Stem Cell. 2009 Jan 9;4(1):80-93. doi: 10.1016/j.stem.2008.11.011.

11.

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P.

Genome Res. 2009 Feb;19(2):255-65. doi: 10.1101/gr.084541.108. Epub 2008 Dec 11.

12.

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Core LJ, Waterfall JJ, Lis JT.

Science. 2008 Dec 19;322(5909):1845-8. doi: 10.1126/science.1162228. Epub 2008 Dec 4.

13.

Divergent transcription from active promoters.

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Science. 2008 Dec 19;322(5909):1849-51. doi: 10.1126/science.1162253. Epub 2008 Dec 4.

14.

High-resolution human core-promoter prediction with CoreBoost_HM.

Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ.

Genome Res. 2009 Feb;19(2):266-75. doi: 10.1101/gr.081638.108. Epub 2008 Nov 7.

15.

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.

Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, Calabrese JM, Dennis LM, Volkert TL, Gupta S, Love J, Hannett N, Sharp PA, Bartel DP, Jaenisch R, Young RA.

Cell. 2008 Aug 8;134(3):521-33. doi: 10.1016/j.cell.2008.07.020.

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.

17.

Transcription regulation through promoter-proximal pausing of RNA polymerase II.

Core LJ, Lis JT.

Science. 2008 Mar 28;319(5871):1791-2. doi: 10.1126/science.1150843.

18.

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.

19.

Genome-wide approaches to studying chromatin modifications.

Schones DE, Zhao K.

Nat Rev Genet. 2008 Mar;9(3):179-91. doi: 10.1038/nrg2270. Review.

PMID:
18250624
20.

Generic eukaryotic core promoter prediction using structural features of DNA.

Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y.

Genome Res. 2008 Feb;18(2):310-23. Epub 2007 Dec 20.

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