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Items: 1 to 20 of 44

1.

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R.

Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111.

2.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

3.

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 J, 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.

4.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

5.

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes.

Ingolia NT, Lareau LF, Weissman JS.

Cell. 2011 Nov 11;147(4):789-802. doi: 10.1016/j.cell.2011.10.002. Epub 2011 Nov 3.

6.

The evolution of RNAs with multiple functions.

Dinger ME, Gascoigne DK, Mattick JS.

Biochimie. 2011 Nov;93(11):2013-8. doi: 10.1016/j.biochi.2011.07.018. Epub 2011 Jul 23.

PMID:
21802485
7.

The reality of pervasive transcription.

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS.

PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. doi: 10.1371/journal.pbio.1000625. Epub 2011 Jul 12. No abstract available.

8.

YY1 tethers Xist RNA to the inactive X nucleation center.

Jeon Y, Lee JT.

Cell. 2011 Jul 8;146(1):119-33. doi: 10.1016/j.cell.2011.06.026.

9.

Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events.

Ulveling D, Francastel C, Hubé F.

Biochimie. 2011 Nov;93(11):2024-7. doi: 10.1016/j.biochi.2011.06.019. Epub 2011 Jun 26.

PMID:
21729736
10.

Autoantigen discovery with a synthetic human peptidome.

Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, Gakidis MA, Church GM, Kesari S, Leproust EM, Solimini NL, Elledge SJ.

Nat Biotechnol. 2011 May 22;29(6):535-41. doi: 10.1038/nbt.1856.

11.

Global quantification of mammalian gene expression control.

Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M.

Nature. 2011 May 19;473(7347):337-42. doi: 10.1038/nature10098. Erratum in: Nature. 2013 Mar 7;495(7439):126-7.

PMID:
21593866
12.

MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA.

Lipovich L, Johnson R, Lin CY.

Biochim Biophys Acta. 2010 Sep;1799(9):597-615. doi: 10.1016/j.bbagrm.2010.10.001. Epub 2010 Oct 14. Review. Erratum in: Biochim Biophys Acta. 2011 Jan;1809(1):63.

PMID:
20951849
13.

UPF1 association with the cap-binding protein, CBP80, promotes nonsense-mediated mRNA decay at two distinct steps.

Hwang J, Sato H, Tang Y, Matsuda D, Maquat LE.

Mol Cell. 2010 Aug 13;39(3):396-409. doi: 10.1016/j.molcel.2010.07.004. Epub 2010 Aug 5.

14.

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.

Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL.

Cell. 2010 Aug 6;142(3):409-19. doi: 10.1016/j.cell.2010.06.040.

15.

Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis.

Kondo T, Plaza S, Zanet J, Benrabah E, Valenti P, Hashimoto Y, Kobayashi S, Payre F, Kageyama Y.

Science. 2010 Jul 16;329(5989):336-9. doi: 10.1126/science.1188158.

16.

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.

Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY.

Nature. 2010 Apr 15;464(7291):1071-6. doi: 10.1038/nature08975.

17.

Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells.

Sheik Mohamed J, Gaughwin PM, Lim B, Robson P, Lipovich L.

RNA. 2010 Feb;16(2):324-37. doi: 10.1261/rna.1441510. Epub 2009 Dec 21.

18.

The UCSC Genome Browser.

Karolchik D, Hinrichs AS, Kent WJ.

Curr Protoc Bioinformatics. 2009 Dec;Chapter 1:Unit1.4. doi: 10.1002/0471250953.bi0104s28.

19.

H19 acts as a trans regulator of the imprinted gene network controlling growth in mice.

Gabory A, Ripoche MA, Le Digarcher A, Watrin F, Ziyyat A, Forné T, Jammes H, Ainscough JF, Surani MA, Journot L, Dandolo L.

Development. 2009 Oct;136(20):3413-21. doi: 10.1242/dev.036061. Epub 2009 Sep 17.

20.

Global discovery of primate-specific genes in the human genome.

Tay SK, Blythe J, Lipovich L.

Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12019-24. doi: 10.1073/pnas.0904569106. Epub 2009 Jul 6. Erratum in: Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):14180.

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