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Results: 1 to 20 of 115

1.

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.

PMID:
24753594
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Diversity and dynamics of the Drosophila transcriptome.

Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE.

Nature. 2014 Mar 16. doi: 10.1038/nature12962. [Epub ahead of print]

PMID:
24670639
[PubMed - as supplied by publisher]
3.

RAMPAGE: promoter activity profiling by paired-end sequencing of 5'-complete cDNAs.

Batut P, Gingeras TR.

Curr Protoc Mol Biol. 2013 Nov 11;104:Unit 25B.11. doi: 10.1002/0471142727.mb25b11s104.

PMID:
24510412
[PubMed - in process]
4.

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.

Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E.

Genome Res. 2013 Oct;23(10):1601-14. doi: 10.1101/gr.157271.113. Epub 2013 Jun 28.

PMID:
23811145
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation.

Livyatan I, Harikumar A, Nissim-Rafinia M, Duttagupta R, Gingeras TR, Meshorer E.

Nucleic Acids Res. 2013 Jul;41(12):6300-15. doi: 10.1093/nar/gkt316. Epub 2013 Apr 29.

PMID:
23630323
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

STAR: ultrafast universal RNA-seq aligner.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.

Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

PMID:
23104886
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22955988
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.

Genome Res. 2012 Sep;22(9):1658-67. doi: 10.1101/gr.136838.111.

PMID:
22955978
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.

Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R.

Genome Res. 2012 Sep;22(9):1616-25. doi: 10.1101/gr.134445.111.

PMID:
22955974
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22955620
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Modeling gene expression using chromatin features in various cellular contexts.

Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z.

Genome Biol. 2012 Jun 13;13(9):R53. doi: 10.1186/gb-2012-13-9-r53.

PMID:
22950368
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR.

Genome Res. 2013 Jan;23(1):169-80. doi: 10.1101/gr.139618.112. Epub 2012 Aug 30.

PMID:
22936248
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An effort to make sense of antisense transcription in bacteria.

Lasa I, Toledo-Arana A, Gingeras TR.

RNA Biol. 2012 Aug;9(8):1039-44. doi: 10.4161/rna.21167. Epub 2012 Aug 1.

PMID:
22858676
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Molecular biology: RNA discrimination.

Kowalczyk MS, Higgs DR, Gingeras TR.

Nature. 2012 Feb 15;482(7385):310-1. doi: 10.1038/482310a. No abstract available.

PMID:
22337043
[PubMed - indexed for MEDLINE]
15.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

PMID:
22238572
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genome-wide antisense transcription drives mRNA processing in bacteria.

Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penadés JR, Valle J, Solano C, Gingeras TR.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20172-7. doi: 10.1073/pnas.1113521108. Epub 2011 Nov 28.

PMID:
22123973
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM.

Nat Genet. 2011 Oct 23;43(12):1179-85. doi: 10.1038/ng.948.

PMID:
22019781
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Synthetic spike-in standards for RNA-seq experiments.

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B.

Genome Res. 2011 Sep;21(9):1543-51. doi: 10.1101/gr.121095.111. Epub 2011 Aug 4.

PMID:
21816910
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
21765801
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The developmental transcriptome of Drosophila melanogaster.

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

PMID:
21179090
[PubMed - indexed for MEDLINE]
Free PMC Article

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