Format
Sort by

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 51

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.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

3.

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.

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.

The GENCODE pseudogene resource.

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB.

Genome Biol. 2012 Sep 26;13(9):R51. doi: 10.1186/gb-2012-13-9-r51.

6.

Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy.

Cartault F, Munier P, Benko E, Desguerre I, Hanein S, Boddaert N, Bandiera S, Vellayoudom J, Krejbich-Trotot P, Bintner M, Hoarau JJ, Girard M, Génin E, de Lonlay P, Fourmaintraux A, Naville M, Rodriguez D, Feingold J, Renouil M, Munnich A, Westhof E, Fähling M, Lyonnet S, Henrion-Caude A.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4980-5. doi: 10.1073/pnas.1111596109. Epub 2012 Mar 12.

7.

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
8.

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.

9.

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.

Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP.

Cell. 2011 Dec 23;147(7):1537-50. doi: 10.1016/j.cell.2011.11.055. Erratum in: Cell. 2012 Oct 26;151(3):684-6.

10.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL.

Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024.

11.

The evolution of gene expression levels in mammalian organs.

Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H.

Nature. 2011 Oct 19;478(7369):343-8. doi: 10.1038/nature10532.

PMID:
22012392
12.

Molecular mechanisms of long noncoding RNAs.

Wang KC, Chang HY.

Mol Cell. 2011 Sep 16;43(6):904-14. doi: 10.1016/j.molcel.2011.08.018. Review.

13.

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.

14.

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

Lin MF, Jungreis I, Kellis M.

Bioinformatics. 2011 Jul 1;27(13):i275-82. doi: 10.1093/bioinformatics/btr209.

15.

Initial impact of the sequencing of the human genome.

Lander ES.

Nature. 2011 Feb 10;470(7333):187-97. doi: 10.1038/nature09792. Review.

PMID:
21307931
16.

Ensembl 2011.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM.

Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6. doi: 10.1093/nar/gkq1064. Epub 2010 Nov 2.

17.

The UCSC Genome Browser database: update 2011.

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. doi: 10.1093/nar/gkq963. Epub 2010 Oct 18.

18.

Most "dark matter" transcripts are associated with known genes.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR.

PLoS Biol. 2010 May 18;8(5):e1000371. doi: 10.1371/journal.pbio.1000371.

19.

Alternative splicing and evolution: diversification, exon definition and function.

Keren H, Lev-Maor G, Ast G.

Nat Rev Genet. 2010 May;11(5):345-55. doi: 10.1038/nrg2776. Epub 2010 Apr 8. Review.

PMID:
20376054
20.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

Items per page

Supplemental Content

Write to the Help Desk