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Results: 1 to 20 of 175

Similar articles for PubMed (Select 22955987)

1.

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.

2.

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

3.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.

Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111.

4.

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.

5.

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

Thierry-Mieg D, Thierry-Mieg J.

Genome Biol. 2006;7 Suppl 1:S12.1-14. Epub 2006 Aug 7.

6.

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.

Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS.

Bioinformatics. 2012 Dec 1;28(23):3042-50. doi: 10.1093/bioinformatics/bts582. Epub 2012 Oct 7.

8.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.

9.

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions.

Khatun J, Yu Y, Wrobel JA, Risk BA, Gunawardena HP, Secrest A, Spitzer WJ, Xie L, Wang L, Chen X, Giddings MC.

BMC Genomics. 2013 Feb 28;14:141. doi: 10.1186/1471-2164-14-141.

10.

Functional transcriptomics in the post-ENCODE era.

Mudge JM, Frankish A, Harrow J.

Genome Res. 2013 Dec;23(12):1961-73. doi: 10.1101/gr.161315.113. Epub 2013 Oct 30.

11.

GENCODE pseudogenes.

Frankish A, Harrow J.

Methods Mol Biol. 2014;1167:129-55. doi: 10.1007/978-1-4939-0835-6_10.

PMID:
24823776
12.

Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Fong JH, Murphy TD, Pruitt KD.

BMC Genomics. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654.

13.

Long noncoding RNAs are rarely translated in two human cell lines.

Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L.

Genome Res. 2012 Sep;22(9):1646-57. doi: 10.1101/gr.134767.111.

14.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.

BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18.

15.

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions.

Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R.

BMC Genomics. 2013 Jul 23;14:498. doi: 10.1186/1471-2164-14-498.

16.

The GENCODE exome: sequencing the complete human exome.

Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ, Palotie A.

Eur J Hum Genet. 2011 Jul;19(7):827-31. doi: 10.1038/ejhg.2011.28. Epub 2011 Mar 2.

17.

Incorporating RNA-seq data into the zebrafish Ensembl genebuild.

Collins JE, White S, Searle SM, Stemple DL.

Genome Res. 2012 Oct;22(10):2067-78. doi: 10.1101/gr.137901.112. Epub 2012 Jul 12.

18.

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T.

Genome Res. 2011 May;21(5):756-67. doi: 10.1101/gr.114272.110. Epub 2011 Apr 1.

19.

Genome-wide computational identification and manual annotation of human long noncoding RNA genes.

Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L.

RNA. 2010 Aug;16(8):1478-87. doi: 10.1261/rna.1951310. Epub 2010 Jun 29.

20.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE, Harrow JL.

BMC Genomics. 2009 Dec 15;10:606. doi: 10.1186/1471-2164-10-606.

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