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Results: 1 to 20 of 101

1.

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A.

Genome Res. 2007 Jun;17(6):746-59.

PMID:
17567994
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.

Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M.

Genome Biol. 2008 Jan 3;9(1):R3. doi: 10.1186/gb-2008-9-1-r3.

PMID:
18173853
[PubMed - indexed for MEDLINE]
Free PMC Article
3.
4.

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.

Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z.

Genome Res. 2007 Jun;17(6):720-31.

PMID:
17567992
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22955987
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.

Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):886-97. Epub 2006 Nov 21.

PMID:
17119069
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):732-45.

PMID:
17567993
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays.

Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H, Kumamoto CA, Whiteway M, Nantel A.

Genome Biol. 2010;11(7):R71. doi: 10.1186/gb-2010-11-7-r71. Epub 2010 Jul 9.

PMID:
20618945
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Direct isolation and identification of promoters in the human genome.

Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B.

Genome Res. 2005 Jun;15(6):830-9. Epub 2005 May 17.

PMID:
15899964
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
16925838
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Characterization of 954 bovine full-CDS cDNA sequences.

Harhay GP, Sonstegard TS, Keele JW, Heaton MP, Clawson ML, Snelling WM, Wiedmann RT, Van Tassell CP, Smith TP.

BMC Genomics. 2005 Nov 23;6:166.

PMID:
16305752
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23448259
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury.

Maia RM, Valente V, Cunha MA, Sousa JF, Araujo DD, Silva WA Jr, Zago MA, Dias-Neto E, Souza SJ, Simpson AJ, Monesi N, Ramos RG, Espreafico EM, Paçó-Larson ML.

BMC Genomics. 2007 Jul 24;8:249.

PMID:
17650329
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Identification of a 1.2 Kb cDNA fragment from a region on 9p21 commonly deleted in multiple tumor types.

Gursky S, Olopade OI, Rowley JD.

Cancer Genet Cytogenet. 2001 Sep;129(2):93-101.

PMID:
11566337
[PubMed - indexed for MEDLINE]
15.

Multiple transcription start sites and alternative splicing in the methylenetetrahydrofolate reductase gene result in two enzyme isoforms.

Tran P, Leclerc D, Chan M, Pai A, Hiou-Tim F, Wu Q, Goyette P, Artigas C, Milos R, Rozen R.

Mamm Genome. 2002 Sep;13(9):483-92.

PMID:
12370778
[PubMed - indexed for MEDLINE]
16.
17.

Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences.

Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG, Andrade LE, Cruz LO, Degaki TL, Faria M Jr, Festa F, Giannella-Neto D, Giorgi RR, Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CV, Marie SK, Martinez-Rossi NM, Oba-Shinjo SM, Pardini MI, Rahal P, Rainho CA, Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva ID, da Silva NP, de Souza SJ, Tajara EH, Silva WA Jr, Simpson AJ, Sogayar MC, Camargo AA, Carraro DM.

Genet Mol Res. 2004 Dec 30;3(4):493-511.

PMID:
15688316
[PubMed - indexed for MEDLINE]
Free Article
18.

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.

Salehi-Ashtiani K, Lin C, Hao T, Shen Y, Szeto D, Yang X, Ghamsari L, Lee H, Fan C, Murray RR, Milstein S, Svrzikapa N, Cusick ME, Roth FP, Hill DE, Vidal M.

Genome Res. 2009 Dec;19(12):2334-42. doi: 10.1101/gr.098640.109. Epub 2009 Oct 2.

PMID:
19801531
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Identification of novel transcribed sequences on human chromosome 22 by expressed sequence tag mapping.

Hirosawa M, Nagase T, Murahashi Y, Kikuno R, Ohara O.

DNA Res. 2001 Feb 28;8(1):1-9.

PMID:
11258795
[PubMed - indexed for MEDLINE]
Free Article
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.

PMID:
19581580
[PubMed - indexed for MEDLINE]
Free PMC Article

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