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Results: 1 to 20 of 105

1.

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
2.

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays.

Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR.

Genome Res. 2005 Jul;15(7):987-97.

PMID:
15998911
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
4.

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

Zhang Z, Pang AW, Gerstein M.

BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S14.

PMID:
17288572
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver.

Folkers ME, Delker DA, Maxwell CI, Nelson CA, Schwartz JJ, Nix DA, Hagedorn CH.

PLoS One. 2011 Feb 16;6(2):e14697. doi: 10.1371/journal.pone.0014697.

PMID:
21359205
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
20502517
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Efficient targeted transcript discovery via array-based normalization of RACE libraries.

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, Harrow J, Makrythanasis P, Vidal M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigó R.

Nat Methods. 2008 Jul;5(7):629-35. doi: 10.1038/nmeth.1216. Epub 2008 May 25.

PMID:
18500348
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Global identification and characterization of transcriptionally active regions in the rice genome.

Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW.

PLoS One. 2007 Mar 14;2(3):e294.

PMID:
17372628
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
10.

Global identification of human transcribed sequences with genome tiling arrays.

Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M.

Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.

PMID:
15539566
[PubMed - indexed for MEDLINE]
Free Article
11.

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.

PMID:
22955982
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

Novel transcribed regions in the human genome.

Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M.

Cold Spring Harb Symp Quant Biol. 2006;71:111-6.

PMID:
17381286
[PubMed - indexed for MEDLINE]
14.

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.

Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J.

Nature. 2008 Jun 26;453(7199):1239-43. doi: 10.1038/nature07002. Epub 2008 May 18.

PMID:
18488015
[PubMed - indexed for MEDLINE]
15.

A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription.

Babak T, Blencowe BJ, Hughes TR.

BMC Genomics. 2005 Aug 5;6:104.

PMID:
16083503
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome.

Philippe N, Bou Samra E, Boureux A, Mancheron A, Rufflé F, Bai Q, De Vos J, Rivals E, Commes T.

Nucleic Acids Res. 2014 Mar;42(5):2820-32. doi: 10.1093/nar/gkt1300. Epub 2013 Dec 18.

PMID:
24357408
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Transcriptional and post-transcriptional profile of human chromosome 21.

Nikolaev SI, Deutsch S, Genolet R, Borel C, Parand L, Ucla C, Schütz F, Duriaux Sail G, Dupré Y, Jaquier-Gubler P, Araud T, Conne B, Descombes P, Vassalli JD, Curran J, Antonarakis SE.

Genome Res. 2009 Aug;19(8):1471-9. doi: 10.1101/gr.089425.108. Epub 2009 Jul 6.

PMID:
19581486
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Unexpected observations after mapping LongSAGE tags to the human genome.

Keime C, Sémon M, Mouchiroud D, Duret L, Gandrillon O.

BMC Bioinformatics. 2007 May 15;8:154.

PMID:
17504516
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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
20.

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array.

Coram TE, Settles ML, Chen X.

BMC Genomics. 2009 May 29;10:253. doi: 10.1186/1471-2164-10-253.

PMID:
19480707
[PubMed - indexed for MEDLINE]
Free PMC Article

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