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Items: 1 to 20 of 131

1.

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.

2.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP.

BMC Genomics. 2009 Nov 16;10:531. doi: 10.1186/1471-2164-10-531.

3.

trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.

Renaud G, LaFave MC, Liang J, Wolfsberg TG, Burgess SM.

BMC Bioinformatics. 2014 Oct 13;15:329. doi: 10.1186/1471-2105-15-329.

4.

Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.

Seok J, Xu W, Jiang H, Davis RW, Xiao W.

PLoS One. 2012;7(2):e31440. doi: 10.1371/journal.pone.0031440. Epub 2012 Feb 1.

5.

RNA-eXpress annotates novel transcript features in RNA-seq data.

Forster SC, Finkel AM, Gould JA, Hertzog PJ.

Bioinformatics. 2013 Mar 15;29(6):810-2. doi: 10.1093/bioinformatics/btt034. Epub 2013 Feb 8.

6.

Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.

Watanabe KA, Homayouni A, Tufano T, Lopez J, Ringler P, Rushton P, Shen QJ.

DNA Res. 2015 Oct;22(5):319-29. doi: 10.1093/dnares/dsv015. Epub 2015 Sep 3.

7.

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

Hoeppner MP, Lundquist A, Pirun M, Meadows JR, Zamani N, Johnson J, Sundström G, Cook A, FitzGerald MG, Swofford R, Mauceli E, Moghadam BT, Greka A, Alföldi J, Abouelleil A, Aftuck L, Bessette D, Berlin A, Brown A, Gearin G, Lui A, Macdonald JP, Priest M, Shea T, Turner-Maier J, Zimmer A, Lander ES, di Palma F, Lindblad-Toh K, Grabherr MG.

PLoS One. 2014 Mar 13;9(3):e91172. doi: 10.1371/journal.pone.0091172. eCollection 2014.

8.

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.

9.

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome.

Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA.

BMC Genomics. 2011 Apr 20;12:202. doi: 10.1186/1471-2164-12-202.

10.

The transcriptional landscape of Chlamydia pneumoniae.

Albrecht M, Sharma CM, Dittrich MT, Müller T, Reinhardt R, Vogel J, Rudel T.

Genome Biol. 2011 Oct 11;12(10):R98. doi: 10.1186/gb-2011-12-10-r98.

11.

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF.

Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8.

12.

Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.

Xiong J, Lu X, Zhou Z, Chang Y, Yuan D, Tian M, Zhou Z, Wang L, Fu C, Orias E, Miao W.

PLoS One. 2012;7(2):e30630. doi: 10.1371/journal.pone.0030630. Epub 2012 Feb 7.

13.

A platform independent RNA-Seq protocol for the detection of transcriptome complexity.

Calabrese C, Mangiulli M, Manzari C, Paluscio AM, Caratozzolo MF, Marzano F, Kurelac I, D'Erchia AM, D'Elia D, Licciulli F, Liuni S, Picardi E, Attimonelli M, Gasparre G, Porcelli AM, Pesole G, Sbisà E, Tullo A.

BMC Genomics. 2013 Dec 5;14:855. doi: 10.1186/1471-2164-14-855.

14.

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing.

Cui P, Lin Q, Ding F, Xin C, Gong W, Zhang L, Geng J, Zhang B, Yu X, Yang J, Hu S, Yu J.

Genomics. 2010 Nov;96(5):259-65. doi: 10.1016/j.ygeno.2010.07.010. Epub 2010 Aug 3.

15.

Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.

Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ.

BMC Biol. 2008 Jul 8;6:30. doi: 10.1186/1741-7007-6-30.

16.

Grape RNA-Seq analysis pipeline environment.

Knowles DG, Röder M, Merkel A, Guigó R.

Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17.

17.

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing.

Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD.

Nat Biotechnol. 2004 Aug;22(8):1006-11. Epub 2004 Jul 11.

PMID:
15247925
18.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

19.

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM.

BMC Genomics. 2014 Jun 2;15:419. doi: 10.1186/1471-2164-15-419.

20.

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.

Rallapalli G, Kemen EM, Robert-Seilaniantz A, Segonzac C, Etherington GJ, Sohn KH, MacLean D, Jones JD.

BMC Genomics. 2014 May 6;15:341. doi: 10.1186/1471-2164-15-341.

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