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Results: 1 to 20 of 114

1.

Probabilistic error correction for RNA sequencing.

Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.

Nucleic Acids Res. 2013 May 1;41(10):e109. doi: 10.1093/nar/gkt215. Epub 2013 Apr 4.

PMID:
23558750
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data.

Duan J, Xia C, Zhao G, Jia J, Kong X.

BMC Genomics. 2012 Aug 14;13:392. doi: 10.1186/1471-2164-13-392.

PMID:
22891638
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.

Yang Y, Smith SA.

BMC Genomics. 2013 May 14;14:328. doi: 10.1186/1471-2164-14-328.

PMID:
23672450
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy.

Nat Biotechnol. 2012 Jul 1;30(7):693-700. doi: 10.1038/nbt.2280.

PMID:
22750884
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
21507250
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A context-based approach to identify the most likely mapping for RNA-seq experiments.

Bonfert T, Csaba G, Zimmer R, Friedel CC.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S9. doi: 10.1186/1471-2105-13-S6-S9.

PMID:
22537048
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identification and correction of systematic error in high-throughput sequence data.

Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L.

BMC Bioinformatics. 2011 Nov 21;12:451. doi: 10.1186/1471-2105-12-451.

PMID:
22099972
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.

Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S2. doi: 10.1186/1471-2105-12-S14-S2.

PMID:
22373417
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

RNA-Seq read alignments with PALMapper.

Jean G, Kahles A, Sreedharan VT, De Bona F, R├Ątsch G.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.6. doi: 10.1002/0471250953.bi1106s32.

PMID:
21154708
[PubMed - indexed for MEDLINE]
10.

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.

Sacomoto GA, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot MF, Peterlongo P, Lacroix V.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S5. doi: 10.1186/1471-2105-13-S6-S5.

PMID:
22537044
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

Hassan MA, Melo MB, Haas B, Jensen KD, Saeij JP.

BMC Genomics. 2012 Dec 12;13:696. doi: 10.1186/1471-2164-13-696.

PMID:
23231500
[PubMed - indexed for MEDLINE]
Free PMC Article
12.
13.

STAR: ultrafast universal RNA-seq aligner.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.

Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

PMID:
23104886
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.

Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA.

BMC Genomics. 2010 Dec 1;11:681. doi: 10.1186/1471-2164-11-681.

PMID:
21122097
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

Francis WR, Christianson LM, Kiko R, Powers ML, Shaner NC, D Haddock SH.

BMC Genomics. 2013 Mar 12;14:167. doi: 10.1186/1471-2164-14-167.

PMID:
23496952
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Overview of available methods for diverse RNA-Seq data analyses.

Chen G, Wang C, Shi T.

Sci China Life Sci. 2011 Dec;54(12):1121-8. doi: 10.1007/s11427-011-4255-x. Epub 2012 Jan 7. Review.

PMID:
22227904
[PubMed - indexed for MEDLINE]
17.

[RNA-Seq and its applications: a new technology for transcriptomics].

Qi YX, Liu YB, Rong WH.

Yi Chuan. 2011 Nov;33(11):1191-202. Review. Chinese.

PMID:
22120074
[PubMed - indexed for MEDLINE]
18.

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN.

Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18.

PMID:
20022975
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Brooks MJ, Rajasimha HK, Roger JE, Swaroop A.

Mol Vis. 2011;17:3034-54. Epub 2011 Nov 23.

PMID:
22162623
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

RNA-Seq improves annotation of protein-coding genes in the cucumber genome.

Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K.

BMC Genomics. 2011 Nov 2;12:540. doi: 10.1186/1471-2164-12-540.

PMID:
22047402
[PubMed - indexed for MEDLINE]
Free PMC Article

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