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Results: 1 to 20 of 118

1.

EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY.

Bioinformatics. 2013 Apr 15;29(8):1004-10. doi: 10.1093/bioinformatics/btt092. Epub 2013 Mar 1.

PMID:
23457040
[PubMed - indexed for MEDLINE]
Free Article
2.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Schulz MH, Zerbino DR, Vingron M, Birney E.

Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

PMID:
22368243
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Comparative analysis of de novo transcriptome assembly.

Clarke K, Yang Y, Marsh R, Xie L, Zhang KK.

Sci China Life Sci. 2013 Feb;56(2):156-62. doi: 10.1007/s11427-013-4444-x. Epub 2013 Feb 8.

PMID:
23393031
[PubMed - indexed for MEDLINE]
4.

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences.

Bao E, Jiang T, Girke T.

Bioinformatics. 2013 May 15;29(10):1250-9. doi: 10.1093/bioinformatics/btt127. Epub 2013 Mar 14.

PMID:
23493323
[PubMed - indexed for MEDLINE]
Free Article
5.

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
6.

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
7.

CLASS: constrained transcript assembly of RNA-seq reads.

Song L, Florea L.

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.

PMID:
23734605
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

PMID:
21572440
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.

Li W, Jiang T.

Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.

PMID:
23060617
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels.

Peng Y, Leung HC, Yiu SM, Lv MJ, Zhu XG, Chin FY.

Bioinformatics. 2013 Jul 1;29(13):i326-34. doi: 10.1093/bioinformatics/btt219.

PMID:
23813001
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A.

Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11.

PMID:
23845962
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

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
14.

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq.

Lu B, Zeng Z, Shi T.

Sci China Life Sci. 2013 Feb;56(2):143-55. doi: 10.1007/s11427-013-4442-z. Epub 2013 Feb 8.

PMID:
23393030
[PubMed - indexed for MEDLINE]
15.

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.

PMID:
19289445
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

LeGault LH, Dewey CN.

Bioinformatics. 2013 Sep 15;29(18):2300-10. doi: 10.1093/bioinformatics/btt396. Epub 2013 Jul 11.

PMID:
23846746
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Li B, Dewey CN.

BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323.

PMID:
21816040
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.

PMID:
24130305
[PubMed - indexed for MEDLINE]
19.

SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.

Safikhani Z, Sadeghi M, Pezeshk H, Eslahchi C.

Genomics. 2013 Nov-Dec;102(5-6):507-14. doi: 10.1016/j.ygeno.2013.10.003. Epub 2013 Oct 23.

PMID:
24161398
[PubMed - indexed for MEDLINE]
20.

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.

Nariai N, Hirose O, Kojima K, Nagasaki M.

Bioinformatics. 2013 Sep 15;29(18):2292-9. doi: 10.1093/bioinformatics/btt381. Epub 2013 Jul 2.

PMID:
23821651
[PubMed - indexed for MEDLINE]

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