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1.

Comparing reference-based RNA-Seq mapping methods for non-human primate data.

Benjamin AM, Nichols M, Burke TW, Ginsburg GS, Lucas JE.

BMC Genomics. 2014 Jul 7;15:570. doi: 10.1186/1471-2164-15-570.

2.

A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.

Finseth FR, Harrison RG.

PLoS One. 2014 Oct 3;9(10):e108550. doi: 10.1371/journal.pone.0108550. eCollection 2014.

3.

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.

5.

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics.

Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG.

Nucleic Acids Res. 2013 Jan;41(Database issue):D906-14. doi: 10.1093/nar/gks1268. Epub 2012 Nov 29.

6.

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.

Vijay N, Poelstra JW, Künstner A, Wolf JB.

Mol Ecol. 2013 Feb;22(3):620-34. doi: 10.1111/mec.12014. Epub 2012 Sep 24.

PMID:
22998089
7.

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.

8.

454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes.

Hook SE, Twine NA, Simpson SL, Spadaro DA, Moncuquet P, Wilkins MR.

Aquat Toxicol. 2014 Aug;153:73-88. doi: 10.1016/j.aquatox.2013.11.022. Epub 2013 Dec 12.

PMID:
24434169
9.

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.

Liu Y, Koyutürk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR.

BMC Genomics. 2014 Aug 16;15:685. doi: 10.1186/1471-2164-15-685.

10.

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J.

Nucleic Acids Res. 2012 Nov 1;40(20):10084-97. doi: 10.1093/nar/gks804. Epub 2012 Sep 10.

11.

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.

Tulin S, Aguiar D, Istrail S, Smith J.

Evodevo. 2013 Jun 3;4:16. doi: 10.1186/2041-9139-4-16. eCollection 2013.

12.

De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology.

Crawford JE, Guelbeogo WM, Sanou A, Traoré A, Vernick KD, Sagnon N, Lazzaro BP.

PLoS One. 2010 Dec 2;5(12):e14202. doi: 10.1371/journal.pone.0014202.

13.

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.

Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW.

PLoS One. 2011;6(7):e22953. doi: 10.1371/journal.pone.0022953. Epub 2011 Jul 29.

14.

Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads.

Zhao S.

PLoS One. 2014 Jul 3;9(7):e101374. doi: 10.1371/journal.pone.0101374. eCollection 2014.

15.

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.

16.

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.

17.

Towards an improved apple reference transcriptome using RNA-seq.

Bai Y, Dougherty L, Xu K.

Mol Genet Genomics. 2014 Jun;289(3):427-38. doi: 10.1007/s00438-014-0819-3. Epub 2014 Feb 16.

PMID:
24532088
18.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL.

Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36.

19.

Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches.

Chen G, Wang C, Shi L, Tong W, Qu X, Chen J, Yang J, Shi C, Chen L, Zhou P, Lu B, Shi T.

Hum Genet. 2013 Aug;132(8):899-911. doi: 10.1007/s00439-013-1300-9. Epub 2013 Apr 10.

PMID:
23572138
20.

RNA-Seq technology and its application in fish transcriptomics.

Qian X, Ba Y, Zhuang Q, Zhong G.

OMICS. 2014 Feb;18(2):98-110. doi: 10.1089/omi.2013.0110. Epub 2013 Dec 31. Review.

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