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Items: 1 to 20 of 126

1.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.

Nucleic Acids Res. 2012 Mar;40(6):e42. doi: 10.1093/nar/gkr1248. Epub 2011 Dec 22.

2.

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.

3.

Designing a transcriptome next-generation sequencing project for a nonmodel plant species.

Strickler SR, Bombarely A, Mueller LA.

Am J Bot. 2012 Feb;99(2):257-66. doi: 10.3732/ajb.1100292. Epub 2012 Jan 19. Review.

4.

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.

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML.

Nucleic Acids Res. 2010 Jun;38(10):e112. doi: 10.1093/nar/gkq041. Epub 2010 Feb 11.

6.

RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.

van Delft J, Gaj S, Lienhard M, Albrecht MW, Kirpiy A, Brauers K, Claessen S, Lizarraga D, Lehrach H, Herwig R, Kleinjans J.

Toxicol Sci. 2012 Dec;130(2):427-39. doi: 10.1093/toxsci/kfs250. Epub 2012 Aug 13.

PMID:
22889811
7.

Design and validation issues in RNA-seq experiments.

Fang Z, Cui X.

Brief Bioinform. 2011 May;12(3):280-7. doi: 10.1093/bib/bbr004. Epub 2011 Apr 15. Review.

PMID:
21498551
9.

Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.

Pollier J, Rombauts S, Goossens A.

Methods Mol Biol. 2013;1011:305-15. doi: 10.1007/978-1-62703-414-2_24.

PMID:
23616006
10.

TrueSight: a new algorithm for splice junction detection using RNA-seq.

Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J.

Nucleic Acids Res. 2013 Feb 1;41(4):e51. doi: 10.1093/nar/gks1311. Epub 2012 Dec 18.

11.

DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression.

George NI, Chang CW.

BMC Bioinformatics. 2014 Mar 31;15:92. doi: 10.1186/1471-2105-15-92.

12.

Detection and quantification of alternative splicing variants using RNA-seq.

Bryant DW Jr, Priest HD, Mockler TC.

Methods Mol Biol. 2012;883:97-110. doi: 10.1007/978-1-61779-839-9_7.

PMID:
22589127
13.

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A.

Bioinformatics. 2012 Apr 15;28(8):1184-5. doi: 10.1093/bioinformatics/bts084. Epub 2012 Feb 17.

PMID:
22345621
14.

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.

15.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72. doi: 10.1073/pnas.1113972108. Epub 2011 Dec 1.

16.

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
17.

Bias detection and correction in RNA-Sequencing data.

Zheng W, Chung LM, Zhao H.

BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.

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.

19.

R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.

Mittal VK, McDonald JF.

Nucleic Acids Res. 2012 May;40(9):e67. doi: 10.1093/nar/gks047. Epub 2012 Jan 28.

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

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