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Results: 1 to 20 of 85

Similar articles for PubMed (Select 23056304)

1.

Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.

Palmieri N, Nolte V, Suvorov A, Kosiol C, Schlötterer C.

PLoS One. 2012;7(10):e46415. doi: 10.1371/journal.pone.0046415. Epub 2012 Oct 3.

2.

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment.

Zhang Z, Huang S, Wang J, Zhang X, Pardo Manuel de Villena F, McMillan L, Wang W.

Bioinformatics. 2013 Jul 1;29(13):i291-9. doi: 10.1093/bioinformatics/btt216.

3.

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

Zhang Y, Lameijer EW, 't Hoen PA, Ning Z, Slagboom PE, Ye K.

Bioinformatics. 2012 Feb 15;28(4):479-86. doi: 10.1093/bioinformatics/btr712. Epub 2012 Jan 4.

4.

PASTA: splice junction identification from RNA-sequencing data.

Tang S, Riva A.

BMC Bioinformatics. 2013 Apr 4;14:116. doi: 10.1186/1471-2105-14-116.

6.

Assessing the impact of human genome annotation choice on RNA-seq expression estimates.

Wu PY, Phan JH, Wang MD.

BMC Bioinformatics. 2013;14 Suppl 11:S8. doi: 10.1186/1471-2105-14-S11-S8. Epub 2013 Nov 4.

7.

Computational approaches for isoform detection and estimation: good and bad news.

Angelini C, De Canditiis D, De Feis I.

BMC Bioinformatics. 2014 May 9;15:135. doi: 10.1186/1471-2105-15-135.

8.

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.

9.

Supersplat--spliced RNA-seq alignment.

Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC.

Bioinformatics. 2010 Jun 15;26(12):1500-5. doi: 10.1093/bioinformatics/btq206. Epub 2010 Apr 21.

10.

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213.

Reddy JS, Kumar R, Watt JM, Lawrence ML, Burgess SC, Nanduri B.

BMC Bioinformatics. 2012;13 Suppl 15:S4. doi: 10.1186/1471-2105-13-S15-S4. Epub 2012 Sep 11.

11.

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.

12.

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.

13.

Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data.

Zhou A, Breese MR, Hao Y, Edenberg HJ, Li L, Skaar TC, Liu Y.

BMC Genomics. 2012;13 Suppl 8:S10. doi: 10.1186/1471-2164-13-S8-S10. Epub 2012 Dec 17.

14.

UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.

Burns PD, Li Y, Ma J, Borodovsky M.

Nucleic Acids Res. 2014 Feb;42(4):e25. doi: 10.1093/nar/gkt1141. Epub 2013 Nov 19.

15.

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker SE, Brown JB.

Nat Biotechnol. 2014 Apr;32(4):341-6. doi: 10.1038/nbt.2850. Epub 2014 Mar 16.

16.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

17.

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.

18.

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.

Wang Y, Ghaffari N, Johnson CD, Braga-Neto UM, Wang H, Chen R, Zhou H.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S5. doi: 10.1186/1471-2105-12-S10-S5.

19.

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.

20.

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.

Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.

BMC Genomics. 2010 Nov 24;11:663. doi: 10.1186/1471-2164-11-663.

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