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Items: 1 to 20 of 572

1.

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA.

Bioinformatics. 2011 Sep 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19.

2.

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.

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.

JAGuaR: junction alignments to genome for RNA-seq reads.

Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJ, Birol İ.

PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. eCollection 2014.

5.

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.

6.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium..

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

7.

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data.

Kumar PK, Hoang TV, Robinson ML, Tsonis PA, Liang C.

Sci Rep. 2015 Aug 25;5:13443. doi: 10.1038/srep13443.

8.

Mapping RNA-seq Reads with STAR.

Dobin A, Gingeras TR.

Curr Protoc Bioinformatics. 2015 Sep 3;51:11.14.1-19. doi: 10.1002/0471250953.bi1114s51. Review.

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.

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.

Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR.

Bioinformatics. 2015 Dec 15;31(24):3938-45. doi: 10.1093/bioinformatics/btv488. Epub 2015 Sep 3.

11.

A probabilistic framework for aligning paired-end RNA-seq data.

Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J.

Bioinformatics. 2010 Aug 15;26(16):1950-7. doi: 10.1093/bioinformatics/btq336. Epub 2010 Jun 23.

12.

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.

13.

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.

Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C.

Nucleic Acids Res. 2013 May 1;41(10):5149-63. doi: 10.1093/nar/gkt216. Epub 2013 Apr 9.

14.

RNA-Seq read alignments with PALMapper.

Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G.

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

PMID:
21154708
15.

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF.

Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8.

16.

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level.

Zhang Z, Wang W.

Bioinformatics. 2014 Jun 15;30(12):i283-i292. doi: 10.1093/bioinformatics/btu288.

17.

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW.

New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.

18.

SplicingCompass: differential splicing detection using RNA-seq data.

Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R.

Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.

PMID:
23449093
19.

SNPlice: variants that modulate Intron retention from RNA-sequencing data.

Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A.

Bioinformatics. 2015 Apr 15;31(8):1191-8. doi: 10.1093/bioinformatics/btu804. Epub 2014 Dec 6.

20.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.

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