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Results: 1 to 20 of 32

1.

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.

Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y.

Nucleic Acids Res. 2012 Apr;40(8):e61. doi: 10.1093/nar/gkr1291. Epub 2012 Jan 20.

PMID:
22266656
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ.

Bioinformatics. 2011 Nov 1;27(21):3010-6. doi: 10.1093/bioinformatics/btr508. Epub 2011 Sep 6.

PMID:
21896509
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
21824971
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

Improving RNA-Seq expression estimates by correcting for fragment bias.

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L.

Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22. Epub 2011 Mar 16.

PMID:
21410973
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

CD44 splice isoform switching in human and mouse epithelium is essential for epithelial-mesenchymal transition and breast cancer progression.

Brown RL, Reinke LM, Damerow MS, Perez D, Chodosh LA, Yang J, Cheng C.

J Clin Invest. 2011 Mar;121(3):1064-74. doi: 10.1172/JCI44540.

PMID:
21393860
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Katz Y, Wang ET, Airoldi EM, Burge CB.

Nat Methods. 2010 Dec;7(12):1009-15. doi: 10.1038/nmeth.1528. Epub 2010 Nov 7.

PMID:
21057496
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Alternative expression analysis by RNA sequencing.

Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJ, Tai IT, Marra MA.

Nat Methods. 2010 Oct;7(10):843-7. doi: 10.1038/nmeth.1503. Epub 2010 Sep 12.

PMID:
20835245
[PubMed - indexed for MEDLINE]
9.

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.

Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27.

PMID:
20802226
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.

Srivastava S, Chen L.

Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670. Epub 2010 Jul 29.

PMID:
20671027
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
20576625
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

rQuant.web: a tool for RNA-Seq-based transcript quantitation.

Bohnert R, R├Ątsch G.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W348-51. doi: 10.1093/nar/gkq448. Epub 2010 Jun 15.

PMID:
20551130
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

PMID:
20436464
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

Au KF, Jiang H, Lin L, Xing Y, Wong WH.

Nucleic Acids Res. 2010 Aug;38(14):4570-8. doi: 10.1093/nar/gkq211. Epub 2010 Apr 5.

PMID:
20371516
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

De novo assembly of human genomes with massively parallel short read sequencing.

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.

Genome Res. 2010 Feb;20(2):265-72. doi: 10.1101/gr.097261.109. Epub 2009 Dec 17.

PMID:
20019144
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Sequence-non-specific effects of RNA interference triggers and microRNA regulators.

Olejniczak M, Galka P, Krzyzosiak WJ.

Nucleic Acids Res. 2010 Jan;38(1):1-16. doi: 10.1093/nar/gkp829. Epub 2009 Oct 20. Review.

PMID:
19843612
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

ErbB4 splice variants Cyt1 and Cyt2 differ by 16 amino acids and exert opposing effects on the mammary epithelium in vivo.

Muraoka-Cook RS, Sandahl MA, Strunk KE, Miraglia LC, Husted C, Hunter DM, Elenius K, Chodosh LA, Earp HS 3rd.

Mol Cell Biol. 2009 Sep;29(18):4935-48. doi: 10.1128/MCB.01705-08. Epub 2009 Jul 13.

PMID:
19596786
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

De novo transcriptome assembly with ABySS.

Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ.

Bioinformatics. 2009 Nov 1;25(21):2872-7. doi: 10.1093/bioinformatics/btp367. Epub 2009 Jun 15.

PMID:
19528083
[PubMed - indexed for MEDLINE]
Free Article
19.

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
20.

Statistical inferences for isoform expression in RNA-Seq.

Jiang H, Wong WH.

Bioinformatics. 2009 Apr 15;25(8):1026-32. doi: 10.1093/bioinformatics/btp113. Epub 2009 Feb 25.

PMID:
19244387
[PubMed - indexed for MEDLINE]
Free PMC Article

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