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Results: 1 to 20 of 94

1.

GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.

Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y.

Genome Biol. 2013 Jul 22;14(7):R74. doi: 10.1186/gb-2013-14-7-r74.

PMID:
23876401
[PubMed - in process]
Free PMC Article
2.

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
3.

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

Tokheim C, Park JW, Xing Y.

Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001. Epub 2014 Apr 18.

PMID:
24747190
[PubMed - indexed for MEDLINE]
Free Article
4.

rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test.

Shi Y, Jiang H.

PLoS One. 2013 Nov 18;8(11):e79448. doi: 10.1371/journal.pone.0079448. eCollection 2013.

PMID:
24260225
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ARH-seq: identification of differential splicing in RNA-seq data.

Rasche A, Lienhard M, Yaspo ML, Lehrach H, Herwig R.

Nucleic Acids Res. 2014 Oct 1;42(14):e110. doi: 10.1093/nar/gku495. Epub 2014 Jun 11.

PMID:
24920826
[PubMed - in process]
Free Article
6.

Integrative analysis of many RNA-seq datasets to study alternative splicing.

Li W, Dai C, Kang S, Zhou XJ.

Methods. 2014 Jun 1;67(3):313-24. doi: 10.1016/j.ymeth.2014.02.024. Epub 2014 Feb 28.

PMID:
24583115
[PubMed - in process]
Free Article
7.

Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.

Park JW, Tokheim C, Shen S, Xing Y.

Methods Mol Biol. 2013;1038:171-9. doi: 10.1007/978-1-62703-514-9_10.

PMID:
23872975
[PubMed - indexed for MEDLINE]
8.

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
[PubMed - indexed for MEDLINE]
Free Article
9.

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.

PMID:
24209455
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A statistical method for the detection of alternative splicing using RNA-seq.

Wang L, Xi Y, Yu J, Dong L, Yen L, Li W.

PLoS One. 2010 Jan 8;5(1):e8529. doi: 10.1371/journal.pone.0008529.

PMID:
20072613
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.

Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM.

Genome Res. 2011 Oct;21(10):1728-37. doi: 10.1101/gr.119784.110. Epub 2011 Aug 26.

PMID:
21873452
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
23557086
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.

Wang X, Cairns MJ.

BMC Bioinformatics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2105-14-S5-S16. Epub 2013 Apr 10.

PMID:
23734663
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21775302
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser.

Gulledge AA, Vora H, Patel K, Loraine AE.

Methods Mol Biol. 2014;1158:123-37. doi: 10.1007/978-1-4939-0700-7_8.

PMID:
24792048
[PubMed - in process]
Free PMC Article
16.

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq.

Feng H, Qin Z, Zhang X.

Cancer Lett. 2013 Nov 1;340(2):179-91. doi: 10.1016/j.canlet.2012.11.010. Epub 2012 Nov 27. Review.

PMID:
23196057
[PubMed - indexed for MEDLINE]
17.

Detecting differential usage of exons from RNA-seq data.

Anders S, Reyes A, Huber W.

Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111. Epub 2012 Jun 21.

PMID:
22722343
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Identification of genetic variants associated with alternative splicing using sQTLseekeR.

Monlong J, Calvo M, Ferreira PG, Guigó R.

Nat Commun. 2014 Aug 20;5:4698. doi: 10.1038/ncomms5698.

PMID:
25140736
[PubMed - in process]
Free PMC Article
19.

Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.

Suo C, Calza S, Salim A, Pawitan Y.

Bioinformatics. 2014 Feb 15;30(4):506-13. doi: 10.1093/bioinformatics/btt704. Epub 2013 Dec 3.

PMID:
24307704
[PubMed - indexed for MEDLINE]
20.

Towards reliable isoform quantification using RNA-SEQ data.

Howard BE, Heber S.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S6. doi: 10.1186/1471-2105-11-S3-S6.

PMID:
20438653
[PubMed - indexed for MEDLINE]
Free PMC Article

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