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Items: 1 to 20 of 106

1.

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.

2.

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq.

Li Y, Rao X, Mattox WW, Amos CI, Liu B.

PLoS One. 2015 Sep 1;10(9):e0136653. doi: 10.1371/journal.pone.0136653. eCollection 2015.

3.

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.

4.

IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data.

Niu L, Huang W, Umbach DM, Li L.

BMC Genomics. 2014 Oct 6;15:862. doi: 10.1186/1471-2164-15-862.

5.

Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data.

Badr E, ElHefnawi M, Heath LS.

PLoS One. 2016 Nov 18;11(11):e0166978. doi: 10.1371/journal.pone.0166978. eCollection 2016.

6.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J.

BMC Genomics. 2008 Nov 7;9:529. doi: 10.1186/1471-2164-9-529. Erratum in: BMC Genomics. 2009 Mar 23;10. doi: 10.1186/1471-2164-10-121.

7.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S.

Nucleic Acids Res. 2010 Jan;38(Database issue):D86-90. doi: 10.1093/nar/gkp984. Epub 2009 Dec 7.

8.

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.

9.

Identification of human-specific transcript variants induced by DNA insertions in the human genome.

Kim DS, Hahn Y.

Bioinformatics. 2011 Jan 1;27(1):14-21. doi: 10.1093/bioinformatics/btq612. Epub 2010 Oct 29.

PMID:
21037245
10.

Identifying differentially spliced genes from two groups of RNA-seq samples.

Wang W, Qin Z, Feng Z, Wang X, Zhang X.

Gene. 2013 Apr 10;518(1):164-70. doi: 10.1016/j.gene.2012.11.045. Epub 2012 Dec 8.

PMID:
23228854
11.

Prediction and Quantification of Splice Events from RNA-Seq Data.

Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R.

PLoS One. 2016 May 24;11(5):e0156132. doi: 10.1371/journal.pone.0156132. eCollection 2016.

12.

Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments.

Lu H, Lin L, Sato S, Xing Y, Lee CJ.

PLoS Comput Biol. 2009 Dec;5(12):e1000608. doi: 10.1371/journal.pcbi.1000608. Epub 2009 Dec 18.

13.

A non-EST-based method for exon-skipping prediction.

Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R.

Genome Res. 2004 Aug;14(8):1617-23.

14.

SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

Sun X, Zuo F, Ru Y, Guo J, Yan X, Sablok G.

Comput Methods Programs Biomed. 2015 Apr;119(1):53-62. doi: 10.1016/j.cmpb.2015.02.004. Epub 2015 Feb 14.

PMID:
25720307
15.

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.

16.

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq.

Hartley SW, Mullikin JC.

Nucleic Acids Res. 2016 Sep 6;44(15):e127. doi: 10.1093/nar/gkw501. Epub 2016 Jun 1.

17.

Genome-wide association between DNA methylation and alternative splicing in an invertebrate.

Flores K, Wolschin F, Corneveaux JJ, Allen AN, Huentelman MJ, Amdam GV.

BMC Genomics. 2012 Sep 15;13:480. doi: 10.1186/1471-2164-13-480.

18.

Multiple sequence variants of BRCA2 exon 7 alter splicing regulation.

Gaildrat P, Krieger S, Di Giacomo D, Abdat J, Révillion F, Caputo S, Vaur D, Jamard E, Bohers E, Ledemeney D, Peyrat JP, Houdayer C, Rouleau E, Lidereau R, Frébourg T, Hardouin A, Tosi M, Martins A.

J Med Genet. 2012 Oct;49(10):609-17. doi: 10.1136/jmedgenet-2012-100965. Epub 2012 Sep 7.

PMID:
22962691
19.

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

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

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

20.

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.

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