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Items: 1 to 20 of 228

1.

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.

Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ.

Nat Genet. 2008 Dec;40(12):1413-5. doi: 10.1038/ng.259. Epub 2008 Nov 2. Erratum in: Nat Genet. 2009 Jun;41(6):762.

PMID:
18978789
2.

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML.

Science. 2008 Aug 15;321(5891):956-60. doi: 10.1126/science.1160342. Epub 2008 Jul 3.

3.

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
4.

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
5.

Quantitative analysis of alternative splicing options of human plasma membrane calcium pump genes.

Stauffer TP, Hilfiker H, Carafoli E, Strehler EE.

J Biol Chem. 1993 Dec 5;268(34):25993-6003. Erratum in: J Biol Chem. 1994 Dec 16;269(50):32022.

6.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.

Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, Chen L, Tian W, Tao Y, Kristiansen K, Zhang X, Li S, Yang H, Wang J, Wang J.

Genome Res. 2010 May;20(5):646-54. doi: 10.1101/gr.100677.109. Epub 2010 Mar 19.

7.

Estimating accuracy of RNA-Seq and microarrays with proteomics.

Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P.

BMC Genomics. 2009 Apr 16;10:161. doi: 10.1186/1471-2164-10-161.

8.

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.

9.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ.

BMC Genomics. 2006 Sep 29;7:246.

10.

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.

11.

A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.

He C, Zhou F, Zuo Z, Cheng H, Zhou R.

PLoS One. 2009;4(3):e4732. doi: 10.1371/journal.pone.0004732. Epub 2009 Mar 6.

12.

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. Epub 2008 May 30.

PMID:
18516045
13.

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.

14.

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.

15.

Genome-wide detection of testis- and testicular cancer-specific alternative splicing.

He C, Zuo Z, Chen H, Zhang L, Zhou F, Cheng H, Zhou R.

Carcinogenesis. 2007 Dec;28(12):2484-90. Epub 2007 Aug 27.

PMID:
17724370
16.

Alternative splicing: global insights.

Hallegger M, Llorian M, Smith CW.

FEBS J. 2010 Feb;277(4):856-66. doi: 10.1111/j.1742-4658.2009.07521.x. Epub 2010 Jan 15. Review.

17.

Observations on novel splice junctions from RNA sequencing data.

Wang L, Wang X, Wang X, Liang Y, Zhang X.

Biochem Biophys Res Commun. 2011 Jun 3;409(2):299-303. doi: 10.1016/j.bbrc.2011.05.005. Epub 2011 May 7.

PMID:
21575597
18.

Inferring global levels of alternative splicing isoforms using a generative model of microarray data.

Shai O, Morris QD, Blencowe BJ, Frey BJ.

Bioinformatics. 2006 Mar 1;22(5):606-13. Epub 2006 Jan 10.

PMID:
16403798
19.

A study of alternative splicing in the pig.

Nygard AB, Cirera S, Gilchrist MJ, Gorodkin J, Jørgensen CB, Fredholm M.

BMC Res Notes. 2010 May 5;3:123. doi: 10.1186/1756-0500-3-123.

20.

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.

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