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Items: 14

1.

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.

2.

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.

3.

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.

4.

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Richard H, Schulz MH, Sultan M, N├╝rnberger 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.

5.

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.

Ramsk├Âld D, Wang ET, Burge CB, Sandberg R.

PLoS Comput Biol. 2009 Dec;5(12):e1000598. doi: 10.1371/journal.pcbi.1000598.

6.

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.

7.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25.

8.

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.

9.

RNA-Seq: a revolutionary tool for transcriptomics.

Wang Z, Gerstein M, Snyder M.

Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484. Review.

10.

Alternative isoform regulation in human tissue transcriptomes.

Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB.

Nature. 2008 Nov 27;456(7221):470-6. doi: 10.1038/nature07509.

11.

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.

12.

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y.

Genome Res. 2008 Sep;18(9):1509-17. doi: 10.1101/gr.079558.108.

13.

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.

PMID:
18516045
14.

The transcriptional landscape of the yeast genome defined by RNA sequencing.

Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M.

Science. 2008 Jun 6;320(5881):1344-9. doi: 10.1126/science.1158441.

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