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Items: 15

1.

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. Epub 2009 Mar 4.

2.

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.

3.

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.

4.

Cross-hybridization modeling on Affymetrix exon arrays.

Kapur K, Jiang H, Xing Y, Wong WH.

Bioinformatics. 2008 Dec 15;24(24):2887-93. doi: 10.1093/bioinformatics/btn571. Epub 2008 Nov 4.

5.

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Nucleic Acids Res. 2008 Sep;36(16):e105. doi: 10.1093/nar/gkn425. Epub 2008 Jul 26.

6.

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.

Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M.

Biotechniques. 2008 Jul;45(1):81-94. doi: 10.2144/000112900.

7.

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. Epub 2008 Jun 11.

8.

Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM.

Nat Methods. 2008 Jul;5(7):613-9. doi: 10.1038/nmeth.1223. Epub 2008 May 30.

PMID:
18516046
9.

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
10.

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. Epub 2008 May 1.

11.

Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR.

Cell. 2008 May 2;133(3):523-36. doi: 10.1016/j.cell.2008.03.029.

12.

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

Faulkner GJ, Forrest AR, Chalk AM, Schroder K, Hayashizaki Y, Carninci P, Hume DA, Grimmond SM.

Genomics. 2008 Mar;91(3):281-8. doi: 10.1016/j.ygeno.2007.11.003.

13.

The UCSC Known Genes.

Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D.

Bioinformatics. 2006 May 1;22(9):1036-46. Epub 2006 Feb 24.

PMID:
16500937
14.

Statistical modeling of sequencing errors in SAGE libraries.

Beissbarth T, Hyde L, Smyth GK, Job C, Boon WM, Tan SS, Scott HS, Speed TP.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i31-9.

PMID:
15262778
15.

A strategy of DNA sequencing employing computer programs.

Staden R.

Nucleic Acids Res. 1979 Jun 11;6(7):2601-10.

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