rnaseq references

[Wang2009RNA] Z. Wang, M. Gerstein, and M. Snyder. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10(1):57-63, Jan 2009. [ bib | DOI | http | .pdf | Abstract ]
[Jiang2009Statistical] H. Jiang and W. H. Wong. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics, 25(8):1026-1032, Apr 2009. [ bib | DOI | http | .pdf | Abstract ]
[Bohnert2009Transcript] R. Bohnert, J. Behr, and G. Rätsch. Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10 (Suppl 13):P5, 2009. [ bib | DOI | http | .pdf ]
[Trapnell2009TopHat] C. Trapnell, L. Pachter, and S. L. Salzberg. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9):1105-1111, May 2009. [ bib | DOI | http | .pdf | Abstract ]
[Trapnell2010Transcript] C. Trapnell, B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter. Transcript assembly and quantification by rna-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 28(5):511-515, May 2010. [ bib | DOI | http | .pdf | Abstract ]
[Roberts2011Improving] A. Roberts, C. Trapnell, J. Donaghey, J. L. Rinn, and L. Pachter. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol, 12(3):R22, 2011. [ bib | DOI | http | .pdf | Abstract ]
[Roberts2011Identification] A. Roberts, H. Pimentel, C. Trapnell, and L. Pachter. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27(17):2325-2329, Sep 2011. [ bib | DOI | http | .pdf | Abstract ]
[Li2011IsoLasso] W. Li, J. Feng, and T. Jiang. Isolasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. J Comput Biol, 18(11):1693-1707, Nov 2011. [ bib | DOI | http | .pdf | Abstract ]
[Li2011Sparse] J. J. Li, C.-R. Jiang, J. B. Brown, H. Huang, and P. J. Bickel. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc. Natl. Acad. Sci. USA, 108(50):19867-19872, December 2011. [ bib | DOI | http | .pdf | Abstract ]
[Trapnell2012Differential] C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D. R. Kelley, H. Pimentel, S. L. Salzberg, J. L. Rinn, and L. Pachter. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 7(3):562-578, Mar 2012. [ bib | DOI | http | .pdf | Abstract ]
[Trapnell2013Differential] C. Trapnell, D. G. Hendrickson, M. Sauvageau, L. Goff, J. L. Rinn, and L. Pachter. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol, 31(1):46-53, Jan 2013. [ bib | DOI | http | .pdf | Abstract ]
[Mezlini2013iReckon] A. M. Mezlini, E. J. M. Smith, M. Fiume, O. Buske, G. L. Savich, S. Shah, S. Aparicio, D. Y. Chiang, A. Goldenberg, and M. Brudno. iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res, 23(3):519-529, Mar 2013. [ bib | DOI | http | .pdf | Abstract ]

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