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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. Haas BJ, et al. Among authors: dewey cn. Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. Nat Protoc. 2013. PMID: 23845962 Free PMC article.
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project; Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Stark A, et al. Among authors: dewey cn. Nature. 2007 Nov 8;450(7167):219-32. doi: 10.1038/nature06340. Nature. 2007. PMID: 17994088 Free PMC article.
RNA-Seq gene expression estimation with read mapping uncertainty.
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. Li B, et al. Among authors: dewey cn. Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18. Bioinformatics. 2010. PMID: 20022975 Free PMC article.
Evaluation of de novo transcriptome assemblies from RNA-Seq data.
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Li B, et al. Among authors: dewey cn. Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5. Genome Biol. 2014. PMID: 25608678 Free PMC article.
57 results