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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.
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.
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.
Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN. Stewart R, et al. Among authors: dewey cn. PLoS Comput Biol. 2013;9(3):e1002936. doi: 10.1371/journal.pcbi.1002936. Epub 2013 Mar 7. PLoS Comput Biol. 2013. PMID: 23505351 Free PMC article.
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.
57 results