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STAR: ultrafast universal RNA-seq aligner.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. Dobin A, et al. Among authors: davis ca. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. Bioinformatics. 2013. PMID: 23104886 Free PMC article.
Synthetic spike-in standards for RNA-seq experiments.
Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Jiang L, et al. Among authors: davis ca. Genome Res. 2011 Sep;21(9):1543-51. doi: 10.1101/gr.121095.111. Epub 2011 Aug 4. Genome Res. 2011. PMID: 21816910 Free PMC article.
Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Gerstein MB, et al. Among authors: davis ca. Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424. Nature. 2014. PMID: 25164755 Free PMC article.
Comparison of the transcriptional landscapes between human and mouse tissues.
Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. Lin S, et al. Among authors: davis ca. Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17224-9. doi: 10.1073/pnas.1413624111. Epub 2014 Nov 20. Proc Natl Acad Sci U S A. 2014. PMID: 25413365 Free PMC article.
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.
Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Pervouchine DD, et al. Among authors: davis ca. Nat Commun. 2015 Jan 13;6:5903. doi: 10.1038/ncomms6903. Nat Commun. 2015. PMID: 25582907 Free PMC article.
A benchmark for RNA-seq quantification pipelines.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Teng M, et al. Among authors: davis ca. Genome Biol. 2016 Apr 23;17:74. doi: 10.1186/s13059-016-0940-1. Genome Biol. 2016. PMID: 27107712 Free PMC article.
Erratum to: A benchmark for RNA-seq quantification pipelines.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Teng M, et al. Among authors: davis ca. Genome Biol. 2016 May 23;17(1):107. doi: 10.1186/s13059-016-0986-0. Genome Biol. 2016. PMID: 27215799 Free PMC article. No abstract available.
Gene-specific patterns of expression variation across organs and species.
Breschi A, Djebali S, Gillis J, Pervouchine DD, Dobin A, Davis CA, Gingeras TR, Guigó R. Breschi A, et al. Among authors: davis ca. Genome Biol. 2016 Jul 8;17(1):151. doi: 10.1186/s13059-016-1008-y. Genome Biol. 2016. PMID: 27391956 Free PMC article.
Erratum to: A benchmark for RNA-seq quantification pipelines.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Teng M, et al. Among authors: davis ca. Genome Biol. 2016 Sep 30;17(1):203. doi: 10.1186/s13059-016-1060-7. Genome Biol. 2016. PMID: 27716375 Free PMC article. No abstract available.
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.
Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R. Lagarde J, et al. Among authors: davis c. Nat Genet. 2017 Dec;49(12):1731-1740. doi: 10.1038/ng.3988. Epub 2017 Nov 6. Nat Genet. 2017. PMID: 29106417 Free PMC article.
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