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Page 1
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: gingeras tr. 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: gingeras tr. Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424. Nature. 2014. PMID: 25164755 Free PMC article.
The developmental transcriptome of Drosophila melanogaster.
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. Graveley BR, et al. Among authors: gingeras tr. Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22. Nature. 2011. PMID: 21179090 Free PMC article.
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. Derrien T, et al. Among authors: gingeras tr. Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111. Genome Res. 2012. PMID: 22955988 Free PMC article.
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: gingeras tr. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. Bioinformatics. 2013. PMID: 23104886 Free PMC article.
Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium. Engström PG, et al. Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. Nat Methods. 2013. PMID: 24185836 Free PMC article.
Dynamics of microRNA expression during mouse prenatal development.
Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei LH, Drenkow J, Scavelli A, Gingeras TR, Wold BJ, Myers RM, Guigó R, Mortazavi A. Rahmanian S, et al. Among authors: gingeras tr. Genome Res. 2019 Nov;29(11):1900-1909. doi: 10.1101/gr.248997.119. Epub 2019 Oct 23. Genome Res. 2019. PMID: 31645363 Free PMC article.
The transcriptional diversity of 25 Drosophila cell lines.
Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P. Cherbas L, et al. Among authors: gingeras tr. Genome Res. 2011 Feb;21(2):301-14. doi: 10.1101/gr.112961.110. Epub 2010 Dec 22. Genome Res. 2011. PMID: 21177962 Free PMC article.
172 results