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High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. Batut P, et al. Among authors: carninci p. Genome Res. 2013 Jan;23(1):169-80. doi: 10.1101/gr.139618.112. Epub 2012 Aug 30. Genome Res. 2013. PMID: 22936248 Free PMC article.
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes.
Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y. Carninci P, et al. Genome Res. 2000 Oct;10(10):1617-30. doi: 10.1101/gr.145100. Genome Res. 2000. PMID: 11042159 Free PMC article.
Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library.
Konno H, Fukunishi Y, Shibata K, Itoh M, Carninci P, Sugahara Y, Hayashizaki Y. Konno H, et al. Among authors: carninci p. Genome Res. 2001 Feb;11(2):281-9. doi: 10.1101/gr.gr-1457r. Genome Res. 2001. PMID: 11157791 Free PMC article.
A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs.
Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, Hayashizaki Y. Osato N, et al. Among authors: carninci p. Genome Res. 2002 Jul;12(7):1127-34. doi: 10.1101/gr.75202. Genome Res. 2002. PMID: 12097351 Free PMC article.
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
Kochiwa H, Suzuki R, Washio T, Saito R, Bono H, Carninci P, Okazaki Y, Miki R, Hayashizaki Y, Tomita M; RIKEN Genome Exploration Research Group Phase II Team. Kochiwa H, et al. Among authors: carninci p. Genome Res. 2002 Aug;12(8):1286-93. doi: 10.1101/gr.220302. Genome Res. 2002. PMID: 12176936 Free PMC article.
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.
Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin GM. Stapleton M, et al. Among authors: carninci p. Genome Res. 2002 Aug;12(8):1294-300. doi: 10.1101/gr.269102. Genome Res. 2002. PMID: 12176937 Free PMC article.
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y. Carninci P, et al. Genome Res. 2003 Jun;13(6B):1273-89. doi: 10.1101/gr.1119703. Genome Res. 2003. PMID: 12819125 Free PMC article.
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.
Wells CA, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume DA, Lyons PA; RIKEN GER Group; GSL Members. Wells CA, et al. Among authors: carninci p. Genome Res. 2003 Jun;13(6B):1360-5. doi: 10.1101/gr.1056103. Genome Res. 2003. PMID: 12819134 Free PMC article.
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y. Shiraki T, et al. Among authors: carninci p. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15776-81. doi: 10.1073/pnas.2136655100. Epub 2003 Dec 8. Proc Natl Acad Sci U S A. 2003. PMID: 14663149 Free PMC article.
Alternate transcription of the Toll-like receptor signaling cascade.
Wells CA, Chalk AM, Forrest A, Taylor D, Waddell N, Schroder K, Himes SR, Faulkner G, Lo S, Kasukawa T, Kawaji H, Kai C, Kawai J, Katayama S, Carninci P, Hayashizaki Y, Hume DA, Grimmond SM. Wells CA, et al. Among authors: carninci p. Genome Biol. 2006;7(2):R10. doi: 10.1186/gb-2006-7-2-r10. Epub 2006 Feb 17. Genome Biol. 2006. PMID: 16507160 Free PMC article.
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