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Transcriptome tomography for brain analysis in the web-accessible anatomical space.
Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y, Nishimura M, Kasukawa T, Masumoto KH, Nikaido I, Shigeyoshi Y, Ueda HR, Song G, Gee J, Himeno R, Yokota H. Okamura-Oho Y, et al. Among authors: shimokawa k. PLoS One. 2012;7(9):e45373. doi: 10.1371/journal.pone.0045373. Epub 2012 Sep 19. PLoS One. 2012. PMID: 23028969 Free PMC article.
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks.
Morita M, Shimokawa K, Nishimura M, Nakamura S, Tsujimura Y, Takemoto S, Tawara T, Yokota H, Wemler S, Miyamoto D, Ikeno H, Sato A, Furuichi T, Kobayashi N, Okumura Y, Yamaguchi Y, Okamura-Oho Y. Morita M, et al. Among authors: shimokawa k. Nucleic Acids Res. 2019 Jan 8;47(D1):D859-D866. doi: 10.1093/nar/gky951. Nucleic Acids Res. 2019. PMID: 30371824 Free PMC article.
Expression analysis for inverted effects of serotonin transporter inactivation.
Ichikawa M, Okamura-Oho Y, Shimokawa K, Kondo S, Nakamura S, Yokota H, Himeno R, Lesch KP, Hayashizaki Y. Ichikawa M, et al. Among authors: shimokawa k. Biochem Biophys Res Commun. 2008 Mar 28;368(1):43-9. doi: 10.1016/j.bbrc.2008.01.041. Epub 2008 Jan 22. Biochem Biophys Res Commun. 2008. PMID: 18211820
Large-scale clustering of CAGE tag expression data.
Shimokawa K, Okamura-Oho Y, Kurita T, Frith MC, Kawai J, Carninci P, Hayashizaki Y. Shimokawa K, et al. BMC Bioinformatics. 2007 May 21;8:161. doi: 10.1186/1471-2105-8-161. BMC Bioinformatics. 2007. PMID: 17517134 Free PMC article.
Genome-wide analysis of mammalian promoter architecture and evolution.
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y. Carninci P, et al. Among authors: shimokawa k. Nat Genet. 2006 Jun;38(6):626-35. doi: 10.1038/ng1789. Epub 2006 Apr 28. Nat Genet. 2006. PMID: 16645617
The transcriptional landscape of the mammalian genome.
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, … See abstract for full author list ➔ Carninci P, et al. Among authors: shimokawa k. Science. 2005 Sep 2;309(5740):1559-63. doi: 10.1126/science.1112014. Science. 2005. PMID: 16141072
352 results