バイオインフォマティクス研究開発ユニット

生命現象は、生命を構成する部品が相互作用することで実現されます。DNAシーケンサーの技術革新により、生命の部品である遺伝子産物の量やその相互作用を包括的に測定できるようになりました。しかしシーケンサーから得らえるデータは多様かつ巨大で、よくコントロールされた実験と高度なデータ解析技術が必須です。当ユニットでは、理研各所のシーケンス施設と連携し、実験生物学者と実験をデザインしながら、多様な生命情報を定量・統合し、理解するデータ解析手法やソフトウェアの研究開発を行います。さらに、理研共通のデータ解析プラットフォームの構築や教育を通じて、実験生物学者のデータ解析リテラシー向上へ貢献します。

研究分野

生物学 & 生化学 / 分子生物 & 遺伝学 / コンピューター科学

研究テーマ

• 階層的オミックスの新しいデータ解析手法と実験手法の開発
• 実験生物学者との共同研究やバイオインフォマティクス教育による支援

主要論文

1. Sasagawa Y*, Nikaido I*, Hayashi T, Danno H, Uno KD, Imai T and Ueda HR.
   Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity.
   Genome Biology. 14. (*Equally contributions)(2013)
2. Kasukawa T*, Masumoto KH*, Nikaido I*, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR.:
   Quantitative expression profile of distinct functional regions in the adult mouse brain.
   PLoS One. 2011;6(8):e23228. Epub 2011 Aug 12. (*Equally contributions) (2011)
3. Tokuzawa Y, Yagi K, Yamashita Y, Nakachi Y, Nikaido I, Bono H, Ninomiya Y, Kanesaki-Yatsuka Y, Akita M, Motegi H, Wakana S, Noda T, Sablitzky F, Arai S, Kurokawa R, Fukuda T, Katagiri T, Schönbach C, Suda T, Mizuno Y, Okazaki Y.:
   Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation.
   PLoS Genet. Jul 8;6(7):e1001019. (2010)
4. Nakachi Y, Yagi K, Nikaido I, Bono H, Tonouchi M, Schönbach C, Okazaki Y.:
   Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation.
   Biochem Biophys Res Commun. Jul 25;372(2):362-6. Epub 2008 May 19. (2008)
5. Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y.:
   EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.
   Nucleic Acids Res. Jan 1;32:D548-51. (2004)
6. Nikaido I, Saito C, Mizuno Y, Meguro M, Bono H, Kadomura M, Kono T, Morris GA, Lyons PA, Oshimura M, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.
   Genome Res. Jun;13(6B):1402-9. (2003)
7. Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members. Comprehensive analysis of the mouse metabolome based on the transcriptome.
   Genome Res. Jun;13(6B):1345-9. (2003)
8. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.:
   Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
   Nature. Dec 5;420(6915):563-73. (2002)
9. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium.:
   Functional annotation of a full-length mouse cDNA collection.
   Nature. Feb 8;409(6821):685-90. (2001)
10. Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S.:
    Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis
    DNA Res. Jun 30;7(3):223-7. (2000)