Bioinformatics Research Unit

Life is complicated interactions of various biochemical components. Recently, massively parallel sequencers have changed life science. The sequencer can quantify miscellaneous biological phenomenon. However, it is difficult to reveal biological knowledge from huge and various sequencing data for experimental biologists. In our research unit, we are challenging to research and develop novel methods and software to integrate various sequencing data and understand complex biological phenomenon. Furthermore, we will collaborate with experimental biologist in RIKEN to support analysis for sequencing data.

Research Fields

Biology & Biochemistry / Molecular Biology & Genetics / Computer Science

Research Subjects

• Research and development of data analysis for multilayer omics data
• Collaboration with experimental biologist in RIKEN to support analysis for sequencing data

Publications

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)