Centers & Labs

Advanced Center for Computing and Communication

Bioinformatics Research Unit

Unit Leader: Itoshi Nikaido (Ph.D.)
Itoshi  Nikaido(Ph.D.)

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.

Main Research Field

Informatics

Related Research Fields

Biological Sciences

Keywords

  • Bioinformatics
  • Single-cell RNA-sequencing
  • Epigenome
  • Cloud Computing

Selected Publications

  1. Matsumoto H, Kiryu H, Furusawa C, Ko MSH, Ko SBH, Gouda N, Hayashi T, Nikaido I.:
    “SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation”
    Bioinformatics.(2017).
  2. G. Morota, F. Peñagaricano, J. L. Petersen, D. C. Ciobanu, K. Tsuyuzaki and I.Nikaido.:
    An application of MeSH enrichment analysis in livestock.
    Animal Genetics.(2015).
  3. Koki Tsuyuzaki, Gota Morota, Takeru Nakazato, Satoru Miyazaki and Itoshi Nikaido.:
    MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis.
    BMC Bioinformatics. 16:45.(2015)
  4. Kenjiro Adachi*, Itoshi Nikaido*, Hiroshi Ohta, Satoshi Ohtsuka, Hiroki Ura, Teruhiko Wakayama, Hiroki R. Ueda & Hitoshi Niwa.:
    Context-Dependent Wiring of Sox2 Regulatory Networks for Self-Renewal of Embryonic and Trophoblast Stem Cells.
    Molecular Cell. (2013)(*Equally contributions)
  5. 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. (2013) (*Equally contributions)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)

Lab Members

Principal Investigator

Itoshi Nikaido
Unit Leader

Core Members

Yohei Sasagawa
Senior Scientist
Tetsutaro Hayashi
Research Scientist
Akihiro Matsushima
Technical Scientist
Manabu Ishii
Technical Staff I
Mana Umeda
Technical Staff I
Mika Yoshimura
Technical Staff I
Koki Tsuyuzaki
Postdoctoral Researcher
Haruka Ozaki
Special Postdoctoral Researcher
Matsumoto Hirotaka
Visiting Researcher

Contact information

Room 311, 3F, Information Science Building
2-1 Hirosawa, Wako, Saitama 351-0198, Japan

Email: itoshi.nikaido [at] riken.jp

Related links