Centers & Labs

RIKEN Center for Developmental Biology

Single-cell Omics Research Unit

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

A multicellular organism is orchestrated by cell growth, death, differentiation, and communication at the single-cell level. To understand various crucial biological phenomena, we should massively perturb and measure transcriptomes and epigenomes at the single-cell level.

Our group will develop novel methods of comprehensive analysis and perturbation of transcriptome and epigenome at the single-cell level, in particular, by applying massively parallel DNA sequencing, genome editing, microfluidics, and machine learning. We focus on developing methods for quantifying and controlling cell function, fate, and cell-cell communication at the single-cell level.

We have already reported novel single-cell RNA-sequencing methods, such as Quartz-Seq and RamDA-seq, which are highly reproducible and sensitive methods of quantifying single-cell transcriptomes. Our unit will not only develop new techniques but also collaborate with life scientists both within and outside of RIKEN using our new sequencing technologies.

With these techniques, our group seeks to promote social well-being by contributing to the insights into how humans can achieve health and longevity.

We are located at the RIKEN Center for Computing and Communication near Tokyo and the RIKEN Center for Developmental Biology in Kobe.

Main Research Field


Related Research Fields

Biological Sciences


  • 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. Volume 33, Issue 15, 2314–2321, 1 August 2017
  2. 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
  3. 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. Aug;46(4):381-7. 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. Volume 52, Issue 3, p380–392, 7 November 2013
  5. Sasagawa Y*, Nikaido I*, Hayashi T, Danno H, Uno KD, Imai T and Ueda HR.: (*Equally contributions)
    "Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity"
    Genome Biology. 14. 2013
  6. Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y, Nishimura M, Kasukawa T, Masumoto K, Nikaido I, Shigeyoshi Y, Ueda HR, Song G, Gee J, Himeno R, Yokota H.:
    "Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space"
    PLoS ONE 7(9): e45373. 2012
  7. 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. Aug 12. 2011
  8. 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.
  9. 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.
  10. 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

Contact information

312 Information Science Building,
2-1 Hirosawa,
Wako, Saitama
351-0198, Japan
Tel: +81-(0)48-467-9398
Fax: +81-(0)48-462-4395

Email: itoshi.nikaido [at]

Related links