Laboratory for Bioinformatics Research | RIKEN BDR

Laboratory for Bioinformatics Research

Team Leader

Itoshi NikaidoPh.D.

Photo of principal investigator

  • Location:Kobe / Developmental Biology Buildings, Wako / Information Science Bldg.
  • E-mail:itoshi.nikaido[at]riken.jpPlease replace [at] with @.
  • Lab Website

Research Summary

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 team 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 the development of 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 transcriptome. Our team will not only develop new techniques but also collaborate with various life scientists within and outside of RIKEN using our new sequencing technologies.

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

Quartz-Seq2: a high throughput single-cell RNA-sequencing method

Overview of RT-RamDA and single-cell RamDA-seq for detection of full-length total RNAs

Research Theme

  • Development of novel single-cell omics techniques
  • Collaboration with various biologists to apply novel single-cell omics technologies

Main Publications List

  • Mishina T, Tabata N, Hayashi T, et al.
    Single-oocyte transcriptome analysis reveals aging-associated effects influenced by life stage and calorie restriction.
    Aging Cell (2021) doi: 10.1111/acel.13428
  • Ishihara S, Sasagawa Y, Kameda T, et al.
    Local states of chromatin compaction at transcription start sites control transcription levels.
    Nucleic Acids Research gkab587 (2021) doi: 10.1093/nar/gkab587
  • Yamada A, Hirasawa T, Nishimura K, et al.
    Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra Syndrome.
    iScience 24, 102741 (2021) doi: 10.1016/j.isci.2021.102741
  • Morita R, Sanzen N, Sasaki H, et al.
    Tracing the origin of hair follicle stem cells.
    Nature (2021) doi: 10.1038/s41586-021-03638-5
  • Ochiai H, Hayashi T, Umeda M, et al.
    Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells
    Science Advances 6(25): eaaz6699 (2020) doi: 10.1126/sciadv.aaz6699
  • Mereu E, Lafzi A, Moutinho C, et al.
    Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
    Nature Biotechnology (2020) doi: 10.1038/s41587-020-0469-4
  • Ozaki H, Hayashi T, Umeda M, Nikaido I.
    Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.
    BMC Genomics 21, 177 (2020) doi: 10.1186/s12864-020-6542-z
  • Tsuyuzaki K, Sato H, Sato K, Nikaido I.
    Benchmarking principal component analysis for large-scale single-cell RNA-sequencing.
    Genome Biology 21, 9 (2020) doi: 10.1186/s13059-019-1900-3
  • Sato K, Tsuyuzaki K, Shimizu K, Nikaido I.
    CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing.
    Genome Biology 20: 31 (2019) doi: 10.1186/s13059-019-1639-x
  • Hayashi T, Ozaki H, Sasagawa Y, et al.
    Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
    Nature Communications 9. 619 (2018) doi: 10.1038/s41467-018-02866-0
  • Matsumoto H, Kiryu H, Furusawa C, et al.
    SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.
    Bioinformatics 33(15). 2314–2321 (2017) doi: 10.1093/bioinformatics/btx194
  • Tsuyuzaki K, Morota G, Ishii M, et al.
    MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis.
    BMC Bioinformatics 16. 45 (2015) doi: 10.1186/s12859-015-0453-z
  • Sasagawa Y, Nikaido I, Hayashi T, et al.
    Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.
    Genome Biology 14. 3097 (2013) doi: 10.1186/gb-2013-14-4-r31
  • Adachi K, Nikaido I, Ohta H, et al.
    Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.
    Molecular Cell 52. 380–392 (2013) doi: 10.1016/j.molcel.2013.09.002
  • Sasagawa Y, Danno H, Takada H et al.
    Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.
    Genome Biology 19. 29 (2018) doi: 10.1186/s13059-018-1407-3

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