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RIKEN Center for Biosystems Dynamics Research Laboratory for Prediction of Cell Systems Dynamics

Team Leader: Katsuyuki Shiroguchi (Ph.D.)

Research Summary

Katsuyuki  Shiroguchi(Ph.D.)

I had been working on single molecule observation of molecular motors by optical microscopy, and have jumped into genomics research field. Based on these experiences, we are making a new platform which enables to combine imaging and sequencing. Using this system, we would like to understand biological systems, and to contribute to medical sciences. We have developed other techniques as well, for example, molecular barcoding which provides digital RNA sequencing (dRNA-seq), and a novel bacterial microbiota analysis based on single-base identification and single-cell level quantification. We often collaborate with biologists and/or medical scientists in order to study, e.g., immune cells, and/or diseases.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Complex Systems
  • Interdisciplinary Science & Engineering
  • Biology


  • Quantitative genomics
  • Single cell analysis
  • Digital quantification
  • Sequencing
  • Bio-imaging

Selected Publications

  • 1.Tenno M., Shiroguchi K., Muroi S., Kawakami E., Koseki K., Kryukov K., Imanishi T., Ginhoux F., Taniuchi I.
    "Cbfβ2-deficiency preserves Langerhans cell precursors by lack of selective TGFβ receptor signaling"
    J. Exp. Med. accepted.
  • 2.Suzuki, H. Mitsuno K., Shiroguchi K., Tsugane M., Okano T., Dohi T., Tsuji T.
    "One-step Micromolding of Complex 3D Microchambers for Single-Cell Analysis"
    Lab. Chip. 17, 647-652 (2017).
  • 3.Chen H.*, Shiroguchi K.*, Ge H., Xie X.S.
    "Genome-wide study of mRNA degradation and transcript elongation in E.coli"
    Mol. Syst. Biol. 11, 781 (2015) (*equal contribution)
  • 4.Miyazaki M. Kinosita Jr. K., Shiroguchi K.
    "Accurate polarity control and parallel alignment of actin filaments for myosin-powered transport systems"
    RSC Adv. 3, 8728-8733 (2013)
  • 5.* Shiroguchi K., Jia T.Z., Sims P.A., Xie X.S.
    "Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single molecule barcodes"
    Proc. Natl. Acad. Sci. USA, 109, 1347-1352 (2012).
  • 6.* Shiroguchi, K.*, Chin, H.F., Hannemann, D.E., Muneyuki, E., De La Cruz, E.M.*, Kinosita Jr. K.
    "Direct observation of the Myosin Va recovery stroke that contributes to unidirectional stepping along actin"
    PLoS Biol. 9: e1001031 (2011) *Corresponding author.
  • 7.* Shiroguchi K., Kinosita Jr. K.
    "Myosin V walks by lever action and Brownian motion"
    Science, 316, 1208-1212 (2007).

Recent Research Results

Related Links

Lab Members

Principal investigator

Katsuyuki Shiroguchi
Team Leader

Core members

Taisaku Ogawa
Special Postdoctoral Researcher
Jianshi Jin
Visiting Researcher
Kaori Fukuhara
Technical Staff I
Reiko Yamamoto
Part-time Worker