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Laboratory for Integrative Omics

Katsuyuki Shiroguchi


Unit Leader

Katsuyuki Shiroguchi (Ph.D.)

Shiroguchi of RIKEN

Original HP

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.

Research Topics

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

Selected Publications

  • Ogawa, T., Kryukov, K., Imanishi, T. & Shiroguchi, K.
    "The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules"
    Sci. Rep. 7, 13576 (2017) doi:10.1038/s41598-017-13529-3
  • Tenno, M., Shiroguchi, K., Muroi, S., Kawakami, E., Koseki, K., Kryukov, K., et al.
    "Cbfβ2-deficiency preserves Langerhans cell precursors by lack of selective TGFβ receptor signaling"
    J. Exp. Med. 214, 2933-2946 (2017) doi:10.1084/jem.20170729
  • Suzuki, H., Mitsuno, K., Shiroguchi, K., Tsugane, M., Okano, T., Dohi, T., et al.
    "One-step micromolding of complex 3D microchambers for single-cell analysis"
    Lab Chip 17, 647-652 (2017) doi:10.1039/c6lc01313a
  • Chen, H. Y.*, Shiroguchi, K.*, Ge, H. & Xie, X. S. (*Equal first authors)
    "Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli"
    Mol. Syst. Biol. 11, 781 (2015) doi:10.15252/msb.20145794
  • Miyazaki, M., Kinosita, K. & Shiroguchi, K.
    "Accurate polarity control and parallel alignment of actin filaments for myosin-powered transport systems"
    RSC Adv. 3, 8728-8733 (2013) doi:10.1039/c3ra41112e
  • 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. U.S.A. 109, 1347-1352 (2012) doi:10.1073/pnas.1118018109
  • Shiroguchi, K., Chin, H. F., Hannemann, D. E., Muneyuki, E., Cruz, E. M. & Kinosita, K.
    "Direct Observation of the Myosin Va Recovery Stroke That Contributes to Unidirectional Stepping along Actin"
    PLoS Biol. 9, e1001031 (2011) doi:10.1371/journal.pbio.1001031
  • Shiroguchi, K. & Kinosita, K.
    "Myosin V walks by lever action and Brownian motion"
    Science 316, 1208-1212 (2007) doi:10.1126/science.1140468