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Research

Research

BDR researchers coming from diverse research fields are working together to achieve higher goals.

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BDR hosts annual symposium and regular seminars inviting international scientists in life science.

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BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.

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About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Katsuyuki Shiroguchi

Team Leader
Katsuyuki Shiroguchi Ph.D.

Laboratory for Prediction of Cell Systems Dynamics

LocationOsaka / Quantitative Biology Buildings

E-mailkatsuyuki.shiroguchi[at]riken.jp

Please replace [at] with @.

Unraveling biological systems and contributing to medical sciences by a combination of biophysics and quantitative genomics.

I had been working on single molecule observation of molecular motors by optical microscopy, and have jumped into the genomics research field. Based on these experiences, we are making a new platform enabled by the combination of imaging, sequencing, and machine learning. 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 immune cells and diseases.

Research Theme

  • Molecular barcodes for digital quantification of nucleic acid molecules
  • Digital RNA sequencing (dRNA-seq)
  • Novel bacterial microbiota analysis
  • Combination of bio-imaging, sequencing, and machine learning
  • Organoid studies
  • Cell-Cell interaction

Selected Publications

Jin J, Yamamoto R, Takeuchi T, et al.
High-throughput identification and quantification of single bacterial cells in the microbiota
Nature Communications 13, 863 (2022) doi: 10.1038/s41467-022-28426-1

Zhang B, Vogelzang A, Miyajima M, et al.
B cell-derived GABA elicits IL-10+ macrophages to limit anti-tumour immunity.
Nature 599(7885), 471-476 (2021) doi: 10.1038/s41586-021-04082-1

Nishida M, Yamashita N, Ogawa T, et al.
Mitochondrial reactive oxygen species trigger metformin-dependent antitumor immunity via activation of Nrf2/mTORC1/p62 axis in tumor-infiltrating CD8T lymphocytes.
Journal for immunotherapy of cancer 9, e002954 (2021) doi: 10.1136/jitc-2021-002954

Aso H, Nagaoka S, Kawakami E, et al.
Multiomics investigation revealing the characteristics 1 of HIV-1-infected cells.
Cell Reports 32, 107887 (2020)

Kimura S, Nakamura Y, Kobayashi N, et al.
Osteoprotegerin-dependent M cell self-regulation balances gut infection and immunity.
Nature Communications 11, 234 (2020) doi: 10.1038/s41467-019-13883-y

Yazaki J, Kawashima Y, Ogawa T, et al.
HaloTag-based conjugation of proteins to barcoding-oligonucleotides.
Nucleic Acids Research 48, e8 (2020) doi: 10.1093/nar/gkz1086

Miyamoto C, Kojo S, Yamashita M, et al.
Runx/Cbfβ complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation.
Nature Communications 10, 447 (2019) doi: 10.1038/s41467-019-08365-0

Ise W, Fujii K, Shiroguchi K, et al.
T follicular helper cell-germinal center B cell interaction strength regulates entry into plasma cell or recycling GC cell fate.
Immunity 48, 702-715 (2018) doi: 10.1016/j.immuni.2018.03.027

Tenno M, Kojo S, Lawir DF, et al.
Cbfβ2 controls differentiation of and confers homing capacity to prethymic progenitors.
Journal of Experimental Medicine 215, 595-610 (2018) doi: 10.1084/jem.20171221

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.
Scientific Reports 7, 13576 (2017) doi: 10.1038/s41598-017-13529-3

Tenno M, Shiroguchi K, Muroi S, et al.
Cbfβ2-deficiency preserves Langerhans cell precursors by lack of selective TGFβ receptor signaling.
Journal of Experimental Medicine 214(10), 2933-2946 (2017) doi: 10.1084/jem.20170729

Suzuki H, Mitsuno K, Shiroguchi K, et al.
One-step micromolding of complex 3D microchambers for single-cell analysis.
Lab on a Chip 17(4), 647-652 (2017) doi: 10.1039/c6lc01313a

Chen HY*, Shiroguchi K*, Ge H, Xie XS.
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.
Molecular Systems Biology 11(1), 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 Advances 3(23), 8728-8733 (2013) doi: 10.1039/c3ra41112e

Shiroguchi K, Jia TZ, Sims PA, Xie XS.
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.
Proceedings of the National Academy of Sciences of the United States of America 109(4), 1347-1352 (2012) doi: 10.1073/pnas.1118018109

Shiroguchi K, Chin HF, Hannemann DE, et al.
Direct Observation of the Myosin Va Recovery Stroke That Contributes to Unidirectional Stepping along Actin.
PLOS Biology 9(4), e1001031 (2011) doi: 10.1371/journal.pbio.1001031

Shiroguchi K, Kinosita K.
Myosin V walks by lever action and Brownian motion.
Science 316(5828), 1208-1212 (2007) doi: 10.1126/science.1140468

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