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 @.
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
Takahashi S, Ochiai S, Jin J, et al.
Sensory neuronal STAT3 is critical for IL-31 receptor expression and inflammatory itch
Cell Reports
Tue Nov 28 00:00:00 JST 2023
doi: /10.1016/j.celrep.2023.113433
Jin J, Yamamoto R, Shiroguchi K, et al.
High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ
Nature Protocols
Mon Nov 27 00:00:00 JST 2023
doi: /10.1038/s41596-023-00906-8
Cui G, Shimba A, Jin J, et al.
CD45 Alleviates Airway Inflammation and Lung Fibrosis by Limiting Expansion and Activation of ILC2s.
Proceedings of the National Academy of Sciences of the United States of America
120(36), e2215941120 Wed Aug 30 00:00:00 JST 2023
doi: 10.1073/pnas.2215941120
Fujimura T, Enomoto Y, Katsura H, et al.
Identifying a Lung Stem Cell Subpopulation by Combining Single-Cell Morphometrics, Organoid Culture, and Transcriptomics.
Stem Cells
41(8), 809-820 Wed Aug 30 00:00:00 JST 2023
doi: 10.1093/stmcls/sxad044
Jin J, Ogawa T, Hojo N, et al.
Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes.
Proceedings of the National Academy of Sciences of the United States of America
120(1), e2210283120 Tue Jan 03 00:00:00 JST 2023
doi: 10.1073/pnas.2210283120
Cui G, Shimba A, Jin J, et al.
A circulating subset of iNKT cells mediates antitumor and antiviral immunity.
Science Immunology
7(76), eabj8760 Fri Oct 28 00:00:00 JST 2022
doi: 10.1126/sciimmunol.abj8760
Jin J, Yamamoto R, Takeuchi T, et al.
High-throughput identification and quantification of single bacterial cells in the microbiota.
Nature Communications
13, 863 Tue Feb 22 00:00:00 JST 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 Mon Nov 01 00:00:00 JST 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 Wed Sep 01 00:00:00 JST 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 Tue Dec 01 00:00:00 JST 2020
Kimura S, Nakamura Y, Kobayashi N, et al.
Osteoprotegerin-dependent M cell self-regulation balances gut infection and immunity.
Nature Communications
11, 234 Tue Dec 01 00:00:00 JST 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 Sun Nov 01 00:00:00 JST 2020
doi: 10.1093/nar/gkz1086
