RIKEN Center for Integrative Medical Sciences Laboratory for Integrated Cellular Systems
Team Leader: Katsuyuki Yugi (Ph.D.)
Research Summary

Our research interest is to understand intracellular metabolism and its regulatory mechanism as a system of biochemical reactions in dynamic, macroscopic, and quantitative contexts. We employ the methodology of 'trans-omics' that reconstructs multi-layered metabolic regulatory networks by integration of multiple omic data on the basis of reaction kinetics. Interdisciplinary approaches such as 'wet' biology experiments and 'dry' analysis such as databases and mathematical models are utilized to characterize the global metabolic regulatory networks. We eventually aim at revealing chain of logic from individual biochemical reaction to omics-scale systems.
Main Research Fields
- Biological Sciences
Related Research Fields
- Informatics
- Complex Systems
- Mathematical & Physical Sciences
- Biology
- System genome science
Keywords
- Metabolism
- Systems biology
- Trans-omics
- Reaction kinetics
- Mathematical model
Selected Publications
Papers with an asterisk(*) are based on research conducted outside of RIKEN.
- 1.
Nishida, K., Maruyama, J., Kaizu, K., Takahashi, K., and Yugi, K.:
"Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks”
npj Syst. Biol. Appl. 10, 16 (2024) - 2.
Takeuchi, T., Kubota, T., Nakanishi, Y., Tsugawa, H., Suda, W,. Kwon, A.T., Yazaki, J., Ikeda, K., Nemoto, S., Mochizuki, Y., Kitami, T., Yugi, K., Mizuno, Y., Yamamichi, N., Yamazaki, T., Takamoto, I., Kubota, N., Kadowaki, T., Arner, E., Carninci, P., Ohara, O., Arita, M., Hattori, M., Koyasu, S., and Ohno, H.
"Gut microbial carbohydrate metabolism contributes to insulin resistance”
Nature 621(7978), 389-395 (2023) - 3.
Okamoto, L., Watanabe, S., Deno, S., Nie, X., Maruyama, J., Tomita, M., Hatano, A., Yugi, K.,
"Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach"
Neurosci. Res. 175, 82-97 (2022) - 4.
Quek, L.E., Krycer, J.R., Ohno, S., Yugi, K., Fazakerley, D.J., Scalzo, R., Elkington, S.D., Dai, Z,, Hirayama, A., Ikeda, S., Shoji, F., Suzuki, K., Locasale, J.W., Soga, T., James, D.E., and Kuroda, S.:
"Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin"
iScience 23(2), 100855 (2020). - 5.
†Kawata, K., †Hatano, A., †Yugi, K., Kubota, H., Sano, T., Fujii, M., Tomizawa, Y., Kokaji, T., Tanaka, K.Y., Uda, S., Suzuki, Y., Matsumoto, M., Nakayama, K.I., Saitoh, K., Kato, K., Ueno, A., Ohishi, M., Hirayama, A., Soga, T., and Kuroda, S.:
"Trans-omic analysis reveals selective responses to induced and basal insulin across signaling, transcriptional, and metabolic networks"
iScience 7, 212-229 (2018) (Cover Article; † These authors contributed equally). - 6.
Yugi, K., and Kuroda, S.:
"Metabolism as a signal generator across trans-omic networks at distinct time scales"
Curr. Opin. Syst. Biol. 8, 59-66 (2018). - 7.
*†Krycer, J.R., †Yugi, K., Hirayama, A., Fazakerley, D.J., Quek, L.E., Scalzo, R., Ohno, S., Hodson, M.P., Ikeda, S., Soji, F., Suzuki, K., Domanova, W., Parker, B.K., Nelson, M.E., Humphrey, S.J., Turner, N., Hoehn, K.L., Cooney, G.J., Soga, T., Kuroda, S., and James, D.E.:
"Dynamic metabolomics reveals that insulin primes the adipocyte for glucose metabolism"
Cell Rep. 21(12), 3536-3547 (2017) - 8.
Yugi, K., and Kuroda, S.:
"Metabolism-Centric Trans-Omics"
Cell Syst. 4(1), 19-20 (2017). - 9.
*Yugi, K., Kubota, H., Hatano, A., and Kuroda, S.:
"Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic' Layers"
Trends Biotechnol. 34(4), 276-290 (2016) (Cover Article). - 10.
*Yugi, K., Kubota, H., Toyoshima, Y., Noguchi, R., Kawata, K., Komori, Y., Uda, S., Kunida, K., Tomizawa, Y., Funato, Y., Miki, H., Matsumoto, M., Nakayama, K.I., Kashikura, K., Endo, K., Ikeda, K., Soga, T., and Kuroda, S.:
"Reconstruction of insulin signal flow from phosphoproteome and metabolome data"
Cell Rep. 8(4), 1171-1183 (2014)
Related Links
Lab Members
Principal investigator
- Katsuyuki Yugi
- Team Leader
Core members
- Junichi Maruyama
- Research Scientist
- Xiang Nie
- Visiting Researcher
- Satoko Tsugawa
- Technical Staff I
Contact Information
N407
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Email: katsuyuki.yugi@riken.jp