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RIKEN Center for Integrative Medical Sciences Laboratory for Integrated Cellular Systems

Team Leader: Katsuyuki Yugi (Ph.D.)

Research Summary

Katsuyuki Yugi (Ph.D.)

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. 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).
  • 2. Yugi, K., Ohno, S., Krycer, J.R., James, D.E., and Kuroda, S.:
    "Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics"
    Curr. Opin. Syst. Biol. 15, 109-120 (2019).
  • 3. †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).
  • 4. 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).
  • 5. †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) († These authors contributed equally).
  • 6. Yugi, K., and Kuroda, S.:
    "Metabolism-Centric Trans-Omics"
    Cell Syst. 4(1), 19-20 (2017).
  • 7. *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).
  • 8. *†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) († These authors contributed equally).
  • 9. *Noguchi, R., Kubota, H., Yugi, K., Toyoshima, Y., Komori, Y., Soga, T., and Kuroda, S.:
    "The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns"
    Mol. Syst. Biol. 9, 664 (2013).
  • 10. *Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P.Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., and Tomita, M.:
    "Multiple high-throughput analyses monitor the response of E. coli to perturbations"
    Science 316(5824), 593-7 (2007).

Related Links

Lab Members

Principal investigator

Katsuyuki Yugi
Team Leader

Core members

Satoko Tsugawa
Technical Staff I

Contact Information

N407
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Email: katsuyuki.yugi [at] riken.jp

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