Laboratory for Integrated Cellular Systems

Publication list on PubMed 


Publications related to trans-omics 

  1. Egami, R., Kokaji, T., Hatano, A.Yugi, K.,  Eto, M., Morita, K., Ohno, S., Fujii, M., Hironaka, K. Uematsu, S., Terakawa, A., Bai, U., Pan, Y., Tsuchiya, T., Ozaki, H., Inoue, H., Uda, S., Kubota, H., Suzuki, Y., Matsumoto, M., Nakayama, K.I., Hirayama, A., Soga, T., Kuroda, S., "Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle", iScience, 24(3):102217, 2021.
  2. Kokaji, T., Hatano, A., Ito, Y., Yugi, K., Eto, M., Morita, K., Ohno, S., Fujii, M., Hironaka, K.I., Egami, R., Terakawa, A., Tsuchiyal T., Ozaki, H., Inoue, H., Uda, S., Kubota, H., Suzuki, Y., Ikeda, K., Arita, M., Matsumoto, M., Nakayama, K.I., Hirayama, A., Soga, T., Kuroda, S., "Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity", Sci. Signal. 13(660):eaaz1236, 2020.
  3. Hoshino, D., Kawata, K., Kunida, K., Hatano, A.Yugi, K., Wada, T., Fujii, M., Sano, T., Ito, Y., Furuichi, Y., Manabe, Y., Suzuki, Y., Fujii, N.L., Soga, T., Kuroda, S., "Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes", iScience 23(10):101558, 2020.
  4. Ohno, S., Quek, L.E., Krycer, J.R., Yugi, K., Hirayama, A., Ikeda, S., Shoji, F., Suzuki, K., Soga, T., James, D.E., Kuroda, S., "Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes", iScience 23(9):101479, 2020.
  5. 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.
  6. 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.​
  7. †Kawata, K., †Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K.I., Kuroda, S., "Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data", Genes Cells. 24(1):82-93, 2019 († These authors contributed equally).
  8. 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., 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).
  9. 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.  
  10. †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., 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).
  11. Yugi, K. and Kuroda, S. "Metabolism-Centric Trans-Omics", Cell Syst. 4(1):19-20, 2017.
  12. Sano, T., Kawata, K., Ohno S., Yugi, K., Kakuda, H., Kubota, H., Uda, S., Fujii, M., Kunida, K., Hoshino, D., Hatano, A., Ito, Y., Sato, M., Suzuki, Y., Kuroda S., “Selective Control of Upregulated and Downregulated Genes by Temporal Patterns and Doses of Insulin”, Sci. Signal. 22(9): ra112, 2016.
  13. 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).
  14. 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., Kuroda, S., "Reconstruction of insulin signal flow from phosphoproteome and metabolome data", Cell Rep. 8(4), 1171-1183, 2014. († These authors contributed equally )
  15. 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.
  16. 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.

 


Publications

  1. Miyauchi, K., Adachi, Y., Tonouchi, K., Yajima, T., Harada, Y., Fukuyama, H., Deno, S., Iwakura, Y., Yoshimura, A., Hasegawa, H., Yugi, K., Fujii, S.I., Ohara, O., Takahashi, Y., Kubo, M., "Influenza virus infection expands the breadth of antibody responses through IL-4 signalling in B cells", Nat. Commun., 12(1):3789, 2021.
  2. Egami, R., Kokaji, T., Hatano, A.Yugi, K.,  Eto, M., Morita, K., Ohno, S., Fujii, M., Hironaka, K. Uematsu, S., Terakawa, A., Bai, U., Pan, Y., Tsuchiya, T., Ozaki, H., Inoue, H., Uda, S., Kubota, H., Suzuki, Y., Matsumoto, M., Nakayama, K.I., Hirayama, A., Soga, T., Kuroda, S., "Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle", iScience, 24(3):102217, 2021.
  3. Kokaji, T., Hatano, A., Ito, Y., Yugi, K., Eto, M., Morita, K., Ohno, S., Fujii, M., Hironaka, K.I., Egami, R., Terakawa, A., Tsuchiyal T., Ozaki, H., Inoue, H., Uda, S., Kubota, H., Suzuki, Y., Ikeda, K., Arita, M., Matsumoto, M., Nakayama, K.I., Hirayama, A., Soga, T., Kuroda, S., "Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity", Sci. Signal. 13(660):eaaz1236, 2020.
  4. Hoshino, D., Kawata, K., Kunida, K., Hatano, A.Yugi, K., Wada, T., Fujii, M., Sano, T., Ito, Y., Furuichi, Y., Manabe, Y., Suzuki, Y., Fujii, N.L., Soga, T., Kuroda, S., "Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes", iScience 23(10):101558, 2020.
  5. Ohno, S., Quek, L.E., Krycer, J.R., Yugi, K., Hirayama, A., Ikeda, S., Shoji, F., Suzuki, K., Soga, T., James, D.E., Kuroda, S., "Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes", iScience 23(9):101479, 2020.
  6. 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., Kuroda, S. (2020) Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin. iScience 23(2):100855.
  7. 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.​
  8. †Kawata, K., †Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K.I., Kuroda, S., "Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data", Genes Cells. 24(1):82-93, 2019 († These authors contributed equally).
  9. 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., 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).
  10. 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.  
  11. †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., 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)
  12. Yugi, K. and Kuroda, S. "Metabolism-Centric Trans-Omics", Cell Syst. 4(1):19-20, 2017.
  13. Sano, T., Kawata, K., Ohno S., Yugi, K., Kakuda, H., Kubota, H., Uda, S., Fujii, M., Kunida, K., Hoshino, D., Hatano, A., Ito, Y., Sato, M., Suzuki, Y., Kuroda S., “Selective Control of Upregulated and Downregulated Genes by Temporal Patterns and Doses of Insulin”, Sci. Signal. 22(9): ra112, 2016.
  14. 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).
  15. 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., Kuroda, S., "Reconstruction of insulin signal flow from phosphoproteome and metabolome data", Cell Rep. 8(4), 1171-1183, 2014 († These authors contributed equally).
  16. Akimoto, Y., Yugi, K., Uda, S., Kudo, T., Komori, Y., Kubota, H., Kuroda, S., "The Extraction of Simple Relationships in Growth Factor-Specific Multiple-Input and Multiple-Output Systems in Cell-Fate Decisions by Backward Elimination PLS Regression", PLoS ONE 8(9) e72780, 2013.
  17. 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.
  18. Watanabe, K., Akimoto, Y., Yugi, K., Uda, S., Chung, J., Nakamuta, S., Kaibuchi, K. and Kuroda, S., "Latent process genes for cell differentiation are common decoders of neurite extension length", J. Cell Sci. 125(Pt 9):2198-211, 2012.
  19. Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. and Kiga, D. "Construction of a genetic AND gate under a new standard for assembly of genetic parts.", BMC Genomics 11(Suppl 4):S16, 2010.
  20. Matsunaga-Udagawa, R., Fujita, Y., Yoshiki, S., Terai, K., Kamioka, Y., Kiyokawa, E., Yugi, K., Aoki, K. and Matsuda, M. "The scaffold protein Shoc2/SUR-8 accelerates the interaction of Ras and Raf", J. Biol. Chem. 285(10):7818-26, 2010.
  21. Jo, H., Yugi, K., Ogawa, S., Suzuki, Y. and Sakakibara, Y. "Molecular basis of chemical chaperone effects of the chemical chaperone N-octyl-β-valienamine on human-β-glucosidase in low/neutral pH conditions", J. Proteomics Bioinform. 3:104-112, 2010.
  22. Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. and Sakakibara, Y., "Operon structure optimization by random self-assembly", Nat. Comput, 9:173, 2010.
  23. Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. and Kiga, D., "SYANAC: SYnthetic biological automaton for noughts and crosses", IET Synthetic Biology 1(1-2):64-67, 2007.
  24. 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.
  25. Yugi, K., Nakayama, Y., Kojima, S. Kitayama, T. and Tomita, M., "A microarray data-based semi-kinetic method for predicting quantitative dynamics of large-scale genetic networks", BMC Bioinformatics 6:299-307, 2005.
  26.  Yugi, K.,  Nakayama, Y., Kinoshita, A. and Tomita, M., "Hybrid dynamic/static method for large-scale simulation of metabolism", Theor. Biol. Med. Model. 2:42-52, 2005 († These authors contributed equally).
  27. Yugi, K. and Tomita, M., "A general computational model of mitochondrial metabolism in a whole organelle scale", Bioinformatics 20:1795-1796, 2004.
  28. Takahashi, K., Yugi, K., Hashimoto, K., Yamada, Y., Pickett, C. and Tomita, M., "Computational challenges in cell simulation", IEEE Intelligent Systems 17:64-71, 2002.
  29. Tomita, M., Hashimoto, K., Takahashi, K., Matsuzaki, Y., Matsushima, R., Saito K., Yugi K., Miyoshi, F., Nakano, H., Tanida, S., Saito, Y., Kawase, A., Watanabe, N., Shimizu, T. and Nakayama, Y., "The E-CELL Project: Towards integrative simulation of cellular processes", New Generation Computing 18:1-12, 2000.
  30. Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi K., Venter J.C. and Hutchison, C.A., "E-CELL: Software environment for whole cell simulation", Bioinformatics 15:72-84, 1999

 


Reviewed International Conference Papers

  1. Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. and Sakakibara, Y., “Operon Structure Optimization by Random Self-Assembly” The 14th International Meeting on DNA Computing, Prague, Czech Republic, 2008.
  2. Sakakibara, Y., Nakagawa, H., Nakashima, Y. and Yugi, K., “Implementing in vivo cellular automata using toggle switch and inter-bacterial communication mechanism”, BIONETICS2007 Workshop on Computing and Communications from Biological Systems, Budapest, Hungary, 2007.
  3. Tomita, M., Hashimoto, K., Takahashi, K., Matsuzaki, Y., Matsushima, R., Yugi, K., Miyoshi, F., Nakano, H., Saito, Y., Shimizu, T.S., Nakayama, Y., "The E-CELL project: towards integrative simulation of cellular processes", Proceedings of the fourth annual international conference on Computational molecular biology 290-298, 2000. 
  4. Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J.C. and Hutchison, C.A., "E-CELL: Software Environment for Whole Cell Simulation", Genome Informatics 8:147-155, 1997.