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 1999. 3
B.A. (Honors) Keio University, Faculty of Environment and Information Studies
2001
M.A. Keio University, Graduate School of Media and Governance
2002-2004
Research Associate of Keio University 21st Century COE Program
2003-2005
Research Trainee, National Institute of Neuroscience, Department of Mental Retardation and Birth Defect Research
2004-2006
Visiting Researcher, Keio Research Institute at SFC
2005
Ph.D. Keio University, Advisor: Masaru Tomita
2006-2010
Keio University (Sakakibara Lab.)
2010-
University of Tokyo (Kuroda Lab.)
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Research Associate: |
YUGI, Katsuyuki |
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yugi AT bs.s.u-tokyo.ac.jp |
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| Primers for Mathematical Methods in Systems Biology
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Chapter 2
Bifurcation Analysis
[text] [slide]
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Chapter 5
Flux Balance Analysis
[text] [slide]
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Chapter 6
Metabolic Control Analysis
[text] [slide]
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Chapter 9
Deriving Reaction Kinetics from Physics
[text][slide]
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Chapter 10
Stochastic Simulation Methods
[text][slide]
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Chapter 11
Multivariate Analysis in Systems Biology
[text][slide]
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Copyright © 2011 YUGI, Katsuyuki All Rights Reserved.
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Yugi, K., Kubota, H, Hatano, A, Kuroda, S.,, "Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers", Trends Biotechnol. 34(4):276-290, 2016.
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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.
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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.
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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.
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Yugi K., "Dynamic kinetic modelling of mitochondrial energy metabolism." In: Arjunan, S.N.V., Pawan, K.D, and Tomita, M., eds. E-Cell System: Basic Concepts and Applications. Austin: Landes Bioscience, 2013.
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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.
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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.
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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.
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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.
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Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. and Sakakibara, Y., "Operon structure optimization by random self-assembly", Natural Computing 9(1):173-181 2010.
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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.
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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.
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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.
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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.
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Yugi, K. and Tomita, M., "A general computational model of mitochondrial metabolism in a whole organelle scale", Bioinformatics 20:1795-1796, 2004. [supplementary]
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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.
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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.
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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.
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| International Conferences
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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.
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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.
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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.
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[総説2] 柚木克之, 久保田浩行、黒田真也「トランスオミクスによる代謝制御ネットワークの再構築」, 実験医学 32(8):1215-1222, 2014.
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柚木克之, 冨田勝, 「E-Cell」, (今中忠行 監修「ゲノミクス・プロテオミクスの新展開生物情報の解析と応用」pp.920-929, エヌ・ティー・エス刊, 2004 所収)
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Michael Snyder Lab., Stanford Univ., 6 Feb. 2012
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Bernhald O. Palsson Lab., UC San Diego, 3 Feb. 2012
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Lewis Cantley Lab., Harvard Medical School, 27 Jan. 2012
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Joshua D. Rabinowitz Lab., Princeton Univ., 26 Jan. 2012
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Michiyuki Matsuda Lab., Kyoto Univ., 7 Nov. 2007, "Underlying mechanisms of biochemical oscillations"
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Poster Prize, The CREST Seminar "Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics", Daiba, Japan, 25 Nov. 2013.
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Metabolomic Profiling Forum Young Scientist Poster Prize, 9th International Conference of the Metabolomics Society, Glasgow, Scotland, 4 Jul. 2013.
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Poster Prize, The CREST Exhibition Symposium "The Dynamic Mechanism of and Fundamental Technology for Biological Systems", Akihabara, Japan, 25 Feb. 2013.
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Best Cooperation and Collaboration Prize (1st place) and Best Part Prize (Runner-up), International Genetically Engineered Machine Competition 2006, Boston, USA, 6 Nov. 2006
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