Katsuyuki Yugi
Katsuyuki Yugi
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Cited by
E-CELL: software environment for whole-cell simulation.
M Tomita, K Hashimoto, K Takahashi, TS Shimizu, Y Matsuzaki, F Miyoshi, ...
Bioinformatics (Oxford, England) 15 (1), 72-84, 1999
Multiple high-throughput analyses monitor the response of E. coli to perturbations
N Ishii, K Nakahigashi, T Baba, M Robert, T Soga, A Kanai, T Hirasawa, ...
Science 316 (5824), 593-597, 2007
Trans-omics: how to reconstruct biochemical networks across multiple ‘omic’layers
K Yugi, H Kubota, A Hatano, S Kuroda
Trends in biotechnology 34 (4), 276-290, 2016
The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns
R Noguchi, H Kubota, K Yugi, Y Toyoshima, Y Komori, T Soga, S Kuroda
Molecular systems biology 9 (1), 664, 2013
Computational challenges in cell simulation: a software engineering approach
K Takahashi, K Yugi, K Hashimoto, Y Yamada, CJF Pickett, M Tomita
IEEE Intelligent Systems 17 (5), 64-71, 2002
Reconstruction of insulin signal flow from phosphoproteome and metabolome data
K Yugi, H Kubota, Y Toyoshima, R Noguchi, K Kawata, Y Komori, S Uda, ...
Cell reports 8 (4), 1171-1183, 2014
The scaffold protein Shoc2/SUR-8 accelerates the interaction of Ras and Raf
R Matsunaga-Udagawa, Y Fujita, S Yoshiki, K Terai, Y Kamioka, ...
Journal of biological chemistry 285 (10), 7818-7826, 2010
A general computational model of mitochondrial metabolism in a whole organelle scale
K Yugi, M Tomita
Bioinformatics 20 (11), 1795-1796, 2004
Dynamic metabolomics reveals that insulin primes the adipocyte for glucose metabolism
JR Krycer, K Yugi, A Hirayama, DJ Fazakerley, LE Quek, R Scalzo, ...
Cell reports 21 (12), 3536-3547, 2017
The E-CELL project: towards integrative simulation of cellular processes
M Tomita, K Hashimoto, K Takahashi, Y Matsuzaki, R Matsushima, K Yugi, ...
Proceedings of the fourth annual international conference on Computational …, 2000
Hybrid dynamic/static method for large-scale simulation of metabolism
K Yugi, Y Nakayama, A Kinoshita, M Tomita
Theoretical Biology and Medical Modelling 2, 1-11, 2005
E-CELL: Software environment for whole cell simulation
M Tomita, T Shimizu, K Saito, JC Venter, K Hashimoto, Y Matsuzaki, ...
Genome Informatics 8, 147-155, 1997
Trans-omic analysis reveals selective responses to induced and basal insulin across signaling, transcriptional, and metabolic networks
K Kawata, A Hatano, K Yugi, H Kubota, T Sano, M Fujii, Y Tomizawa, ...
IScience 7, 212-229, 2018
Latent process genes for cell differentiation are common decoders of neurite extension length
K Watanabe, Y Akimoto, K Yugi, S Uda, J Chung, S Nakamuta, K Kaibuchi, ...
Journal of cell science 125 (9), 2198-2211, 2012
Metabolism-centric trans-omics
K Yugi, S Kuroda
Cell Systems 4 (1), 19-20, 2017
Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin
T Sano, K Kawata, S Ohno, K Yugi, H Kakuda, H Kubota, S Uda, M Fujii, ...
Science Signaling 9 (455), ra112-ra112, 2016
Metabolism as a signal generator across trans-omic networks at distinct time scales
K Yugi, S Kuroda
Current Opinion in Systems Biology 8, 59-66, 2018
Influenza virus infection expands the breadth of antibody responses through IL-4 signalling in B cells
K Miyauchi, Y Adachi, K Tonouchi, T Yajima, Y Harada, H Fukuyama, ...
Nature communications 12 (1), 3789, 2021
Dynamic 13C flux analysis captures the reorganization of adipocyte glucose metabolism in response to insulin
LE Quek, JR Krycer, S Ohno, K Yugi, DJ Fazakerley, R Scalzo, ...
Iscience 23 (2), 2020
Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle
R Egami, T Kokaji, A Hatano, K Yugi, M Eto, K Morita, S Ohno, M Fujii, ...
IScience 24 (3), 2021
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