| 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 | 1089 | 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 | 792 | 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 | 283 | 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 | 111 | 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 | 111 | 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 | 87 | 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 | 80 | 2010 |
| A general computational model of mitochondrial metabolism in a whole organelle scale K Yugi, M Tomita Bioinformatics 20 (11), 1795-1796, 2004 | 68 | 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 | 60 | 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 | 51 | 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 | 45 | 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 | 45 | 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 | 36 | 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 | 36 | 2012 |
| Metabolism-centric trans-omics K Yugi, S Kuroda Cell Systems 4 (1), 19-20, 2017 | 31 | 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 | 29 | 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 | 27 | 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 | 26 | 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 | 26 | 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 | 19 | 2021 |
Shinya KurodaBiological Sciences, University of TokyoVerified email at bs.s.u-tokyo.ac.jp
