• Shimo H, Arjunan SNV, Machiyama H, Nishino T, Suematsu M, Fujita H, Tomita M, Takahashi K: Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS computational biology. 11:e1004210 (2015) Open_Access
  • Nishino T, Yachie-Kinoshita A, Hirayama A, Soga T, Suematsu M, Tomita M. Dynamic Simulation and Metabolome Analysis of Long-Term Erythrocyte Storage in Adenine–Guanosine Solution. PLoS One. 8(8):e71060 (2013) Open_Access
  • Okubo C, Sano HI, Naito Y, Tomita M. Contribution of quantitative changes in individual ionic current systems to the embryonic development of ventricular myocytes: a simulation study. J Physiol Sci. 63(5):355-67 (2013) Open_Access PubMed
  • Mugler A, Bailey AG, Takahashi K, ten Wolde PR. Membrane clustering and the role of rebinding in biochemical signaling. Biophys J. 102(5):1069-78 (2012) PubMed
  • Seike M, Saitou T, Kouchi Y, Ohara T, Matsuhisa M, Sakaguchi K, Tomita K, Kosugi K, Kashiwagi A, Kasuga M, Tomita M, Naito Y, Nakajima H. Computational assessment of insulin secretion and insulin sensitivity from 2-h oral glucose tolerance tests for clinical use for type 2 diabetes. J Physiol Sci 61(4):321-30 (2011) Open_Access PubMed
  • Shimo H, Nishino T, Tomita M. Predicting the Kinetic Properties Associated with Redox Imbalance after Oxidative Crisis in G6PD-Deficient Erythrocytes: A Simulation Study. Adv Hematol 2011:398945 (2011) Open_Access PubMed
  • Takahashi K, Tanase-Nicola S, ten Wolde PR. Spatio-temporal correlations can drastically change the response of a MAPK pathway. Proc Natl Acad Sci U S A 107(6):2473-8 (2010) PubMed
  • Yachie-Kinoshita A, Nishino T, Shimo H, Suematsu M, Tomita M. A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment. J Biomed Biotechnol 2010:642420 (2010) PubMed
  • Nishino T, Yachie-Kinoshita A, Hirayama A, Soga T, Suematsu M, Tomita M. In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods. J Biotechnol 144(3):212-23 (2009) PubMed
  • Helmy M, Gohda J, Inoue J, Tomita M, Tsuchiya M, Selvarajoo K. Predicting novel features of toll-like receptor 3 signaling in macrophages. PLoS One 4(3):e4661 (2009) PubMed
  • Ogawa Y, Arakawa K, Kaizu K, Miyoshi F, Nakayama Y, Tomita M. Comparative study of circadian oscillatory network models of Drosophila. Artif Life 14(1):29-48 (2008) PubMed
  • Ohno H, Naito Y, Nakajima H, Tomita M. Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule. Artif Life 14(1):3-28 (2008) PubMed
  • Selvarajoo K, Takada Y, Gohda J, Helmy M, Akira S, Tomita M, Tsuchiya M, Inoue J, Matsuo K. Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One 3(10):e3430 (2008) PubMed
  • Ishii N, Nakayama Y, Tomita M. Distinguishing enzymes using metabolome data for the hybrid dynamic/static method. Theor Biol Med Model 4:19 (2007) PubMed
  • Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, 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, Tomita M. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316(5824):593-7 (2007) PubMed
  • Kinoshita A, Tsukada K, Soga T, Hishiki T, Ueno Y, Nakayama Y, Tomita M, Suematsu M. Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysis. J Biol Chem 282(14):10731-41 (2007) PubMed
  • Kinoshita A, Nakayama Y, Kitayama T, Tomita M. Simulation study of methemoglobin reduction in erythrocytes. Differential contributions of two pathways to tolerance to oxidative stress. FEBS J 274(6):1449-58 (2007) PubMed
  • Itoh H, Naito Y, Tomita M. Simulation of developmental changes in action potentials with ventricular cell models. Syst Synth Biol 1(1):11-23 (2007) PubMed
  • Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M. A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. J Biol Rhythms 22(1):69-80 (2007) PubMed
  • Kitayama T, Kinoshita A, Sugimoto M, Nakayama Y, Tomita M. A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles. Theor Biol Med Model 3:24 (2006) PubMed
  • Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M. GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics 7:168 (2006) PubMed
  • Yugi K, Nakayama Y, Kojima S, Kitayama T, Tomita M. A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. BMC Bioinformatics 6:299 (2005) PubMed
  • Yugi K, Nakayama Y, Kinoshita A, Tomita M. Hybrid dynamic/static method for large-scale simulation of metabolism. Theor Biol Med Model 2:42 (2005) PubMed
  • Nakayama Y, Kinoshita A, Tomita M. Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model 2:18 (2005) PubMed
  • Takahashi K, Arjunan SN, Tomita M. Space in systems biology of signaling pathways–towards intracellular molecular crowding in silico. FEBS Lett 579(8):1783-8 (2005) PubMed
  • Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M. Toward large-scale modeling of the microbial cell for computer simulation. J Biotechnol 113(1-3):281-94 (2004) PubMed
  • Yugi K, Tomita M. A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinformatics 20(4):1795-6 (2004) PubMed Supplement
  • Takahashi K, Kaizu K, Hu B, Tomita M. A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20(4):538-46 (2004) PubMed\

    Supplement - Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M. E-Cell 2: multi-platform E-Cell simulation system. Bioinformatics 19(13):1727-9 (2003) PubMed - Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524-31 (2003) PubMed - Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA 3rd. E-CELL: software environment for whole-cell simulation. Bioinformatics 15(1):72-84 (1999) PubMed - Tomita M, Hashimoto K, Takahashi K, Shimizu T, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA. E-CELL: Software Environment for Whole Cell Simulation. Genome Inform Ser Workshop Genome Inform 8:147-155 (1997) PubMed