Bibliography

Ogawa, Y, Arakawa, K, Kaizu, K, Miyoshi, F, Nakayama, Y, and Tomita, M (2008).
Comparative study of circadian oscillatory network models of Drosophila.
Artif Life, 14(1):29-48.

Ohno, H, Naito, Y, Nakajima, H, and Tomita, M (2008).
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.

Ishii, N, Suga, Y, Hagiya, A, Watanabe, H, Mori, H, Yoshino, M, and Tomita, M (2007).
Dynamic simulation of an in vitro multi-enzyme system.
FEBS Lett, 581(3):413-20.

Itoh, H, Naito, Y, and Tomita, M (2007).
Simulation of developmental changes in action potentials with ventricular cell models
Systems and Synthetic Biology, 1(1):11–23.

Kinoshita, A, Nakayama, Y, Kitayama, T, and Tomita, M (2007).
Simulation study of methemoglobin reduction in erythrocytes. Differential contributions of two pathways to tolerance to oxidative stress.
FEBS J, 274(6):1449-58.

Kinoshita, A, Tsukada, K, Soga, T, Hishiki, T, Ueno, Y, Nakayama, Y, Tomita, M, and Suematsu, M (2007).
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.

Matsuzaki, Y, Kikuchi, S, and Tomita, M (2007).
Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis.
Artif Intell Med, 41(2):145-50.

Miyoshi, F, Nakayama, Y, Kaizu, K, Iwasaki, H, and Tomita, M (2007).
A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria.
J Biol Rhythms, 22(1):69-80.

Nakayama, Y, Kinoshita, A, and Tomita, M (2005).
Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition.
Theor Biol Med Model, 2:18.

Takahashi, K, Arjunan, SNV, and Tomita, M (2005).
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.
FEBS Lett, 579(8):1783-8.

Ishii, N, Robert, M, Nakayama, Y, Kanai, A, and Tomita, M (2004).
Toward large-scale modeling of the microbial cell for computer simulation.
J Biotechnol, 113(1-3):281-94.

Takahashi, K, Kaizu, K, Hu, B, and Tomita, M (2004).
A multi-algorithm, multi-timescale method for cell simulation.
Bioinformatics, 20(4):538-46.

Yugi, K and Tomita, M (2004).
A general computational model of mitochondrial metabolism in a whole organelle scale.
Bioinformatics, 20(11):1795-6.

Kikuchi, S, Fujimoto, K, Kitagawa, N, Fuchikawa, T, Abe, M, Oka, K, Takei, K, and Tomita, M (2003).
Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A.
Neural Netw, 16(9):1389-98.

Kikuchi, S, Tominaga, D, Arita, M, Takahashi, K, and Tomita, M (2003).
Dynamic modeling of genetic networks using genetic algorithm and S-system.
Bioinformatics, 19(5):643-50.

Miyoshi, F, Nakayama, Y, and Tomita, M (2003).
[E-Cell simulation system and its application to the modeling of circadian rhythm]
Seikagaku, 75(1):5-16.

Takahashi, K, Ishikawa, N, Sadamoto, Y, Sasamoto, H, Ohta, S, Shiozawa, A, Miyoshi, F, Naito, Y, Nakayama, Y, and Tomita, M (2003).
E-Cell 2: multi-platform E-Cell simulation system.
Bioinformatics, 19(13):1727-9.

Takahashi, K, Yugi, K, Hashimoto, K, Yamada, Y, Pickett, CJ, and Tomita, M (2002).
Computational Challenges in Cell Simulation: A Software Engineering Approach
IEEE Intelligent Systems, 17(5):64-71.

Tomita, M (2001).
Whole-cell simulation: a grand challenge of the 21st century.
Trends Biotechnol, 19(6):205-10.

Tomita, M, Hashimoto, K, Takahashi, K, Shimizu, TS, Matsuzaki, Y, Miyoshi, F, Saito, K, Tanida, S, Yugi, K, Venter, JC, and Hutchison, CA3 (1999).
E-CELL: software environment for whole-cell simulation.
Bioinformatics, 15(1):72-84.

Tomita, M, Hashimoto, K, Takahashi, K, Shimizu, T, Matsuzaki, Y, Miyoshi, F, Saito, K, Tanida, S, Yugi, K, Venter, JC, and Hutchison, CA (1997).
E-CELL: Software Environment for Whole Cell Simulation.
Genome Inform Ser Workshop Genome Inform, 8:147-155.