bibliographyfolder

This folder holds the following references to publications, sorted by year and author.

There are 21 references in this bibliography folder.

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.