The E-CELL project: towards integrative simulation of cellular processes. - Masaru Tomita; Kenta Hashimoto; Koichi Takahashi; Yuri Matsuzaki; Ryo Matsushima; Katsuyuki Yugi; Fumihiko Miyoshi; Hisako Nakano; Yusuke Saito; Tom Shimizu; Yoichi Nakayama (RECOMB, 2000)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

E-Cell 2: Multi-platform E-Cell simulation system. - Koichi Takahashi; Naota Ishikawa; Yasuhiro Sadamoto; Hiroyuki Sasamoto; Seiji Ohta; Akira Shiozawa; Fumihiko Miyoshi; Yasuhiro Naito; Yoichi Nakayama; Masaru Tomita (Bioinform., 2003)

A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. - Katsuyuki Yugi; Yoichi Nakayama; Shigen Kojima; Tomoya Kitayama; Masaru Tomita (BMC Bioinform., 2005)

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. - Kazuharu Arakawa; Yohei Yamada; Kosaku Shinoda; Yoichi Nakayama; Masaru Tomita (BMC Bioinform., 2006)

GPAC: Benchmarking the Sensitivity of Genome Informatics Analysis to Genome Annotation Completeness. - Kazuharu Arakawa; Yoichi Nakayama; Masaru Tomita (Silico Biol., 2006)

Comparative Study of Circadian Oscillatory Network Models of Drosophila. - Yukino Ogawa; Kazuharu Arakawa; Kazunari Kaizu; Fumihiko Miyoshi; Yoichi Nakayama; Masaru Tomita (Artif. Life, 2008)

Mutual Learning with Many Linear Perceptrons: On-Line Learning Theory. - Kazuyuki Hara; Yoichi Nakayama; Seiji Miyoshi; Masato Okada (ICANN (1), 2009)