E-CELL: software environment for whole-cell simulation. - Masaru Tomita; Kenta Hashimoto; Koichi Takahashi; Thomas Simon Shimizu; Yuri Matsuzaki; Fumihiko Miyoshi; Kanako Saito; Sakura Tanida; Katsuyuki Yugi; J. Craig Venter; Clyde A. Hutchison III (Bioinform., 1999)

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)

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)

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