Cell Illustrator 4.0: A Computational Platform for Systems Biology. - Masao Nagasaki; Ayumu Saito; Euna Jeong; Chen Li 007; Kaname Kojima; Emi Ikeda; Satoru Miyano (Silico Biol., 2010)

CSO validator: improving manual curation workflow for biological pathways. - Euna Jeong; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Ayumu Saito; Satoru Miyano (Bioinform., 2011)

Systems biology model repository for macrophage pathway simulation. - Masao Nagasaki; Ayumu Saito; André Fujita; Georg Tremmel; Kazuko Ueno; Emi Ikeda; Euna Jeong; Satoru Miyano (Bioinform., 2011)

XiP: a computational environment to create, extend and share workflows. - Masao Nagasaki; André Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li 007; Satoru Miyano (Bioinform., 2013)

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML. - Chen Li 007; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Satoru Miyano (Biosyst., 2014)