Searching for amino acid sequence motifs among enzymes: the Enzyme- Reaction Database. - Mikita Suyama; A. Ogiwara; Takaaki Nishioka; J. Oda (Comput. Appl. Biosci., 1993)

LIGAND database for enzymes, compounds and reactions. - Susumu Goto; Takaaki Nishioka; Minoru Kanehisa (Nucleic Acids Res., 1999)

Reconstructing Metabolic Pathways with New Enzyme Classification. - Masanori Arita; Kiyoshi Asai; Takaaki Nishioka (German Conference on Bioinformatics, 2000)

LIGAND: chemical database of enzyme reactions. - Susumu Goto; Takaaki Nishioka; Minoru Kanehisa (Nucleic Acids Res., 2000)

LIGAND: database of chemical compounds and reactions in biological pathways. - Susumu Goto; Yasushi Okuno; Masahiro Hattori; Takaaki Nishioka; Minoru Kanehisa (Nucleic Acids Res., 2002)

MathDAMP: a package for differential analysis of metabolite profiles. - Richard Baran; Hayataro Kochi; Natsumi Saito; Makoto Suematsu; Tomoyoshi Soga; Takaaki Nishioka; Martin Robert; Masaru Tomita (BMC Bioinform., 2006)

Comparison of ESI-MS Spectra in MassBank Database. - Hisayuki Horai; Masanori Arita; Takaaki Nishioka (BMEI (2), 2008)

Time-resolved metabolomics reveals metabolic modulation in rice foliage. - Shigeru Sato; Masanori Arita; Tomoyoshi Soga; Takaaki Nishioka; Masaru Tomita (BMC Syst. Biol., 2008)