KEGG for linking genomes to life and the environment. - Minoru Kanehisa; Michihiro Araki; Susumu Goto; Masahiro Hattori; Mika Hirakawa; Masumi Itoh; Toshiaki Katayama; Shuichi Kawashima; Shujiro Okuda; Toshiaki Tokimatsu; Yoshihiro Yamanishi (Nucleic Acids Res., 2008)

PathPred: an enzyme-catalyzed metabolic pathway prediction server. - Yuki Moriya; Daichi Shigemizu; Masahiro Hattori; Toshiaki Tokimatsu; Masaaki Kotera; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2010)

MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. - Masaaki Kotera; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (BMC Bioinform., 2011)

KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. - Nozomu Sakurai; Takeshi Ara; Yoshiyuki Ogata; Ryosuke Sano; Takashi Ohno; Kenjiro Sugiyama; Atsushi Hiruta; Kiyoshi Yamazaki; Kentaro Yano; Koh Aoki; Asaph Aharoni; Kazuki Hamada; et al. (Nucleic Acids Res., 2011)

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Toshiaki Tokimatsu; Susumu Goto (Bioinform., 2013)

KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Yuki Moriya; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (BMC Syst. Biol., 2013)

Modular Architecture of Metabolic Pathways Revealed by Conserved Sequences of Reactions. - Ai Muto; Masaaki Kotera; Toshiaki Tokimatsu; Zenichi Nakagawa; Susumu Goto; Minoru Kanehisa (J. Chem. Inf. Model., 2013)

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. - Akihiro Nakaya; Toshiaki Katayama; Masumi Itoh; Kazushi Hiranuka; Shuichi Kawashima; Yuki Moriya; Shujiro Okuda; Michihiro Tanaka; Toshiaki Tokimatsu; Yoshihiro Yamanishi; Akiyasu C. Yoshizawa; Minoru Kanehisa; et al. (Nucleic Acids Res., 2013)

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Ai Muto; Yuki Moriya; Toshiaki Tokimatsu; Susumu Goto (Bioinform., 2014)

PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list. - Masaaki Kotera; Yosuke Nishimura; Zenichi Nakagawa; Ai Muto; Yuki Moriya; Shinobu Okamoto; Shuichi Kawashima; Toshiaki Katayama; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (J. Bioinform. Comput. Biol., 2014)

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. - Yuki Moriya; Takuji Yamada; Shujiro Okuda; Zenichi Nakagawa; Masaaki Kotera; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (J. Chem. Inf. Model., 2016)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)