Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites. - Masaaki Kotera; Andrew G. McDonald; Sinéad Boyce; Keith F. Tipton (J. Chem. Inf. Model., 2008)

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. - Yoshihiro Yamanishi; Masahiro Hattori; Masaaki Kotera; Susumu Goto; Minoru Kanehisa (Bioinform., 2009)

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. - Yoshihiro Yamanishi; Masaaki Kotera; Minoru Kanehisa; Susumu Goto (Bioinform., 2010)

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)

Network-Based Analysis and Characterization of Adverse Drug-Drug Interactions. - Masataka Takarabe; Daichi Shigemizu; Masaaki Kotera; Susumu Goto; Minoru Kanehisa (J. Chem. Inf. Model., 2011)

Drug target prediction using adverse event report systems: a pharmacogenomic approach. - Masataka Takarabe; Masaaki Kotera; Yosuke Nishimura; Susumu Goto; Yoshihiro Yamanishi (Bioinform., 2012)

Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces. - Yoshihiro Yamanishi; Edouard Pauwels; Masaaki Kotera (J. Chem. Inf. Model., 2012)

GENIES: gene network inference engine based on supervised analysis. - Masaaki Kotera; Yoshihiro Yamanishi; Yuki Moriya; Minoru Kanehisa; Susumu Goto (Nucleic Acids Res., 2012)

Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints. - Yasuo Tabei; Akihiro Kishimoto; Masaaki Kotera; Yoshihiro Yamanishi (KDD, 2013)

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

Inferring protein domains associated with drug side effects based on drug-target interaction network. - Hiroaki Iwata; Sayaka Mizutani; Yasuo Tabei; Masaaki Kotera; Susumu Goto; Yoshihiro Yamanishi (BMC Syst. Biol., 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)

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)

Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms. - Sayaka Mizutani; Yousuke Noro; Masaaki Kotera; Susumu Goto (Comput. Biol. Chem., 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)

WURCS: The Web3 Unique Representation of Carbohydrate Structures. - Kenichi Tanaka; Kiyoko F. Aoki-Kinoshita; Masaaki Kotera; Hiromichi Sawaki; Shinichiro Tsuchiya; Noriaki Fujita; Toshihide Shikanai; Masaki Kato; Shin Kawano; Issaku Yamada; Hisashi Narimatsu (J. Chem. Inf. Model., 2014)

DINIES: drug-target interaction network inference engine based on supervised analysis. - Yoshihiro Yamanishi; Masaaki Kotera; Yuki Moriya; Ryusuke Sawada; Minoru Kanehisa; Susumu Goto (Nucleic Acids Res., 2014)

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. - Yoshihiro Yamanishi; Yasuo Tabei; Masaaki Kotera (Bioinform., 2015)

Large-Scale Prediction of Beneficial Drug Combinations Using Drug Efficacy and Target Profiles. - Hiroaki Iwata; Ryusuke Sawada; Sayaka Mizutani; Masaaki Kotera; Yoshihiro Yamanishi (J. Chem. Inf. Model., 2015)

Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. - Yasuo Tabei; Yoshihiro Yamanishi; Masaaki Kotera (Bioinform., 2016)

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)

Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. - Kohei Amano; Tsubasa Matsumoto; Kenichi Tanaka; Kimito Funatsu; Masaaki Kotera (BMC Bioinform., 2019)

Network-based characterization of drug-protein interaction signatures with a space-efficient approach. - Yasuo Tabei; Masaaki Kotera; Ryusuke Sawada; Yoshihiro Yamanishi (BMC Syst. Biol., 2019)

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)

Data Transfer Approaches to Improve Seq-to-Seq Retrosynthesis. - Katsuhiko Ishiguro; Kazuya Ujihara; Ryohto Sawada; Hirotaka Akita; Masaaki Kotera (CoRR, 2020)

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)

Comparison and improvement of the predictability and interpretability with ensemble learning models in QSPR applications. - Chia-Hsiu Chen; Kenichi Tanaka; Masaaki Kotera; Kimito Funatsu (J. Cheminformatics, 2020)

Fast Estimation Method for the Stability of Ensemble Feature Selectors. - Rina Onda; Zhengyan Gao; Masaaki Kotera; Kenta Oono (CoRR, 2021)

Multimodal Dish Pairing: Predicting Side Dishes to Serve with a Main Dish. - Taichi Nishimura; Katsuhiko Ishiguro; Keita Higuchi; Masaaki Kotera (CEA++@MM, 2022)

Recipe Recommendation for Balancing Ingredient Preference and Daily Nutrients. - Sara Ozeki; Masaaki Kotera; Katushiko Ishiguro; Taichi Nishimura; Keita Higuchi (CEA++@MM, 2022)