Evaluation of a deductive database system for CAD applications. - Toshihisa Takagi; Takahiko Suzuki; Susumu Goto; Kazuo Ushijima (Syst. Comput. Jpn., 1992)

Object-Oriented Database with Rule-Based Query Interface for Genomic Computation. - Susumu Goto; Norihiro Sakamoto; Toshihisa Takagi (DASFAA, 1993)

A Deductive Object-Oriented Language for Integrated Genome Databaser. - Susumu Goto; Norihiro Sakamoto; Toshihisa Takagi (HICSS (5), 1994)

Metabolic Pathway Interface to Molecular Biology Databases. - Barry Zeeberg; Kevin Watanabe; Susumu Goto; Ross A. Overbeek; Larry Kerschberg; George Michaels (SSDBM, 1998)

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

KEGG: Kyoto Encyclopedia of Genes and Genomes. - Hiroyuki Ogata; Susumu Goto; Kazushige Sato; Wataru Fujibuchi; Hidemasa Bono; Minoru Kanehisa (Nucleic Acids Res., 1999)

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

KEGG: Kyoto Encyclopedia of Genes and Genomes. - Minoru Kanehisa; Susumu Goto (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)

The KEGG databases at GenomeNet. - Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya (Nucleic Acids Res., 2002)

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. - Kiyoko F. Aoki; Atsuko Yamaguchi; Nobuhisa Ueda; Tatsuya Akutsu; Hiroshi Mamitsuka; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2004)

The KEGG resource for deciphering the genome. - Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Yasushi Okuno; Masahiro Hattori (Nucleic Acids Res., 2004)

Fast and accurate database homology search using upper bounds of local alignment scores. - Masumi Itoh; Susumu Goto; Tatsuya Akutsu; Minoru Kanehisa (Bioinform., 2005)

Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. - Shin Kawano; Kosuke Hashimoto; Takashi Miyama; Susumu Goto; Minoru Kanehisa (Bioinform., 2005)

Extraction of phylogenetic network modules from the metabolic network. - Takuji Yamada; Minoru Kanehisa; Susumu Goto (BMC Bioinform., 2006)

From genomics to chemical genomics: new developments in KEGG. - Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F. Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa (Nucleic Acids Res., 2006)

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. - Ali Masoudi-Nejad; Koichiro Tonomura; Shuichi Kawashima; Yuki Moriya; Masanori Suzuki; Masumi Itoh; Minoru Kanehisa; Takashi Endo; Susumu Goto (Nucleic Acids Res., 2006)

ODB: a database of operons accumulating known operons across multiple genomes. - Shujiro Okuda; Toshiaki Katayama; Shuichi Kawashima; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2006)

The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). - Vachiranee Limviphuvadh; Seigo Tanaka; Susumu Goto; Kunihiro Ueda; Minoru Kanehisa (Bioinform., 2007)

Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. - Masashi Fujita; Hisaaki Mihara; Susumu Goto; Nobuyoshi Esaki; Minoru Kanehisa (BMC Bioinform., 2007)

Regulation of metabolic networks by small molecule metabolites. - Alex Gutteridge; Minoru Kanehisa; Susumu Goto (BMC Bioinform., 2007)

Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways. - Mina Oh; Takuji Yamada; Masahiro Hattori; Susumu Goto; Minoru Kanehisa (J. Chem. Inf. Model., 2007)

varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. - C. Nelson Hayes; Diego Diez; Nicolas Joannin; Wataru Honda; Minoru Kanehisa; Mats Wahlgren; Craig E. Wheelock; Susumu Goto (Bioinform., 2008)

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)

KEGG Atlas mapping for global analysis of metabolic pathways. - Shujiro Okuda; Takuji Yamada; Masami Hamajima; Masumi Itoh; Toshiaki Katayama; Peer Bork; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2008)

GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. - Lasse Folkersen; Diego Diez; Craig E. Wheelock; Jesper Z. Haeggström; Susumu Goto; Per Eriksson; Anders Gabrielsen (Bioinform., 2009)

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)

Extraction and Analysis of Chemical Modification Patterns in Drug Development. - Daichi Shigemizu; Michihiro Araki; Shujiro Okuda; Susumu Goto; Minoru Kanehisa (J. Chem. Inf. Model., 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)

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. - Masahiro Hattori; Nobuya Tanaka; Minoru Kanehisa; Susumu Goto (Nucleic Acids Res., 2010)

KEGG for representation and analysis of molecular networks involving diseases and drugs. - Minoru Kanehisa; Susumu Goto; Miho Furumichi; Mao Tanabe; Mika Hirakawa (Nucleic Acids Res., 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)

Relating drug-protein interaction network with drug side effects. - Sayaka Mizutani; Edouard Pauwels; Véronique Stoven; Susumu Goto; Yoshihiro Yamanishi (Bioinform., 2012)

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

KEGG for integration and interpretation of large-scale molecular data sets. - Minoru Kanehisa; Susumu Goto; Yoko Sato; Miho Furumichi; Mao Tanabe (Nucleic Acids Res., 2012)

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

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)

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)

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)

Data, information, knowledge and principle: back to metabolism in KEGG. - Minoru Kanehisa; Susumu Goto; Yoko Sato; Masayuki Kawashima; Miho Furumichi; Mao Tanabe (Nucleic Acids Res., 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)

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)

ViPTree: the viral proteomic tree server. - Yosuke Nishimura; Takashi Yoshida; Megumi Kuronishi; Hideya Uehara; Hiroyuki Ogata; Susumu Goto (Bioinform., 2017)

Discriminating the reaction types of plant type III polyketide synthases. - Yugo Shimizu; Hiroyuki Ogata; Susumu Goto (Bioinform., 2017)

jPOSTrepo: an international standard data repository for proteomes. - Shujiro Okuda; Yu Watanabe; Yuki Moriya; Shin Kawano; Tadashi Yamamoto; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Norie Araki; Akiyasu C. Yoshizawa; Tsuyoshi Tabata; Naoyuki Sugiyama; et al. (Nucleic Acids Res., 2017)

Collective Motion of Repulsive Brownian Particles in Single-File Diffusion with and without Overtaking. - Takeshi Ooshida; Susumu Goto; Michio Otsuki (Entropy, 2018)

Transferring Reservoir Computing: Formulation and Application to Fluid Physics. - Masanobu Inubushi; Susumu Goto (ICANN (Workshop), 2019)

Integrated Growth Media Database by Standardizing Ingredient Information. - Shuichi Kawashima; Toshiaki Katayama; Yuki Moriya; Shinobu Okamoto; Yasunori Yamamoto; Susumu Goto (SWAT4HCLS, 2019)

The jPOST environment: an integrated proteomics data repository and database. - Yuki Moriya; Shin Kawano; Shujiro Okuda; Yu Watanabe; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Yoshinori Yamanouchi; Norie Araki; Akiyasu C. Yoshizawa; Tsuyoshi Tabata; Mio Iwasaki; et al. (Nucleic Acids Res., 2019)

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. - Takuya Aramaki; Romain Blanc-Mathieu; Hisashi Endo; Koichi Ohkubo; Minoru Kanehisa; Susumu Goto; Hiroyuki Ogata (Bioinform., 2020)

TogoID: an exploratory ID converter to bridge biological datasets. - Shuya Ikeda; Hiromasa Ono; Tazro Ohta; Hirokazu Chiba; Yuki Naito; Yuki Moriya; Shuichi Kawashima; Yasunori Yamamoto; Shinobu Okamoto; Susumu Goto; Toshiaki Katayama (Bioinform., 2022)

Enteropathway: the metabolic pathway database for the human gut microbiota. - Hirotsugu Shiroma; Youssef Darzi; Etsuko Terajima; Zenichi Nakagawa; Hirotaka Tsuchikura; Naoki Tsukuda; Yuki Moriya; Shujiro Okuda; Susumu Goto; Takuji Yamada (Briefings Bioinform., 2024)

Can Frontier LLMs Replace Annotators in Biomedical Text Mining? Analyzing Challenges and Exploring Solutions. - Yichong Zhao; Susumu Goto (CoRR, 2025)

Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features. - Shuya Ikeda; Kiyoko F. Aoki-Kinoshita; Hirokazu Chiba; Susumu Goto; Masae Hosoda; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Tazro Ohta; Hiromasa Ono; Terue Takatsuki; Yasunori Yamamoto; et al. (J. Biomed. Semant., 2025)