Use of statistical criteria for screening potential homologies in nucleic acid sequences. - Minoru Kanehisa (Nucleic Acids Res., 1984)

A relational database system for the maintenance and verification of the Los Alamos sequence library. - Minoru Kanehisa; James W. Fickett; W. B. Goad (Nucleic Acids Res., 1984)

Computer analysis and structure prediction of nucleic acids and proteins. - Minoru Kanehisa; P. Klein; P. Greif; Charles DeLisi (Nucleic Acids Res., 1984)

The GenBank nucleic acid sequence database. - Christian Burks; James W. Fickett; W. B. Goad; Minoru Kanehisa; F. I. Lewitter; W. P. Rindone; C. D. Swindell; C. S. Tung; H. S. Bilofsky (Comput. Appl. Biosci., 1985)

Discriminant analysis of promoter regions in Escherichia coli sequences. - Kotoko Nakata; Minoru Kanehisa; Jacob V. Maizel (Comput. Appl. Biosci., 1988)

Multiple sequence alignment by parallel simulated annealing. - Masato Ishikawa; Tomoyuki Toya; Masaki Hoshida; Katsumi Nitta; A. Ogiwara; Minoru Kanehisa (Comput. Appl. Biosci., 1993)

An approach to systematic detection of protein structural motifs. - Yo Matsuo; Minoru Kanehisa (Comput. Appl. Biosci., 1993)

Development of an integrated Database for Genome Mapping and Nucleotide Sequences. - Takahiko Suzuki; Toshihisa Takagi; Satoru Kuhara; Minoru Kanehisa (HICSS (5), 1994)

Systematic Detection of Protein Structural Motifs. - Kentaro Tomii; Minoru Kanehisa (Pattern Discovery in Biomolecular Data, 1999)

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

AAindex: Amino Acid Index Database. - Shuichi Kawashima; Hiroyuki Ogata; 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)

Sequence comparison to graph comparison–a new generation of algorithms for network analysis of interacting molecules (abstract only). - Minoru Kanehisa (RECOMB, 2000)

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)

AAindex: Amino Acid index database. - Shuichi Kawashima; Minoru Kanehisa (Nucleic Acids Res., 2000)

MAGEST: MAboya Gene Expression patterns and Sequence Tags. - Takeshi Kawashima; Shuichi Kawashima; Minoru Kanehisa; Hiroki Nishida; Kazuhiro W. Makabe (Nucleic Acids Res., 2000)

Graph-Driven Feature Extraction From Microarray Data Using Diffusion Kernels and Kernel CCA. - Jean-Philippe Vert; Minoru Kanehisa (NIPS, 2002)

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)

Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. - Takeshi Kawashima; Shuichi Kawashima; Yuji Kohara; Minoru Kanehisa; Kazuhiro W. Makabe (Nucleic Acids Res., 2002)

Extracting active pathways from gene expression data. - Jean-Philippe Vert; Minoru Kanehisa (ECCB, 2003)

Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. - Yoshihiro Yamanishi; Jean-Philippe Vert; Akihiro Nakaya; Minoru Kanehisa (ISMB (Supplement of Bioinformatics), 2003)

Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. - Keun-Joon Park; Minoru Kanehisa (Bioinform., 2003)

Application of a new probabilistic model for recognizing complex patterns in glycans. - Kiyoko F. Aoki; Nobuhisa Ueda; Atsuko Yamaguchi; Minoru Kanehisa; Tatsuya Akutsu; Hiroshi Mamitsuka (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Protein network inference from multiple genomic data: a supervised approach. - Yoshihiro Yamanishi; Jean-Philippe Vert; Minoru Kanehisa (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Clustering under the line graph transformation: application to reaction network. - Jose C. Nacher; Nobuhisa Ueda; Takuji Yamada; Minoru Kanehisa; Tatsuya Akutsu (BMC Bioinform., 2004)

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)

Managing and Analyzing Carbohydrate Data. - Kiyoko F. Aoki; Nobuhisa Ueda; Atsuko Yamaguchi; Tatsuya Akutsu; Minoru Kanehisa; Hiroshi Mamitsuka (SIGMOD Rec., 2004)

A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. - Jean-Marc Schwartz; Minoru Kanehisa (ECCB/JBI, 2005)

Supervised enzyme network inference from the integration of genomic data and chemical information. - Yoshihiro Yamanishi; Jean-Philippe Vert; Minoru Kanehisa (ISMB (Supplement of Bioinformatics), 2005)

A score matrix to reveal the hidden links in glycans. - Kiyoko F. Aoki; Hiroshi Mamitsuka; Tatsuya Akutsu; Minoru Kanehisa (Bioinform., 2005)

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)

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. - Tetsuya Sato 003; Yoshihiro Yamanishi; Minoru Kanehisa; Hiroyuki Toh (Bioinform., 2005)

Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. - Yoshinori Tamada; Hideo Bannai; Seiya Imoto; Toshiaki Katayama; Minoru Kanehisa; Satoru Miyano (J. Bioinform. Comput. Biol., 2005)

A 6-Approximation Algorithm for Computing Smallest Common AoN-Supertree with Application to the Reconstruction of Glycan Trees. - Kiyoko F. Aoki-Kinoshita; Minoru Kanehisa; Ming-Yang Kao; Xiang-Yang Li 001; Weizhao Wang (ISAAC, 2006)

ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. - Kiyoko F. Aoki-Kinoshita; Nobuhisa Ueda; Hiroshi Mamitsuka; Minoru Kanehisa (ISMB (Supplement of Bioinformatics), 2006)

Identification of metabolic units induced by environmental signals. - Jose C. Nacher; Jean-Marc Schwartz; Minoru Kanehisa; Tatsuya Akutsu (ISMB (Supplement of Bioinformatics), 2006)

A new efficient probabilistic model for mining labeled ordered trees. - Kosuke Hashimoto; Kiyoko F. Aoki-Kinoshita; Nobuhisa Ueda; Minoru Kanehisa; Hiroshi Mamitsuka (KDD, 2006)

Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. - Tetsuya Sato 003; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh (Bioinform., 2006)

MIMOX: a web tool for phage display based epitope mapping. - Jian Huang 004; Alex Gutteridge; Wataru Honda; Minoru Kanehisa (BMC Bioinform., 2006)

Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. - Jean-Marc Schwartz; Minoru Kanehisa (BMC Bioinform., 2006)

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)

Inference of Protein-Protein Interactions by Using Co-evolutionary Information. - Tetsuya Sato 003; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh (AB, 2007)

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)

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. - Zhenjun Hu; David M. Ng; Takuji Yamada; Chunnuan Chen; Shuichi Kawashima; Joe Mellor; Bolan Linghu; Minoru Kanehisa; Joshua M. Stuart; Charles DeLisi (Nucleic Acids Res., 2007)

KAAS: an automatic genome annotation and pathway reconstruction server. - Yuki Moriya; Masumi Itoh; Shujiro Okuda; Akiyasu C. Yoshizawa; Minoru Kanehisa (Nucleic Acids Res., 2007)

KEGG for Medical and Pharmaceutical Applications. - Minoru Kanehisa (APBC, 2008)

Mining significant tree patterns in carbohydrate sugar chains. - Kosuke Hashimoto; Ichigaku Takigawa; Motoki Shiga; Minoru Kanehisa; Hiroshi Mamitsuka (ECCB, 2008)

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. - Yoshihiro Yamanishi; Michihiro Araki; Alex Gutteridge; Wataru Honda; Minoru Kanehisa (ISMB, 2008)

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)

AAindex: amino acid index database, progress report 2008. - Shuichi Kawashima; Piotr Pokarowski; Maria Pokarowska; Andrzej Kolinski; Toshiaki Katayama; Minoru Kanehisa (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)

A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology. - Kosuke Hashimoto; Kiyoko F. Aoki-Kinoshita; Nobuhisa Ueda; Minoru Kanehisa; Hiroshi Mamitsuka (ACM Trans. Knowl. Discov. Data, 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)

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)

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)

iPath2.0: interactive pathway explorer. - Takuji Yamada; Ivica Letunic; Shujiro Okuda; Minoru Kanehisa; Peer Bork (Nucleic Acids Res., 2011)

Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering. - Ritsuko Onuki; Ryo Yamada; Rui Yamaguchi; Minoru Kanehisa; Tetsuo Shibuya (J. Comput. Biol., 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)

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)

Automated interpretation of metabolic capacity from genome and metagenome sequences. - Minoru Kanehisa (Quant. Biol., 2013)

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)

KEGG as a reference resource for gene and protein annotation. - Minoru Kanehisa; Yoko Sato; Masayuki Kawashima; Miho Furumichi; Mao Tanabe (Nucleic Acids Res., 2016)

KEGG: new perspectives on genomes, pathways, diseases and drugs. - Minoru Kanehisa; Miho Furumichi; Mao Tanabe; Yoko Sato; Kanae Morishima (Nucleic Acids Res., 2017)

New approach for understanding genome variations in KEGG. - Minoru Kanehisa; Yoko Sato; Miho Furumichi; Kanae Morishima; Mao Tanabe (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)

KEGG: integrating viruses and cellular organisms. - Minoru Kanehisa; Miho Furumichi; Yoko Sato; Mari Ishiguro-Watanabe; Mao Tanabe (Nucleic Acids Res., 2021)

KEGG for taxonomy-based analysis of pathways and genomes. - Minoru Kanehisa; Miho Furumichi; Yoko Sato; Masayuki Kawashima; Mari Ishiguro-Watanabe (Nucleic Acids Res., 2023)