Minoru Kanehisa

Affiliations:
  • Kyoto University, Institute for Chemical Research, Japan


According to our database1, Minoru Kanehisa authored at least 90 papers between 1984 and 2023.

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Bibliography

2023
KEGG for taxonomy-based analysis of pathways and genomes.
Nucleic Acids Res., January, 2023

2021
KEGG: integrating viruses and cellular organisms.
Nucleic Acids Res., 2021

2020
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold.
Bioinform., 2020

2019
New approach for understanding genome variations in KEGG.
Nucleic Acids Res., 2019

2017
KEGG: new perspectives on genomes, pathways, diseases and drugs.
Nucleic Acids Res., 2017

2016
KEGG as a reference resource for gene and protein annotation.
Nucleic Acids Res., 2016

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.
J. Chem. Inf. Model., 2016

2014
DINIES: drug-target interaction network inference engine based on supervised analysis.
Nucleic Acids Res., 2014

Data, information, knowledge and principle: back to metabolism in KEGG.
Nucleic Acids Res., 2014

PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list.
J. Bioinform. Comput. Biol., 2014

2013
Automated interpretation of metabolic capacity from genome and metagenome sequences.
Quant. Biol., 2013

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.
Nucleic Acids Res., 2013

Modular Architecture of Metabolic Pathways Revealed by Conserved Sequences of Reactions.
J. Chem. Inf. Model., 2013

KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics.
BMC Syst. Biol., 2013

2012
GENIES: gene network inference engine based on supervised analysis.
Nucleic Acids Res., 2012

KEGG for integration and interpretation of large-scale molecular data sets.
Nucleic Acids Res., 2012

Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering.
J. Comput. Biol., 2012

2011
iPath2.0: interactive pathway explorer.
Nucleic Acids Res., 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.
Nucleic Acids Res., 2011

Network-Based Analysis and Characterization of Adverse Drug-Drug Interactions.
J. Chem. Inf. Model., 2011

MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites.
BMC Bioinform., 2011

2010
PathPred: an enzyme-catalyzed metabolic pathway prediction server.
Nucleic Acids Res., 2010

KEGG for representation and analysis of molecular networks involving diseases and drugs.
Nucleic Acids Res., 2010

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.
Nucleic Acids Res., 2010

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework.
Bioinform., 2010

2009
Extraction and Analysis of Chemical Modification Patterns in Drug Development.
J. Chem. Inf. Model., 2009

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
Bioinform., 2009

2008
A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology.
ACM Trans. Knowl. Discov. Data, 2008

KEGG Atlas mapping for global analysis of metabolic pathways.
Nucleic Acids Res., 2008

AAindex: amino acid index database, progress report 2008.
Nucleic Acids Res., 2008

KEGG for linking genomes to life and the environment.
Nucleic Acids Res., 2008

varDB: a pathogen-specific sequence database of protein families involved in antigenic variation.
Bioinform., 2008

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Mining significant tree patterns in carbohydrate sugar chains.
Proceedings of the ECCB'08 Proceedings, 2008

KEGG for Medical and Pharmaceutical Applications.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007
KAAS: an automatic genome annotation and pathway reconstruction server.
Nucleic Acids Res., 2007

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
Nucleic Acids Res., 2007

Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways.
J. Chem. Inf. Model., 2007

Regulation of metabolic networks by small molecule metabolites.
BMC Bioinform., 2007

Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.
BMC Bioinform., 2007

The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs).
Bioinform., 2007

Inference of Protein-Protein Interactions by Using Co-evolutionary Information.
Proceedings of the Algebraic Biology, Second International Conference, 2007

2006
ODB: a database of operons accumulating known operons across multiple genomes.
Nucleic Acids Res., 2006

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.
Nucleic Acids Res., 2006

From genomics to chemical genomics: new developments in KEGG.
Nucleic Acids Res., 2006

Extraction of phylogenetic network modules from the metabolic network.
BMC Bioinform., 2006

Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis.
BMC Bioinform., 2006

MIMOX: a web tool for phage display based epitope mapping.
BMC Bioinform., 2006

Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions.
Bioinform., 2006

A new efficient probabilistic model for mining labeled ordered trees.
Proceedings of the Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2006

Identification of metabolic units induced by environmental signals.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

A 6-Approximation Algorithm for Computing Smallest Common AoN-Supertree with Application to the Reconstruction of Glycan Trees.
Proceedings of the Algorithms and Computation, 17th International Symposium, 2006

2005
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
J. Bioinform. Comput. Biol., 2005

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships.
Bioinform., 2005

Prediction of glycan structures from gene expression data based on glycosyltransferase reactions.
Bioinform., 2005

Fast and accurate database homology search using upper bounds of local alignment scores.
Bioinform., 2005

A score matrix to reveal the hidden links in glycans.
Bioinform., 2005

Supervised enzyme network inference from the integration of genomic data and chemical information.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004
Managing and Analyzing Carbohydrate Data.
SIGMOD Rec., 2004

The KEGG resource for deciphering the genome.
Nucleic Acids Res., 2004

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
Nucleic Acids Res., 2004

Clustering under the line graph transformation: application to reaction network.
BMC Bioinform., 2004

Protein network inference from multiple genomic data: a supervised approach.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Application of a new probabilistic model for recognizing complex patterns in glycans.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs.
Bioinform., 2003

Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

Extracting active pathways from gene expression data.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags.
Nucleic Acids Res., 2002

The KEGG databases at GenomeNet.
Nucleic Acids Res., 2002

LIGAND: database of chemical compounds and reactions in biological pathways.
Nucleic Acids Res., 2002

Graph-Driven Feature Extraction From Microarray Data Using Diffusion Kernels and Kernel CCA.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

2000
MAGEST: MAboya Gene Expression patterns and Sequence Tags.
Nucleic Acids Res., 2000

AAindex: Amino Acid index database.
Nucleic Acids Res., 2000

KEGG: Kyoto Encyclopedia of Genes and Genomes.
Nucleic Acids Res., 2000

LIGAND: chemical database of enzyme reactions.
Nucleic Acids Res., 2000

Sequence comparison to graph comparison--a new generation of algorithms for network analysis of interacting molecules (abstract only).
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999
KEGG: Kyoto Encyclopedia of Genes and Genomes.
Nucleic Acids Res., 1999

AAindex: Amino Acid Index Database.
Nucleic Acids Res., 1999

LIGAND database for enzymes, compounds and reactions.
Nucleic Acids Res., 1999

Systematic Detection of Protein Structural Motifs.
Proceedings of the Pattern Discovery in Biomolecular Data: Tools, 1999

1994
Development of an integrated Database for Genome Mapping and Nucleotide Sequences.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994

1993
An approach to systematic detection of protein structural motifs.
Comput. Appl. Biosci., 1993

Multiple sequence alignment by parallel simulated annealing.
Comput. Appl. Biosci., 1993

1988
Discriminant analysis of promoter regions in Escherichia coli sequences.
Comput. Appl. Biosci., 1988

1985
The GenBank nucleic acid sequence database.
Comput. Appl. Biosci., 1985

1984
Computer analysis and structure prediction of nucleic acids and proteins.
Nucleic Acids Res., 1984

A relational database system for the maintenance and verification of the Los Alamos sequence library.
Nucleic Acids Res., 1984

Use of statistical criteria for screening potential homologies in nucleic acid sequences.
Nucleic Acids Res., 1984


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