Minoru Kanehisa

List of Publications

2025

• Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. and Ishiguro-Watanabe, M.; KEGG: biological systems database as a model of the real world. Nucleic Acids Res. 53, D672-D677 (2025). [pubmed] [doi]

2023

• Jin, Z., Sato, Y., Kawashima, M., and Kanehisa, M.; KEGG tools for classification and analysis of viral proteins. Protein Sci. 32, e4820 (2023). [pubmed] [doi]
• Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. and Ishiguro-Watanabe, M.; KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, D587-D592 (2023). [pubmed] [doi]

2022

• Kanehisa, M., Sato, Y., and Kawashima, M.; KEGG mapping tools for uncovering hidden features in biological data. Protein Sci. 31, 47-53 (2022). [pubmed] [doi]

2021

• Kanehisa, M., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M., and Tanabe, M.; KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 49, D545-D551 (2021). [pubmed] [doi]

2020

• Aramaki, T., Blanc-Mathieu, R., Endo, H., Ohkubo, K., Kanehisa, M., Goto, S., and Ogata, H.; KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251-2252 (2020). [pubmed] [doi]
• Kanehisa, M. and Sato, Y.; KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 29, 28-35 (2020). [pubmed] [doi]

2019

• Kanehisa, M; Toward understanding the origin and evolution of cellular organisms. Protein Sci. 28, 1947-1951 (2019). [pubmed] [doi]
• Kanehisa, M., Sato, Y., Furumichi, M., Morishima, K., and Tanabe, M.; New approach for understanding genome variations in KEGG. Nucleic Acids Res. 47, D590-D595 (2019). [pubmed] [doi]

2018

• Kanehisa, M.; Inferring antimicrobial resistance from pathogen genomes in KEGG. In "Data Mining for Systems Biology, Second Edition" (Mamitsuka, H., ed.), Humana Press, Methods Mol. Biol. 1807, 225-239 (2018). [pubmed] [doi]

2017

• Kanehisa, M.; Enzyme annotation and metabolic reconstruction using KEGG. In "Protein Function Prediction: Methods and Protocols" (Kihara, D., ed.), Humana Press, Methods Mol. Biol. 1611, 135-145 (2017). [pubmed] [doi]
• Onuki, R., Yamaguchi, R., Shibuya, T., Kanehisa, M., and Goto, S.; Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks. PLoS One 12, e0176530 (2017). [pubmed] [doi]
• Kanehisa, M.; KEGG GLYCAN. In "A Practical Guide to Using Glycomics Databases" (Aoki-Kinoshita, K.F., ed.), pp. 177-193, Springer (2017). [doi]
• Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017). [pubmed] [doi]

2016

• Moriya, Y., Yamada, T., Okuda, S., Nakagawa, Z., Kotera, M., Tokimatsu, T., Kanehisa, M., and Goto, S.; Identification of enzyme genes using chemical structure alignments of substrate-product pairs. J. Chem. Inf. Model. 56, 510-516 (2016). [pubmed] [doi]
• Kanehisa, M., Sato, Y., and Morishima, K.; BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731 (2016). [pubmed] [doi]
• Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016). [pubmed] [doi]
• Kanehisa, M.; KEGG bioinformatics resource for plant genomics and metabolomics. In "Plant Bioinformatics: Methods and Protocols" (Edwards, D., ed.), Humana Press, Methods Mol. Biol. 1374, 55-70 (2016). [pubmed] [doi]

2015

• Varki, A., et al.; Symbol nomenclature for graphical representations of glycans. Glycobiology 25, 1323-1324 (2015). [pubmed] [doi]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Glycomic analysis using KEGG GLYCAN. In "Glycoinformatics" (Luetteke, T. and Frank, M., eds.), Humana Press, Methods Mol. Biol. 1273, 97-107 (2015). [pubmed] [doi]

2014

• Kotera, M., Nishimura, Y., Nakagawa, Z., Muto, A., Moriya, Y., Okamoto, S., Kawashima, S., Katayama, T., Tokimatsu, T., Kanehisa, M., and Goto, S.; PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list. J. Bioinform. Comput. Biol. 12, 1442001 (2014). [pubmed] [doi]
• Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M., and Goto, S.; DINIES: drug-target interaction network inference engine based on supervised analysis. Nucleic Acids Res. 42, W39-W45 (2014). [pubmed] [doi]
• Kotera, M., Goto, S., and Kanehisa, M.; Predictive genomic and metabolomic analysis for the standardization of enzyme data. Perspectives in Science 1, 24-32 (2014). [doi]
• Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205 (2014). [pubmed] [doi]

2013

• Kotera, M., Tabei, Y., Yamanishi, Y., Moriya, Y., Tokimatsu, T., Kanehisa, M., and Goto, S.; KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst. Biol. 7 Suppl. 6, S2 (2013). [pubmed] [doi]
• Kleensang, A., et al.; t4 Workshop report: Pathways of toxicity. ALTEX 31, 53-61 (2013). [pubmed] [doi]
• Kanehisa, M.; Automated interpretation of metabolic capacity from genome and metagenome sequences. Quant. Biol. 1, 192-200 (2013). [doi]
• Kanehisa, M.; Chemical and genomic evolution of enzyme-catalyzed reaction networks. FEBS Lett. 587, 2731-2737 (2013). [pubmed] [doi] [preprint]
• Muto, A., Kotera, M., Tokimatsu, T., Nakagawa, Z., Goto, S., and Kanehisa, M.; Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J. Chem. Inf. Model. 53, 613-622 (2013). [pubmed] [doi]
• Kanehisa, M.; Molecular network analysis of diseases and drugs in KEGG. In "Data Mining for Systems Biology" (Mamitsuka, H., DeLisi, C., and Kanehisa, M., eds.), Humana Press, Methods Mol. Biol. 939, 263-275 (2013). [pubmed] [doi]
• [Book] Mamitsuka, H., DeLisi, C., and Kanehisa, M. (eds.); "Data Mining for Systems Biology", Humana Press (2013). [nlmcatalog]
• Nakaya, A., Katayama, T., Itoh, M., Hiranuka, K., Kawashima, S., Moriya, Y., Okuda, S., Tanaka, M., Tokimatsu, T., Yamanishi, Y., Yoshizawa, A.C., Kanehisa, M., and Goto, S.; KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res. 41, D353-D357 (2013). [pubmed] [doi]

2012

• Takami, H., Taniguchi, T., Moriya, Y., Kuwahara, Y., Kanehisa, M., and Goto, S.; Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics 13, 699 (2012). [pubmed] [doi]
• Kotera, M., Moriya, Y., Tokimatsu, T., Kanehisa, M., and Goto, S.; KEGG and GenomeNet, new developments, metagenomic analysis. In "Encyclopedia of Metagenomics (Nelson, K.E., ed.), Springer (2012).
• Hayashida, K., Hara, Y., Abe, T., Yamasaki, C., Toyoda, A., Kosuge, T., Suzuki, Y., Sato, Y., Kawashima, S., Katayama, T., Wakaguri, H., Inoue, N., Homma, K., Tada-Umezaki, M., Yagi, Y., Fujii, Y., Habara, T., Kanehisa, M., Watanabe, H., Ito, K., Gojobori, T., Sugawara, H., Imanishi, T., Weir, W., Gardner, M., Pain, A., Shiels, B., Hattori, M., Nene, V., and Sugimoto, C.; Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. MBio 3, e00204-12 (2012). [pubmed] [doi]
• Tanabe, M. and Kanehisa, M.; Using the KEGG database resource. In "Current Protocols in Bioinformatics", Unit 1.12, Wiley (2012). [pubmed] [doi]
• Kotera, M., Yamanishi, Y., Moriya, Y., Kanehisa, M., and Goto, S.; GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res. 40, W162-W167 (2012). [pubmed] [doi]
• Kotera, M., Hirakawa, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. In "Next Generation Microarray Bioinformatics" (Wang, J., Tan, A.C., and Tian, T., eds.), Humana Press, Methods Mol. Biol. 802, 19-39 (2012). [pubmed] [doi]
• Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M.; KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 40, D109-D114 (2012). [pubmed] [doi]
• Onuki, R., Yamada, R., Yamaguchi, R., Kanehisa, M., and Shibuya, T.; Population model-based inter-diplotype similarity measure for accurate diplotype clustering. J. Comput. Biol. 19, 55-67 (2012). [pubmed] [doi]

2011

• Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., and Kanehisa, M.; Network-based analysis and characterization of adverse drug-drug interactions. J. Chem. Inf. Model. 51, 2977-2985 (2011). [pubmed] [doi]
• Kotera, M., Tokimatsu, T., Kanehisa, M., and Goto, S.; MUCHA: multiple chemical alignment algorithm to obtain building block substructures of orphan metabolites. BMC Bioinformatics 12, Suppl 14, S1 (2011). [pubmed] [doi]
• Yamada, T., Letunic, I., Okuda, S., Kanehisa, M., and Bork, P.; iPath2.0: interactive pathway explorer. Nucleic Acids Res. 39, W412-W415 (2011). [pubmed] [doi]
• Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; KEGG and GenomeNet resources for predicting protein function from omics data including KEGG PLANT resource. In "Protein Function Prediction for Omics Era" (Kihara, D., ed.), pp. 271-288, Springer (2011).
• Sakurai, N,. Ara, T., Ogata, Y., Sano, R., Ohno, T., Sugiyama, K., Hiruta, A., Yamazaki, K., Yano, K., Aoki, K., Aharoni, A., Hamada, K., Yokoyama, K., Kawamura, S., Otsuka, H., Tokimatsu, T., Kanehisa, M., Suzuki, H., Saito, K., and Shibata, D.; 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. 39, D677-D684 (2011). [pubmed] [doi]

2010

• Takigawa, I., Hashimoto, K., Shiga, M., Kanehisa, M., and Mamitsuka, H.; Mining patterns from glycan structures. In "Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics" (Hicks, M.G. and Kettner, C., eds.), pp. 13-24, Beilstein-Institut (2010).
• Erguner, B., Hattori, M., Goto, S., and Kanehisa, M.; Characterizing common substructures of ligands for GPCR protein subfamilies. Genome Informatics 24, 31-41 (2010). [pubmed] [doi]
• Kotera, M., Kobayashi, T., Hattori, M., Tokimatsu, T., Goto, S., Mihara, H., and Kanehisa, M.; Comprehensive genomic analysis of sulfur-relay pathway genes. Genome Informatics 24, 104-115 (2010). [pubmed] [doi]
• Mizutani, S., Tanaka, M., Wheelock, C., Kanehisa, M., and Goto, S.; Phylogenetic analysis of lipid mediator GPCRs. Genome Informatics 24, 116-126 (2010). [pubmed] [doi]
• Nishimura, Y., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; Genome-wide analysis of plant UGT family based on sequence and substrate information. Genome Informatics 24, 127-138 (2010). [pubmed] [doi]
• Tamura, T., Yamanishi, Y., Tanabe, M., Goto, S., Kanehisa, M., Horimoto, K., and Akutsu, T.; Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Informatics 24, 193-203 (2010). [pubmed] [doi]
• Sato, T., Yamanishi, Y., Kanehisa, M., Horimoto, K., and Toh, H.; Improvement of the mirrortree method by extracting evolutionary information. In "Sequence and Genome Analysis: Methods and Applications" (Zhao, Z., ed.), iConcept Press (2010). [pdf]
• Yamanishi, Y., Kotera, M., Kanehisa, M., and Goto, S.; Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics 26, i246-i254 (2010). [pubmed] [doi]
• Hattori, M., Tanaka, N., Kanehisa, M., and Goto, S.; SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res. 38, W652-W656 (2010). [pubmed] [doi]
• Moriya, Y., Shigemizu, D., Hattori, M., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 38, W138-W143 (2010). [pubmed] [doi]
• Imada, M., Kawashima, S., Kanehisa, M., Takeuchi, T., and Asai, T.; Characterization of alpha-phosphoglucomutase isozymes from Toxoplasma gondii. Parasitol. Int. 59, 206-210 (2010). [pubmed] [doi]
• Diez, D., Hayes, N., Joannin, N., Normark, J., Kanehisa, M., Wahlgren, M., Wheelock, C.E., and Goto, S.; varDB: a database of antigenic variant sequences -- current status and future prospects. Acta Trop. 14, 144-151 (2010). [pubmed] [doi]
• Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [pubmed] [doi]

2009

• Aoki-Kinoshita, K.F. and Kanehisia, M.; Bioinformatics analysis of glycan structures from a genomic perspective. In "Bioinformatics for Glycobiology and Glycomics: an Introduction" (von der Lieth, C.-W., Luetteke, T., and Frank, M., eds.), pp. 125-141 (2009).
• Hayes, C.N., Diez, D., Joannin, N., Kanehisa, M., Wahlgren, M., Wheelock, C. E., and Goto, S.; Tools for investigating mechanisms of antigenic variation: new extensions to varDB. Genome Informatics 23, 46-59 (2009). [pubmed] [doi] [pdf]
• Onuki, R., Shibuya, T., and Kanehisa, M.; New kernel methods for phenotype prediction from genotype data. Genome Informatics 22, 132-141 (2009). [pubmed] [doi] [pdf]
• Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., and Kanehisa, M.; Characterization and classification of adverse drug interactions. Genome Informatics 22, 167-175 (2009). [pubmed] [doi] [pdf]
• Tanaka, M., Moriya, Y., Goto, S., and Kanehisa, M.; Analysis of a lipid biosynthesis protein family and phospholipid structural variations. Genome Informatics 22, 191-201 (2009). [pubmed] [doi] [pdf]
• Hashimoto, K. and Kanehisa, M.; KEGG GLYCAN for integrated analysis of pathways, genes, and glycan structures. In "Handbook of Glycomics" (Cummings, R.D. and Pierce, J.M., eds.), pp. 197-210, Academic Press (2009).
• Kanehisa, M., Limviphuvadh, V., and Tanabe, M.; Knowledge based analysis of protein interaction networks in neurodegenerative diseases. In "Neuroproteomics" (Alzate, O., ed.), pp. 147-162, CRC Press (2009). [pubmed] [ncbi-bookshelf]
• Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.; E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics 25, i79-i86 (2009). [pubmed] [doi]
• Wheelock, C.E., Wheelock, A.M., Kawashima, S., Diez, D., Kanehisa, M., van Erk, M., Kleemann, R., Haeggstrom, J.Z., and Goto, S.; Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol. Biosyst. 5, 588-602 (2009). [pubmed] [doi]
• Kawashima, T., Kawashima, S., Tanaka, C., Murai, M., Yoneda, M., Putnum, N.H., Rokhsar, D.S., Kanehisa, M., Satoh, N., and Wada H.; Domain shuffling and the evolution of vertebrates. Genome Res. 19, 1393-1403 (2009). [pubmed] [doi]
• Shigemizu, D., Araki, M., Okuda, S., Goto, S., and Kanehisa, M.; Extraction and analysis of chemical modification patterns in drug development. J. Chem. Inf. Model. 49, 1122-1129 (2009). [pubmed] [doi]
• Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A.C., Okuda, S., Goto, S., and Kanehisa, M.; Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr. Res. 344, 881-887 (2009). [pubmed] [doi]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Using KEGG in the transition from genomics to chemical genomics. In "Bioinformatics for Systems Biology" (Krawetz, S., ed.), pp.429-445, Humana Press (2009).
• Hirakawa, M., Nishihara, H., Kanehisa, M., and Okada, N.; Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes. Gene 441, 100-110 (2009). [pubmed] [doi]

2008

• Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.; Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome Informatics 20, 149-158 (2008). [pubmed] [doi] [pdf]
• Takarabe, M., Okuda, S., Itoh, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; Network analysis of adverse drug interactions. Genome Informatics 20, 252-259 (2008). [pubmed] [doi] [pdf]
• Hayes, C.N., Diez, D., Joannin, N., Honda, W., Kanehisa, M., Wahlgren, M., Wheelock, C.E., and Goto, S.; varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 24, 2564-2565 (2008). [pubmed] [doi]
• Hashimoto, K. and Kanehisa, M.; KEGG GLYCAN for integrated analysis of pathways, genes, and structures. In "Experimental Glycoscience" (Taniguchi, N., Suzuki, A., Ito, Y., Narimatsu, H., Kawasaki, T., and Hase, S., eds.), pp. 441-444, Springer (2008).
• Hashimoto, K., Takigawa, I., Shiga, M., Kanehisa, M., and Mamitsuka, H.; Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics 24, i167-i173 (2008). [pubmed] [doi]
• Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., and Kanehisa, M.; Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 24, i232-i240 (2008). [pubmed] [doi]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Systems approach to metabolism. In "Wiley Encyclopedia of Chemical Biology" (Begley, T.P., ed.) wecb589 (2008).
• Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S., and Kanehisa, M.; KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res. 36, W423-W426 (2008). [pubmed] [doi]
• Kojima, K.K. and Kanehisa, M.; Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. Mol. Biol. Evol. 25, 1395-1404 (2008). [pubmed] [doi]
• Hashimoto, K., Aoki-Kinoshita, K.F., Ueda, N., Kanehisa, M., and Mamitsuka, H.; A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology. ACM TKDD, Volume 2, Issue 1, Article No. 6 (2008). [doi]
• Letunic, I., Yamada, T., Kanehisa, M., and Bork P.; iPath: interactive exploration of biochemical pathways and networks. Trends Biochem. Sci. 33, 101-103 (2008). [pubmed] [doi]
• Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.; KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008). [pubmed] [doi]
• Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M.; AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-D205 (2008). [pubmed] [doi]
• Hashimoto, K., Yoshizawa, A.C., Okuda, S., Kuma, K., Goto, S., and Kanehisa, M.; The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J. Lipid Res. 49, 183-191 (2008). [pubmed] [doi] [see Cover]

2007

• Huang, J., Honda, W., and Kanehisa, M.; Predicting B cell epitope residues with network topology based amino acid indices. Genome Informatics 19, 40-49 (2007). [pubmed] [doi] [pdf]
• Kawashima, S., Kawashima, T., Putnam, N.H., Rokhsar, D.S., Wada, H., and Kanehisa, M.; Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes. Genome Informatics 19, 50-60 (2007). [pubmed] [doi] [pdf]
• Huang, J., Kawashima, S., and Kanehisa, M.; New amino acid indices based on residue network topology. Genome Informatics 18, 152-161 (2007). [pubmed] [doi] [pdf]
• Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.; An improved scoring scheme for predicting glycan structures from gene expressison data. Genome Informatics 18, 237-246 (2007). [pubmed] [doi] [pdf]
• Muto, A., Hattori, M., and Kanehisa, M.; Analysis of common substructures of metabolic compounds within the different organism groups. Genome Informatics 18, 299-307 (2007). [pubmed] [doi] [pdf]
• Kadowaki, T., Wheelock, C.E., Adachi, T., Kudo, T., Okamoto, S., Tanaka, N., Tonomura, K., Tsujimoto, G., Mamitsuka, H., Goto, S., and Kanehisa, M.; Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis. Environ. Sci. Technol. 41, 7997-8003 (2007). [pubmed] [doi]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Gene annotation and pathway mapping in KEGG. In "Comparative Genomics Volume 2" (Bergman, N.H., ed.), Humana Press, Methods Mol. Biol. 396, 71-92 (2007). [pubmed] [doi]
• Masoudi-Nejad, A., Goto, S., Endo, T.R., and Kanehisa, M.; KEGG bioinformatics resource for plant genomics research. In "Plant Bioinformatics" (Edwards, D., ed.), Humana Press, Methods Mol. Biol. 406, 437-458 (2007). [pubmed] [doi]
• Fujita, M., Mihara, H., Goto, S., Esaki, N., and Kanehisa, M.; Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. BMC Bioinformatics 8, 225 (2007). [pubmed] [doi]
• Schwartz, J.-M., Gaugain, C., Nacher, J.C., de Daruvar, A., and Kanehisa, M.; Observing metabolic functions at the genome scale. Genome Biol. 8, R123 (2007). [pubmed] [doi]
• Itoh, M., Nacher, J.C., Kuma, K.I., Goto, S., and Kanehisa, M.; Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol. 8, R121 (2007). [pubmed] [doi]
• Limviphuvadh, V., Tanaka, S., Goto, S., Ueda, K., and Kanehisa, M.; The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). Bioinformatics 23, 2129-2138 (2007). [pubmed] [doi]
• Hu, Z., Ng, D.M., Yamada, T., Chen, C., Kawashima, S., Mellor, J., Linghu, B., Kanehisa, M., Stuart, J.M., and Delisi, C.; VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. 35, W625-W632 (2007). [pubmed] [doi]
• Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., and Kanehisa, M.; KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007). [pubmed] [doi]
• Oh, M., Yamada, T., Hattori, M., Goto, S., and Kanehisa, M.; Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf. Model. 47, 1702-1712 (2007). [pubmed] [doi]
• Hu, Z., Mellor, J., Wu, J., Kanehisa, M., Stuart, J.M., and DeLisi, C.; Toward scalable multidimensional maps of the cell. Nat. Biotech. 25, 547-554 (2007). [pubmed] [doi]
• Masoudi-Nejad, A., Goto, S., Jauregui, R., Ito, M., Kawashima, S., Moriya, Y., Endo, T.R., and Kanehisa, M.; EGENES: Transcriptome-based plant database of genes with metabolic pathway information and EST indices in KEGG. Plant Physiol. 144, 857-866 (2007). [pubmed] [doi]
• Minowa, Y., Araki, M., and Kanehisa, M.; Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J. Mol. Biol. 368, 1500-1517 (2007). [pubmed] [doi]
• Yamanishi, Y., Mihara, H., Osaki, M., Muramatsu, H., Esaki, N., Sato, T., Hizukuri, Y., Goto, S., and Kanehisa, M.; Prediction of missing enzyme genes in bacterial metabolic network: a reconstruction of lysine degradation pathway of Pseudomonas aeruginosa. FEBS J. 274, 2262-2273 (2007). [pubmed] [doi]
• Okamoto, S., Yamanishi, Y., Ehira, S., Kawashima, S., Tonomura, K., and Kanehisa, M.; Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis. Proteomics 7, 900-909 (2007). [pubmed] [doi]
• Gutteridge, A., Kanehisa, M., and Goto, S.; Regulation of metabolic networks by small molecule metabolites. BMC Bioinformatics 8, 88 (2007). [pubmed] [doi]
• Okuda, S., Kawashima, S., Kobayashi, K., Ogasawara, N., Kanehisa, M., and Goto, S.; Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics 8, 48 (2007). [pubmed] [doi]
• Sugita, C., Ogata, K., Shikata, M., Jikuya, H., Takano, J., Furumichi, M., Kanehisa, M., Omata, T., Suiura, M., and Sugita, M.; Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: Gene content and organization. Photosynth. Res. 93, 55-67 (2007). [pubmed] [doi]

2006

• Aoki-Kinoshita, K.F. and Kanehisa, M.; Bioinformatics approaches in glycomics and drug discovery. Curr. Opin. Mol. Ther. 8, 514-520 (2006). [pubmed]
• Aoki-Kinoshita, K.F., Kanehisa, M., Kao, M.-Y., Li, X.-Y., and Wang, W.; A 6-approximation algorithm for computing smallest common AoN-supertree with application to the reconstruction of glycan trees. Lecture Notes in Computer Science 4288, 100-110 (2006). [abstract]
• Huang, J., Gutteridge, A., Honda, W., and Kanehisa, M.; MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics 7, 451 (2006). [pubmed] [doi]
• Kadowaki, T., Wheelock, C.E., Hattori, M., Goto, S., and Kanehisa, M.; Structure-activity relationships and pathway analysis of biological degradation processes. J. Pesticide Sci. 31, 273-281 (2006). [doi]
• Hashimoto, K., Yoshizawa, A.C., Saito, K., Yamada, T., and Kanehisa, M.; The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes. Genome Informatics 17(1), 173-183 (2006). [pubmed] [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Metabolite antigens and pathway incompatibility. Genome Informatics 17(1), 184-194 (2006). [pubmed] [pdf]
• Tanaka, M., Yamada, T., Itoh, M., Okuda, S., Goto, S., and Kanehisa M.; Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes. Genome Informatics 17(1), 230-239 (2006). [pubmed] [pdf]
• Hashimoto, K., Aoki-Kinoshita, K., Ueda, N., Kanehisa, M., and Mamitsuka, H.; A new efficient probabilistic model for mining labeled ordered trees. ACM SIGKDD (2006). [doi]
• Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., and Toh, H.; Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics 22, 2488-2492 (2006). [pubmed] [doi]
• Yoshizawa, A.C., Kawashima, S., Okuda, S., Fujita, M., Itoh, M., Moriya, Y., Hattori, M., and Kanehisa, M.; Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic 7, 1104-1118 (2006). [pubmed] [doi]
• Aoki-Kinoshita, K., Ueda, N., Mamitsuka, H., and Kanehisa, M.; ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics 22, e25-e34 (2006). [pubmed] [doi]
• Nacher, J., Schwartz, J.-M., Kanehisa, M., and Akutsu, T.; Identification of metabolic units induced by environmental signals. Bioinformatics 22, e375-e383 (2006). [pubmed] [doi]
• Masoudi-Nejad, A., Tonomura, K., Kawashima, S., Moriya, Y., Suzuki, M., Itoh, M., Kanehisa, M., Endo, T., and Goto, S.; EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res. 34, W459-W462 (2006). [pubmed] [doi]
• Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M.; KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R (2006). [pubmed] [doi] [see Editorial]
• Schwartz, J.M. and Kanehisa, M.; Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 7, 186 (2006). [pubmed] [doi]
• Yamada, T., Kanehisa, M., and Goto, S.; Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics 7, 130 (2006). [pubmed] [doi]
• Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [pubmed] [doi] [see Thomson]
• Okuda, S., Katayama, T., Kawashima, S., Goto, S., and Kanehisa, M.; ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res. 34, D358-D362 (2006). [pubmed] [doi]
• Nacher, J.C., Ochiai, T., Yamada, T., Kanehisa, M., and Akutsu, T.; The role of log-normal dynamics in the evolution of biochemical pathways. BioSystems 83, 26-37 (2006). [pubmed] [doi]

2005

• Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., and Miyano, S.; Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models. J. Bioinform. Comput. Biol. 3, 1295-1313 (2005). [pubmed]
• Aoki, K.F. and Kanehisa, M.; Using the KEGG Database Resource. In "Current Protocols in Bioinformatics", Unit 1.12, Wiley (2005). [pubmed] [doi]
• Schwartz, J.M. and Kanehisa, M.; A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 21, ii204-ii205 (2005). [pubmed] [doi]
• Kawano, S., Hashimoto, K., Miyama, T., Goto, S., and Kanehisa, M.; Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics 21, 3976-3982 (2005). [pubmed] [doi]
• Tamori, A., Yamanishi, Y., Kawashima, S., Kanehisa, M., Enomoto, M., Tanaka, H., Kubo, S., Shiomi, S., and Nishiguchi, S.; Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin. Cancer Res. 15, 5821-5826 (2005). [pubmed] [doi]
• Noguchi, T., Ren, X.Q., Aoki, S., Igarashi, Y., Che, X.F., Nakajima, Y., Takahashi, H., Mitsuo, R., Tsujikawa, K., Sumizawa, T., Haraguchi, M., Kobayashi, M., Goto, S., Kanehisa, M., Aikou, T., Akiyama, S.I., and Furukawa, T.; MRP1 mutated in the L(0) region transports SN-38 but not leukotriene C(4) or estradiol-17 (beta-d-glucuronate). Biochem. Pharmacol. 70, 1056-1065 (2005). [pubmed] [doi]
• Okuda, S., Kawashima, S., Goto, S., and Kanehisa, M.; Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli. Genome Informatics 16(1), 116-124 (2005). [pubmed] [pdf]
• Yamada, T., Kawashima, S., Mamitsuka, H., Goto, S., and Kanehisa, M.; Comprehensive analysis and prediction of synthetic lethality using subcellular locations. Genome Informatics 16(1), 150-158 (2005). [pubmed] [pdf]
• Fujita, M. and Kanehisa, M.; Comparative analysis of DNA-binding proteins between thermophilic and mesophilic bacteria. Genome Informatics 16(1), 174-181 (2005). [pubmed] [pdf]
• Hashimoto, K., Kawano, S., Goto, S., Aoki-Kinoshita, K., Kawashima, M., and Kanehisa, M.; A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Informatics 16(1), 214-222 (2005). [pubmed] [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Autoimmune diseases and peptide variations. Genome Informatics 16(1), 272-280 (2005). [pubmed] [pdf]
• Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., and Kanehisa, M.; Extraction of leukemia specific glycan motifs in human by computational glycomics. Carbohydr. Res. 340, 2270-2278 (2005). [pubmed] [doi]
• Sato, T., Yamanishi, Y., Kanehisa, M., and Toh, H.; The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21, 3482-3489 (2005). [pubmed] [doi]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics 21, i468-i477 (2005). [pubmed] [doi]
• Osanai, T., Kanesaki, Y., Nakano, T., Takahashi, H., Kanehisa, M., Suzuki, I., Murata, N., and Tanaka, K.; Positive regulation of sugar catabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803 by the group 2 sigma factor SigE. J. Biol. Chem. 280, 30653-30659 (2005). [pubmed] [doi]
• Kucho, K., Okamoto, K., Tsuchiya, Y., Nomura, S., Nango, M., Kanehisa, M., and Ishiura, M.; Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J. Bacteriol. 187, 2190-2199 (2005). [pubmed] [doi]
• Nacher, J.C., Ueda, N., Kanehisa, M., and Akutsu, T.; Flexible construction of hierarchical scale-free networks with general exponent. Phys. Rev. E 71, 036132 (2005). [pubmed] [doi]
• Aoki, K.F., Mamitsuka, H., Akutsu, T. and Kanehisa, M.; A score matrix to reveal the hidden links in glycans. Bioinformatics 21, 1457-1463 (2005). [pubmed] [doi]
• Itoh, M., Goto, S., Akutsu, T., and Kanehisa, M.; Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics 21, 912-921 (2005). [pubmed] [doi]
• Nacher, J.C., Yamada, T., Goto, S., Kanehisa, M., and Akutsu, T.; Two complementary representations of a scale-free network. Physica A, 349, 349-363 (2005). [doi]

2004

• Nacher, J.C., Ueda, N., Yamada, T., Kanehisa, M., and Akutsu, T.; Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 5, 207 (2004). [pubmed] [doi]
• Nikitin, F., Rance, B., Itoh, M., Kanehisa, M., and Lisacek, F.; Using protein motif combinations to update KEGG pathway maps and orthologue tables. Genome Informatics 15(2), 266-275 (2004). [pubmed] [pdf]
• Kotera, M., Okuno, Y., Hattori, M., Goto, S., and Kanehisa, M.; Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc. 126, 16487-16498 (2004). [pubmed] [doi]
• Igarashi, Y., Aoki, K.F., Mamitsuka, H., Kuma, K., and Kanehisa, M.; The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes. Mol. Biol. Evol. 21, 2149-2160 (2004). [pubmed] [doi]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Heterogeneous data comparison and gene selection with kernel canonical correlation analysis. In "Kernel Methods in Computational Biology" (Scholkopf, B., Tsuda, K., and Vert, J.-P., eds.), pp. 209-230, MIT Press (2004).
• Aoki, K.F., Ueda, N., Yamaguchi, A., Kanehisa, M., Akutsu, T., and Mamitsuka, H.; Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics 20, i6-i14 (2004). [pubmed] [doi]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Protein network inference from multiple genomic data: a supervised approach. Bioinformatics 20, i363-i370 (2004). [pubmed] [doi]
• Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M.; KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32, W267-W272 (2004). [pubmed] [doi]
• Aoki, K.F., Ueda, N., Yamaguchi, A., Akutsu, T., Kanehisa, M., and Mamitsuka, H.; Managing and analyzing carbohydrate data. ACM SIGMOD Record, Vol. 33, No. 2, pp. 33-38 (2004) [doi]
• Hizukuri, Y., Yamanishi, Y., Hashimoto, K., and Kanehisa, M.; Extraction of species-specific glycan substructures. Genome Informatics 15(1), 69-81 (2004). [pubmed] [pdf]
• Itoh, M., Akutsu, T., and Kanehisa, M.; Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Informatics 15(1), 93-104 (2004). [pubmed] [pdf]
• Yamada, T., Goto, S., and Kanehisa, M.; Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Informatics 15(1), 249-258 (2004). [pubmed] [pdf]
• Levchenko, M.E., Poroikov, M., and Kanehisa, M.; G-protein coupled receptors and and their endogenous ligand in the human genome. Biomeditsinskaya Khimiya (Biomedical Chemistry) 50, 149-158 (2004). [pubmed]
• Imanishi, T., et al.; Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biol. 2, e162 (2004). [pubmed] [doi]
• Kobayashi, M., Ishizuka, T., Katayama, M., Kanehisa, M., Bhattacharyya-Pakrasi, M., Pakrasi, H.B., and Ikeuchi, M.; Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol. 45, 290-299 (2004). [pubmed] [doi]
• Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M.; The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004). [pubmed] [doi]

2003

• Aoki, K.F., Yamaguchi, A., Okuno, Y., Akutsu, T., Ueda, N., Kanehisa, M., and Mamitsuka, H.; Efficient tree-matching methods for accurate carbohydrate database queries. Genome Informatics 14, 134-143 (2003). [pubmed] [pdf]
• Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M.; Heuristics for chemical compound matching. Genome Informatics 14, 144-153 (2003). [pubmed] [pdf]
• Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M.; Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 125, 11853-11865 (2003). [pubmed] [doi]
• Vert, J.-P. and Kanehisa, M.; Extracting active pathways from gene expression data. Bioinformatics 19, ii238-ii234 (2003). [pubmed] [doi]
• Park, K.-J. and Kanehisa, M.; Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 19, 1656-1663 (2003). [pubmed] [doi] [see Thomson]
• Yamanishi, Y., Vert, J.-P., Nakaya, A., and Kanehisa, M.; Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. Bioinformatics 19, i323-i330 (2003). [pubmed] [doi]
• Vert, J.-P. and Kanehisa, M.; Graph-driven features extraction from microarray data using diffusion kernels and kernel CCA. Advances in Neural Information Processing Systems 15 (Becker, S., Thrun, S., and Obermayer, K., eds.), pp. 1425-1432, MIT Press, Cambridge, MA (2003).
• Kanehisa, M. and Bork, P.; Bioinformatics in the post-sequence era. Nature Genetics 33, 305-310 (2003). [pubmed] [doi]
• Hihara, Y., Sonoike, K., Kanehisa, M., and Ikeuchi, M.; DNA microarray analysis of redox responsive genes in the genome of the cyanobacterium Synechocystis sp. PCC 6803. J. Bacteriol. 185, 1719-1725 (2003). [pubmed] [doi]
• Brudler, R., Hitomi, K., Daiyasu, H., Toh, H., Kucho, K., Ishiura, M., Kanehisa, M., Roberts, V.A., Todo, T., Tainer, J.A., and Getzoff, E.D.; Identification of a new cryptochrome class: structure, function and evolution. Mol. Cell 11, 59-67 (2003). [pubmed] [doi]

2002

• Yamanishi, Y., Itoh, M., and Kanehisa, M.; Extraction of organism groups from phylogenetic profiles using independent component analysis. Genome Informatics 13, 61-70 (2002). [pubmed] [pdf]
• Kanehisa, M.; The KEGG database. Novartis Found. Symp. 247, 91-103 (2002). [pubmed] [doi]
• Yamaguchi, K., Suzuki, I., Yamamoto, H., Lyukevich, A., Bodrova, I., Los, D.A., Piven, I., Zinchenko, V., Kanehisa, M., and Murata, N.; A two-component Mn(2+)-sensing system negatively regulates expression of the mntCAB operon in Synechocystis. Plant Cell 14, 2901-2913 (2002). [pubmed] [doi]
• Yoshimura, H., Yanagisawa, S., Kanehisa, M., and Ohmori, M.; Screening for the target gene of cyanobacterrial cAMP receptor protein SYCRP1. Mol. Microbiol. 43, 843-853 (2002). [pubmed] [doi]
• Kanehisa, M. and Goto, S.; KEGG for computational genomics. In "Current Topics in Computational Molecular Biology" (Jiang, T., Xu, Y., and Zhang, M.Q., eds.), pp. 301-315, MIT-Press, Cambridge, MA (2002).
• Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.; The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002). [pubmed] [doi]
• Goto, S., Okuno, Y., Hattori, M., Nishioka, T. and Kanehisa, M.; LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404 (2002). [pubmed] [doi]
• Kawashima, T., Kawashima, S., Kohara, Y., Kanehisa, M., and Makabe, K.W.; Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res. 30, 119-120 (2002). [pubmed] [doi]

2001

• Ohmori, M., Ikeuchi, M., Sato, N., Wolk, P., Kaneko, T., Ogawa, T., Kanehisa, M., Goto, S., Kawashima, S., Okamoto, S. Yoshimura, H., Katoh, H., Fujisawa, T., Ehira, S., Kamei, A., Yoshihara, S., Narikawa, R., and Tabata, S.; Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. Strain PCC 7120. DNA Res. 8, 271-284 (2001). [pubmed] [doi]
• Nakaya, A., Goto, S., and Kanehisa, M.; Extraction of correlated gene clusters by multiple graph comparison. Genome Informatics 12, 44-53 (2001). [pubmed] [pdf]
• Kanehisa, M.; Prediction of higher order functional networks from genomic data. Pharmacogenomics 2, 373-385 (2001). [pubmed] [doi]
• Kihara, D. and Kanehisa, M.; Prediction of membrane proteins in post-genomic era. Recent Res. Devel. Protein Eng. 1, 179-196 (2001).
• Makabe, K.W., Kawashima, T., Kawashima, S., Minokawa, T., Adachi, A., Kawamura, H., Ishikawa, H., Yasuda, R., Yamamoto, H., Kondoh, K., Arioka, S., Sasakura, Y., Kobayashi, A., Yagi, K., Shojima, K., Kondoh, Y., Kido, S., Tsujinami, M., Nishimura, N., Takahashi, M., Nakamura, T., Kanehisa, M., Ogasawara, M., Nishikata, T., and Nishida, H.; Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development. Development 128, 2555-2567 (2001). [pubmed] [pdf]
• Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., Cui, L., Oguchi, A., Aoki, K., Nagai, Y., Lian, J., Ito, T., Kanamori, M., Matsumaru, H., Maruyama, A., Murakami, H., Hosoyama, A., Mizutani-Ui, Y., Takahashi, N.K., Sawano, T., Inoue, R., Kaito, C., Sekimizu, K., Hirakawa, H., Kuhara, S., Goto, S., Yabuzaki, J., Kanehisa, M., Yamashita, A., Oshima, S., Furuya, K., Yoshino, C., Shiba, T., Hattori, M., Ogasawara, N., Hayashi H., and Hiramatsu, K.; Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357, 1225-1240 (2001). [pubmed] [doi]
• Makabe, K.W., Kawashima, T., Kawashima, S., Sasakura, Y., Ishikawa, H., Kawamura, H., Kanehisa, M., Nishikata, T. and Nishida, H.; Maternal genetic information stored in fertilized eggs of the ascidian, Halocynthia roretzi. In "The Biology of Ascidians" (Sawada, H., Yokosawa, H., Lambert, C.C. eds.), pp.165-177, Springer-Verlag, Tokyo (2001).
• Suzuki, I., Kanesaki, Y., Mikami, K., Kanehisa, M., and Murata, N.; Cold-regulated genes under control of the cold sensor Hik33 in Synechocystis. Mol. Microbiol. 40, 235-244 (2001). [pubmed] [doi]
• Hihara, Y., Kamei, A., Kanehisa, M., Kaplan, A., and Ikeuchi, M.; DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 13, 793-806 (2001). [pubmed] [doi]

2000

• Ogata, H., Fujibuchi, W., Goto, S., and Kanehisa, M.; A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 28, 4021-4028 (2000). [pubmed] [doi]
• Fujibuchi, W., Ogata, H., Matsuda, H., and Kanehisa, M.; Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res. 28, 4029-4036 (2000). [pubmed] [doi]
• Kihara, D. and Kanehisa, M.; Tandem clusters of membrane proteins in complete genome sequences. Genome Res. 10, 731-743 (2000). [pubmed] [doi]
• Kanehisa, M.; Pathway databases and higher order function. Adv. Protein Chem. 54, 381-408 (2000). [pubmed] [doi]
• [Book] Kanehisa, M.; "Post-genome Informatics", Oxford University Press (2000). [nlmcatalog]
• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [doi]
• Kawashima, T., Kawashima, S., Kanehisa, M., Nishida, H., and Makabe, K.W.; MAGEST: MAboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res. 28, 133-135 (2000). [pubmed] [doi]
• Kawashima, S. and Kanehisa, M.; AAindex: Amino Acid index database. Nucleic Acids Res. 28, 374 (2000). [pubmed] [doi]
• Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database for enzyme reactions. Nucleic Acids Res. 28, 380-382 (2000). [pubmed] [doi]

1999

• Nakao, M., Bono, H., Kawashima, S., Kamiya, T., Sato, K., Goto, S., and Kanehisa, M.; Genome-scale gene expression analysis and pathway reconstruction in KEGG. Genome Informatics 10, 94-103 (1999). [pubmed] [pdf]
• Tomii, K. and Kanehisa, M.; Systematic detection of protein structural motifs. In "Pattern Discovery in Biomolecular Data" (Wang, J.T.L., Shapiro, B.A., and Shasha, D., eds.), pp.97-110, Oxford Univ. Press (1999)
• Kanehisa, M.; KEGG: From genes to biochemical pathways. In "Bioinformatics: Databases and Systems" (Letovsky, S., ed.), pp. 63-76, Kluwer Academic Publishers (1999).
• Wackett, L.P., Ellis, L.B.M., Speedie, S.M., Hershberger, C.D., Knackmuss, H.-J., Spormann, A.M., Walsh, C.T., Forney, L.J., Punch, W.F., Kazic, T., Kanehisa, M., and Berndt, D.J.; Predicting microbial biodegradation pathways. ASM News 65, 87-93 (1999).
• Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34 (1999). [pubmed] [doi]
• Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND database for enzymes, compounds, and reactions. Nucleic Acids Res. 27, 377-379 (1999). [pubmed] [doi]
• Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 27, 368-369 (1999). [pubmed] [doi]

1998

• Bono, H., Goto, S., Fujibuchi, W., Ogata, H., and Kanehisa, M.; Systematic prediction of orthologous units of genes in the complete genomes. Genome Informatics 9, 32-40 (1998). [pubmed] [pdf]
• Kanehisa, M.; Databases of Biological Information. In "Trends Guide to Bioinformatics" (Brenner, S. and Lewitter, F., eds.), pp. 24-26, Elsevier (1998).
• Tomii, K. and Kanehisa, M.; A comparative analysis of ABC transporters in the complete microbial genomes. Genome Res. 8, 1048-1059 (1998). [pubmed] [doi]
• Kihara, D., Shimizu, T., and Kanehisa, M.; Prediction of membrane proteins based on classification of transmembrane segments. Protein Eng. 11, 961-970 (1998). [pubmed] [doi]
• Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: Chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998). [pubmed] [doi]
• Fujibuchi, W., Sato, K., Ogata, H., Goto, S., and Kanehisa, M.; KEGG and DBGET/LinkDB: Integration of biological relationships in divergenet molecular biology data. In "Knowledge Sharing Across Biological and Medical Knowledge Based Systems", Technical Report WS-98-04, pp. 35-40, AAAI Press (1998).
• Ogata, H., Goto, S., Fujibuchi, W., and Kanehisa, M.; Computation with the KEGG pathway database. BioSystems 47, 119-128 (1998). [pubmed] [doi]
• Kanehisa, M.; Editorial: Grand challenges in bioinformatics. Bioinformatics 14, 309 (1998). [pubmed] [doi]
• Kanehisa, M.; Books etc: Microbiology - on a plate. Trends Genet. 14, 165-166 (1998).
• Bono, H., Ogata, H., Goto, S., and Kanehisa, M.; Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8, 203-210 (1998). [pubmed] [doi]

1997

• Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an Integrated Database Retrieval System. Pacific Symposium on Biocomputing '98, 683-694 (1997). [pubmed] [pdf]
• Kanehisa, M.; Linking databases and organisms - GenomeNet resources in Japan. Trends Biochem. Sci. 22, 442-444 (1997). [pubmed] [doi]
• Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997). [pubmed] [doi]
• Fujibuchi, W. and Kanehisa, M.; Prediction of gene expression specificity by promoter sequence patterns. DNA Res. 4, 81-90 (1997). [pubmed] [doi]
• Kanehisa, M. and Goto, S.; A systematic analysis of gene functions by the metabolic pathway database. In "Theoretical and Computational Methods in Genome Research" (Suhai, S., ed.), pp. 41-55, Plenum (1997).

1996

• Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K., and Kanehisa, M.; Organizing and computing metabolic pathway data in terms of binary relations. Pacific Symposium on Biocomputing '97, 175-186 (1996). [pubmed] [pdf]
• Ogata, H., Bono, H., Fujibuchi, W., Goto, S., and Kanehisa, M.; Analysis of binary relations and hierarchies of enzymes in the metabolic pathways. Genome Informatics 7, 128-136 (1996). [pdf]
• Kanehisa, M.; Toward pathway engineering: a new database of genetic and molecular pathways. Science & Technology Japan, No. 59, pp. 34-38 (1996). [pdf]
• Ogiwara, A., Uchiyama, I., Takagi, T., and Kanehisa, M.; Construction and analysis of a profile library characterizing groups of structurally known proteins. Protein Sci. 5, 1991-1999 (1996). [pubmed] [doi]
• Ogata, H., Fujibuchi, W., and Kanehisa, M.; The size differences among mammalian introns are due to the accumulation of small deletions. FEBS Lett. 390, 99-103 (1996). [pubmed] [doi]
• Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). [pubmed] [doi]

1995

• Ogata, H., Akiyama, Y., and Kanehisa, M.; A genetic algorithm based molecular modeling technique for RNA stem-loop structures. Nucleic Acids Res. 23, 419-426 (1995). [pubmed] [doi]

1994

• Mizuno, M. and Kanehisa, M.; Distribution of base composition around the splice sites in different species. Genome Informatics 5, 130-137 (1994). [pdf]
• Mizuno, M. and Kanehisa, M.; Distribution profiles of GC content around the translation initiation site in different species. FEBS Lett. 352, 7-10 (1994). [pubmed] [doi]
• Uchiyama, I., Ogiwara, A., and Kanehisa, M.; A library of signature pentapeptides for the Protein Data Bank. In "Protein Structures by Distance Analysis" (Bohr, H. and Brunak, S., eds.), pp. 237-246, IOS Press (1994).
• Suzuki, T., Takagi, T., Kuhara, S., and Kanehisa, M.; Development of an integrated database for genome mapping and nucleotide sequences. Proc. 27th Hawaii Int. Conf. on System Sciences, Vol. 5, pp. 68-76 (1994).

1993

• Ohkubo, Z. and Kanehisa, M.; Characterization of spatially close peptide segments in proteins. Bull. Inst. Chem. Res., Kyoto Univ. 71, 327-337 (1993).
• Fujibuchi, W. and Kanehisa, M.; A method to extract functional motifs for transcriptional regulation in eukaryotic sequences. Bull. Inst. Chem. Res., Kyoto Univ. 71, 317-326 (1993).
• Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A., and Kanehisa, M.; Multiple sequence alignment by parallel simulated annealing. Comput. Appl. Biosci. 9, 267-273 (1993). [pubmed]
• Matsuo, Y. and Kanehisa, M.; An approach to systematic detection of protein structural motifs. Comput. Appl. Biosci. 9, 153-159 (1993). [pubmed]

1992

• Nakai, K. and Kanehisa, M.; A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14, 897-911 (1992). [pubmed] [doi]
• Ogiwara, A., Uchiyama, I., Seto, Y., and Kanehisa, M.; Construction of a dictionary of sequence motifs that characterize groups of related proteins. Protein Eng. 5, 479-488 (1992). [pubmed] [doi]
• Horton, P.B. and Kanehisa, M.; An assessment of neural network and statistical approaches for prediction of E.coli promoter sites. Nucleic Acids Res. 20, 4331-4338 (1992). [pubmed] [doi]

1991

• Iijima, T. and Kanehisa, M.; Analysis of DNA functional sites by information contents. Bull. Inst. Chem. Res., Kyoto Univ. 69, 226-233 (1991).
• Nakai, K. and Kanehisa, M.; Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins 11, 95-110 (1991). [pubmed] [doi]

1990

• Seto, Y., Ikeuchi, Y., and Kanehisa, M.; Fragment peptide library for classification and functional prediction of proteins. Proteins 8, 341-351 (1990). [pubmed] [doi]
• Seto, Y., Ikeuchi, Y., and Kanehisa, M.; Peptide sequence library for protein expert system. In "Protein Engineering" (Ikehara, M., ed.), pp. 311-313 (1990).

1989

• Kanehisa, M.; Databases: What's There and What's Needed. In "Biomolecular Data: A Resource in Transition" (Colwell, R.R., ed.), pp. 91-95, Oxford Univ. Press (1989).
• Seto, Y. and Kanehisa, M.; Repeat sequences of amino acids suggest the origin of protein. Bull. Inst. Chem. Res., Kyoto Univ. 66, 461-468 (1989).

1988

• Kanehisa, M. and Lesk, A.M.; The future of computational molecular biology. In "Computational Molecular Biology" (Lesk, A.M., ed.), pp. 223-224, Oxford Univ. Press (1988).
• Nakai, K. and Kanehisa, M.; Prediction of in-vivo modification sites of proteins from their primary structures. J. Biochem. 104, 693-699 (1988). [pubmed] [pdf]
• Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988). [pubmed] [doi]
• Kanehisa, M.; A multivariate analysis method for discriminating protein secondary structural segments. Protein Eng. 2, 87-92 (1988). [pubmed] [doi]

1987

• Kanehisa, M.; Multivariate analysis of amino acid sequences for structural and functional predictions. In "Impact of Knowledge of Amino Acid Sequence Data on Biophysical Research -- Proceedings of the 13th Taniguchi International Symposium on Biophysics" (Tsugita, A., ed.) pp. 75-80, Science Univ. of Tokyo (1987).
• Nishikawa, K., Nakashima, H., Kanehisa, M., and Ooi, T.; Detection of weak sequence homology of proteins for tertiary structure prediction. Protein Seq. Data Anal. 1, 107-116 (1987). [pubmed]

1986

• Kanehisa, M.; Prediction of protein structures by database analysis. In "Proceedings of the International Symposium on Computer Analysis for Life Science" (Kawabata, C. and Bishop, A.R., eds.), pp. 204-211, Ohmsha, Ltd., Tokyo (1986).
• Takagi, J.S., Tokushige, M., Shimura, Y., and Kanehisa, M.; L-Aspartate ammonia-lyase and fumarate hydratase share extensive sequence homology. Biochem. Biophys. Res. Commun. 138, 568-572 (1986). [pubmed] [doi]

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• Nakata, K., Kanehisa, M., and Maizel, J.V.,Jr.; Discriminant analysis of promoter regions in E. coli sequences. Comp. Appl. Biosci. 4, 367-371 (1988). [pubmed]
• Greif, P.C., Nussinov, R., Kanehisa, M., and DeLisi, C.; Nonrandom recurrence of consecutive repeats in noncoding mammalian sequences. Math. Biosci. 81, 43-52 (1986). [doi]

1985

• Burks, C., Fickett, J.W., Goad, W.B., Kanehisa, M., Lewitter, F.I., Rindone, W.P., Swindell, C.D., Tung, C.-S., and Bilofsky, H.S.; The GenBank nucleic acid sequence database. Comp. Appl. Biosci. 1, 225-233 (1985). [pubmed]
• Leonard, W.J., Depper, J.M., Kanehisa, M., Kronke, M., Peffer, N.J., Svetlik, P.B., Sullivan, M., and Greene, W.C.; Structure of the human interleukin-2 receptor gene. Science 230, 633-639 (1985). [pubmed] [doi]
• Nakata, K., Kanehisa, M., and DeLisi, C.; Prediction of splice junctions in mRNA sequences. Nucleic Acids. Res. 13, 5327-5340 (1985). [pubmed] [doi]
• Klein, P., Kanehisa, M., and DeLisi, C.; The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta 815, 468-476 (1985). [pubmed] [doi]
• Norcross, M.A. and Kanehisa, M.; The predicted structure of the Ia beta 1 domain. A hypothesis for the structural basis of MHC-restricted T-cell recognition of antigens. Scand. J. Immunol. 21, 511-523 (1985). [pubmed] [doi]
• Kanehisa, M. and DeLisi, C.; The prediction of a protein and nucleic acid structure: Problems and prospects. Acta Appl. Math. 4, 115-137 (1985). [doi]
• DeLisi, C., Klein, P., and Kanehisa, M.; Some comments on protein taxonomy: Procedures for functional and structural classification. Prog. Clin. Biol. Res. 172A, 431-441 (1985). [pubmed]
• Kanehisa, M. and DeLisi, C.; Sequence homologies of oncogene proteins: A critical review. Prog. Clin. Biol. Res. 172A, 443-452 (1985). [pubmed]

1984

• Klein, P., Kanehisa, M., and DeLisi, C.; Prediction of protein function from sequence properties: A discriminant analysis of a database. Biochim. Biophys. Acta 787, 221-226 (1984). [pubmed] [doi]
• DeLisi, C. and Kanehisa, M.; Assessing the significance of local seqeunce homologies. Math. Biosci. 69, 77-85 (1984). [doi]
• Kanehisa, M.; Use of statistical criteria for screening potential homologies in nucleic acid sequences. Nucleic Acids Res. 12, 203-213 (1984). [pubmed] [doi]
• Kanehisa, M., Klein, P., Greif, P., and DeLisi, C.; Computer analysis and structure prediction of nucleic acid and proteins. Nucleic Acids Res. 12, 417-428 (1984). [pubmed] [doi]

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• Kanehisa, M., Fickett, J.W., and Goad, W.B.; A relational database system for the maintenance and verification of the Los Alamos sequence library. Nucleic Acids Res. 12, 149-158 (1984). [pubmed] [doi]

1982

• Fickett, J., Goad, W., and Kanehisa, M.; Los Alamos sequence library: A database and analysis system for nucleic acid sequences. Los Alamos National Laboratory Technical Report, LA-9274-MS (1982).
• Kanehisa, M.I.; Los Alamos sequence analysis package for nucleic acids and proteins. Nucleic Acids Res. 10, 183-196 (1982). [pubmed] [doi]
• Goad, W.B. and Kanehisa, M.I.; Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries. Nucleic Acids Res. 10, 247-263 (1982). [pubmed] [doi]
• Kanehisa, M.I. and Goad, W.B.; Pattern recognition in nucleic acid sequences. II. An efficient method for finding locally stable secondary structures. Nucleic Acids Res. 10, 265-278 (1982). [pubmed] [doi]

1981

• Kanehisa, M.I.; Kinetics of activation and desensitization in receptor proteins. Biopolymers 20, 787-801 (1981). [pubmed] [doi]

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1980

• Kanehisa, M.I. and Tsong, T.Y.; Local hydrophobicity stabilizes secondary structures in proteins. Biopolymers 19, 1617-1628 (1980). [pubmed] [doi]
• Tsong, T.Y. and Kanehisa, M.I.; Local conformational relaxations and protein folding-unfolding transitions. Biophys. J. 32, 422-424 (1980). [pubmed] [doi]

1979

• Kanehisa, M.I. and Tsong, T.Y.; Kinetic analysis of local structure formations in protein folding. Biopolymers 18, 2913-2928 (1979). [doi]
• Kanehisa, M.I. and Tsong, T.Y.; Slow equilibration of a denatured protein: Comparison of the cluster model with the proline isomerization model. J. Mol. Biol. 133, 279-283 (1979). [pubmed] [doi]
• Kanehisa, M.I. and Tsong, T.Y.; Dynamics of the cluster model of protein folding. Biopolymers 18, 1375-1388 (1979). [doi]

1978

• Kanehisa, M.I. and Tsong, T.Y.; Mechanisms of the multiphasic kinetics in the folding and unfolding of globular proteins. J. Mol. Biol. 124, 177-194 (1978). [pubmed] [doi]
• Kanehisa, M.I. and Tsong, T.Y.; Cluster model of lipid phase transitions with application to passive permeation of molecules and structure relaxations in lipid bilayers. J. Am. Chem. Soc. 100, 424-432 (1978). [doi]

1977

• Tsong, T.Y., Greenberg, M., and Kanehisa, M.I.; Anesthetic action on membrane lipids. Biochemistry 16, 3115-3121 (1977). [pubmed] [doi]
• Tsong, T.Y. and Kanehisa, M.I.; Relaxation phenomena in aqueous dispersions of synthetic lecithins. Biochemistry 16, 2674-2680 (1977). [pubmed] [doi]

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• Kanehisa, M.I. and Ikegami, A.; Structural changes and fluctuations of proteins. II. Analysis of the denaturation of globular proteins. Biophys. Chem. 6, 131-149 (1977). [pubmed] [doi]

1974

• Sakanishi, A., Kanehisa, M.I., Yoshida, S., and Ikegami, A.; Expressions of morphologies of erythrocytes with surface spherical harmonics. Repts. Progr. Polym. Phys. Japan 17, 693-696 (1974).
• Ikegami, A., Kanehisa, M.I., Nakanishi, M., and Tsuboi, M.; Isotope exchange and conformational fluctuation in polypeptides. Adv. Biophys. 6, 1-39 (1974).

1973

• Kanehisa, M.I. and Ikegami, A.; Simulation of the hydrogen-deuterium exchange in short polypeptides. Repts. Progr. Polym. Phys. Japan 16, 625-628 (1973).

1972

• Nakanishi, M., Tsuboi, M., Ikegami, A., and Kanehisa, M.; Fluctuation of an alpha-helix structure. Difference between the central and terminal portions. J. Mol. Biol. 64, 363-378 (1972). [pubmed]