Kanehisa Laboratories

List of GIW/IBSB Poster Presentations

IBSB 2011

• Fujita, M., Tokimatsu, T., Kotera, M., Kanehisa, M., and Goto, S.; Evolutionary analysis of UTR length in the eukaryote transcripts. IBSB 2011 Poster Abstracts, P08 (2011).
• Nishimura, Y., Tokimatsu, T., Kotera, M., Kanehisa, M., and Goto, S.; Functional analysis of miRNA and its overlapping gene in metazoan genomes. IBSB Poster Abstracts, P23 (2011).
• Shimizu, Y., Shigemizu, D., Hu, S., Kanehisa, M., and DeLisi, C.: Analysis of possible repositioning drugs by comparing expression signatures between different cancer types. IBSB Poster Abstracts, P26 (2011).

IBSB 2010

• Honda, W., Kawashima, S., Yamanishi, Y., Goto, S., and Kanehisa, M.; Association of Low Complexity Regions with Autoantigens. IBSB 2010 Poster Abstracts, P7 (2010).
• Sakiyama, T., Goto, S., and Kanehisa, M.; Comprehensive Sequence Analysis for Extended Region in Ubiquitin-conjugating Enzymes. IBSB 2010 Poster Abstracts, P17 (2010).
• Fujita, M., Harada, Y., Yamaguchi, A., Yamada, L., Sawada, H., and Goto, S.; Analysis of Polymorphism of Self-nonself Recognition gene in Ciona intestinalis. IBSB 2010 Poster Abstracts, P18 (2010).
• Hiranuka, K., Diez, D., Goto, S., and Kanehisa, M.; Detection of Segmental Gene Conversion in Antigenic Variant Multigene Families of Protozoan Parasites. IBSB 2010 Poster Abstracts, P22 (2010).
• Jin, Z., Goto, S., and Kanehisa, M.; Analysis of Cancer Pathways Caused by Oncogenic Virus. IBSB 2010 Poster Abstracts, P23 (2010).
• Dong, H., Kotera, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; A Study on Classification of Traditional Chinese Medicines. IBSB 2010 Poster Abstracts, P25 (2010).
• Shimizu, Y., Kotera, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; Comprehensive Analysis of Domain Structures in Polyketide Synthases. IBSB 2010 Poster Abstracts, P27 (2010).

GIW 2009

• Shimizu, Y., Kotera, M., Tokimatsu, T., Hattori, M., Goto, S., and Kanehisa, M.; Comprehensive analysis of polyketide synthase families. GIW 2009 Poster Abstracts, P022 (2009).
• Nishimura, Y., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; Analysis of plant UGT family sequences and substrate specificity. GIW 2009 Poster Abstracts, P027 (2009).
• Kotera, M., Tokimatsu, T., Nakagawa, Z., Moriya, Y., Hattori, M., Goto, S., and Kanehisa, M.; Reclassification of oxidoreductase subclasses based on the relationships of reductants and oxidants. GIW 2009 Poster Abstracts, P124 (2009).
• Tokimatsu, T., Kotera, M., Goto, S., Kanaya, S., and Kanehisa, M.; Structural clustering of plant secondary metabolite to estimate compound classes reflecting their biosynthetic pathway. GIW 2009 Poster Abstracts, P127 (2009).
• Erguner, B., Hattori, M., Goto, S., and Kanehisa, M.; Extracting common substructures of GPCR ligands. GIW 2009 Poster Abstracts, P134 (2009).
• Hattori, M., Kotera, M., Muto, A., Goto, S., and Kanehisa, M.; Chemical continuity of reaction centers along successive metabolic reactions. GIW 2009 Poster Abstracts, P135 (2009).
• Muto, A., and Kanehisa, M.; Structural similarity-based approach to characterize crude drug components. GIW 2009 Poster Abstracts, P137 (2009).
• Liu, C., Hsu, C., Kao, C., Kanehisa, M., Goto, S., and Huang C.F.; Dissecting protein-protein interaction-mediated cross-talk pathways in hepatocellular carcinoma. GIW 2009 Poster Abstracts, T002/P081 (2009).

IBSB 2009

• Kotera, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; Structural clustering of secondary metabolites based on their substructures. IBSB 2009 Boston, USA (2009).
• Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; Estimating the connectivity in secondary metabolite groups based on the structural clustering. IBSB 2009 Boston, USA (2009).
• Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.; Analysis of conserved pattern in enzymatic reactions and its application to EC prediction. IBSB 2009 Boston, USA (2009).

IBSB 2007

• Kuntzer, J., Lenhof, H.-P., Goto, S., and Kanehisa, M.; Network analysis using the biochemical network library. IBSB 2007, P001 (2007).
• Takarabe, M., Okuda, S., Itoh, M., and Kanehisa, M.; Analysis of tissue specific expression patterns of metabolic pathway. IBSB 2007, P007 (2007)
• Onuki, R., Shibuya, T., and Kanehisa, M.; Haplotype inference probability-based genotype clustering. IBSB 2007, P010 (2007).
• Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.; An improved scoring scheme for predicting glycan structures from gene expression data. IBSB 2007, P013 (2007).
• Muto, A., Hattori, M., and Kanehisa, M.; Analysis of common substructures of metabolic compounds within the different organism groups. IBSB 2007, P014 (2007).
• Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.; Analysis of the relationship between EC classification and reaction representations in KEGG RPAIR database. IBSB 2007, P015 (2007).

GIW 2006

• Gutteridge, A., Kanehisa, M., and Goto, S.; Regulation of Metabolic Networks By Small Molecule Metabolites. GIW 2006 Poster Abstracts, P014 (2006).
• Honda, W., Kawashima, S., and Kanehisa, M.; Autoimmune Diseases and Evolutionary Trace of the T-Cell Epitopes. GIW 2006 Poster Abstracts, P041 (2006).
• Takarabe, M., Tsuchida, A., Fujita, M., Okuda, S., Yoshizawa, A.C., Yamada, T., Itoh, M., Goto, S., and Kanehisa, M.; Analysis of Tissue Specific Expression Patterns of Isozymes. GIW 2006 Poster Abstracts, P042 (2006).
• Hayes, N., Normark, J., Nilsson, D., Wheelock, C., Wahlgren, M., and Goto, S.; A Web Application for Identification of Glycosaminoglycan (GAG) Binding Motifs in Plasmodium Falciparum. GIW 2006 Poster Abstracts, P043 (2006).
• Diez, D., Ribacke, U., Wheelock, C., Wahlgren, M., and Goto, S.; Analysis of the Sub-Telomeric Region of the Malaria Parasite P. Falciparum Using aCGH Data. GIW 2006 Poster Abstracts, P044 (2006).
• Huang, J., and Kanehisa, M.; Structural Analysis on Functional Epitope. GIW 2006 Poster Abstracts, P061 (2006).
• Muto, A., Hattori, M., Honda, W., and Kanehisa, M.; Analyses of the Nutrient Dependency of Parasites to Hosts Using KEGG Database. GIW 2006 Poster Abstracts, P084 (2006).
• Kojima, K.K., and Kanehisa, M.; Identification of Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture. GIW 2006 Poster Abstracts, P085 (2006).
• Sato, T., Yamanishi, Y., Ichihara, H., Kuma, K., Kanehisa, M. and Toh, H.; Relationship between Data Size and Accuracy of Prediction of Protein-Protein Interactions by Co-Evolutionary Information. GIW 2006 Poster Abstracts, P102 (2006).
• Moriya, Y., Yamanishi, Y., Itoh, M., Okamoto, S., and Kanehisa, M.; From Function Prediction to Pathway Prediction: A New Pipeline Based on KAAS and GENIES. GIW 2006 Poster Abstracts, P116 (2006).
• Suga, A., Yamanishi, Y., Hashimoto, K., and Kanehisa, M.; Prediction of Glycan Structures from Gene Expression Data Based on Improved Scoring Scheme. GIW 2006 Poster Abstracts, P118 (2006).

IBSB 2006

• Suga, A., Hashimoto, K., Yamanishi, Y., and Kanehisa M.; Predictionof glycan structures from gene expression data based on glycosyltransferase reactions. IBSB 2006, Boston (2006).
• Oh, M., Hattori, M., Yamada, T., Goto, S., and Kanehisa M.; Analysis of characteristic biochemical transformation patterns in metabolic pathways. IBSB 2006, Boston (2006).
• Honda, W., Kawashima, S., and Kanehisa M.; Immunosurveillance against lipid antigens and pathogens' tropism. IBSB 2006, Boston (2006).
• Muto, A., Honda, W., Hattori, M., and Kanehisa M.; Clustering of species by the degree of compound sharing. IBSB 2006, Boston (2006).
• Shigemizu, D., Okuda, S., Araki , M., Goto, S., and Kanehisa M.; Construction of the drug substructure library from the KEGG DRUG database. IBSB 2006, Boston (2006).
• Sakiyama, T., and Kanehisa M.; Sequence analysis of ubiquitin signaling cascade. IBSB 2006, Boston (2006).

GIW 2005

• Moriya, Y., Itoh, M., Okuda, S., and Kanehisa M.; KAAS: KEGG Automatic Annotation Server. GIW 2005 Poster Abstracts, P005 (2005).
• Yamada, T., Hattori, M., Oh, M., Goto, S., and Kanehisa M.; RPAIR: a database of chemical transformation patterns in enzymatic reactions. GIW 2005 Poster Abstracts, P020 (2005).
• Honda, W., Kawashima, S., and Kanehisa M.; Physicochemical and structural characterization of nonapeptides targeted in autoimmune diseases. GIW 2005 Poster Abstracts, P069 (2005).
• Sato, T., Yamanishi, Y., Ichihara, H., Kanehisa M., and Toh, H.; Comparison of prediction methods for protein-protein interactions using co-evolutionary information. GIW 2005 Poster Abstracts, P080 (2005).
• Muto, A., Hattori, M., and Kanehisa M.; Characterization of secondary structure elements in riboswitches. GIW 2005 Poster Abstracts, P081 (2005).
• Tanaka, N., Kadowaki, T., Goto, S., and Kanehisa M.; Automatic assignment of full EC numbers based on structural changes of chemical compounds. GIW 2005 Poster Abstracts, P084 (2005).
• Kadowaki, T., Adachi, T., Okamoto, S., Tanaka, N., Tonomura, K., Tsujimoto, G., and Kanehisa M.; Chemical genomic sutdy of endocrine disrupting chemicals in metabolic pathways. GIW 2005 Poster Abstracts, P085 (2005).
• Sakai, H., Suzuki, Y., Horimoto, K., Sugano, S., and Kanehisa M.; Genome-wide analysis of the alternative splicing based on full-length cDNA Data. GIW 2005 Poster Abstracts, P100 (2005).
• Hashimoto, K., Binder, B., Kanehisa M., Ebenhoeh, O., and Heinrich, R.; Expanding large scale signal transduction networks. GIW 2005 Poster Abstracts, P112 (2005).
• Fujita, M. and Kanehisa M.; Thermal adaptations of DNA-binding proteins. GIW 2005 Poster Abstracts, P129 (2005).
• Oh, M., Liebermeister, W., Kanehisa M., Heinrich, R., and Ebenhoeh, O.; Structural and functional analysis of transiently expressed metabolic networks. GIW 2005 Poster Abstracts, P149 (2005).
• Onuki, R., Aburatani, S., Horimoto, K., and Kanehisa, M.; Evaluation of inference performance by ASIAN in transcriptional regulatory relationships. GIW 2005 Poster Abstracts, P155 (2005).
• Oh, M., Hattori, M., Goto, S., and Kanehisa, M.; Characteristic chemical transformation patterns in biodegradation pathways. GIW 2005 Poster Abstracts, P167 (2005).

IBSB 2005

• Itoh, M., Goto, S., and Kanehisa, M.; Phylogenetic analysis of domain combinations in eukaryotic genomes. IBSB 2005 Poster Abstracts, P7 (2005). [pdf]
• Muto, A., Okuda, S., Hattori, M., and Kanehisa, M.; Analysis of the bacterial mRNAs recognized by RNA-binding proteins and compounds. IBSB 2005 Poster Abstracts, P14 (2005). [pdf]
• Moriya, Y., Itoh, M., and Kanehisa, M.; Automatic construction of KEGG PATHWAY for new genomes. IBSB 2005 Poster Abstracts, P22 (2005). [pdf]
• Sakai, H., Suzuki, Y., Murakami, H., Aburatani, S., Horimoto, K., Sugano, S., and Kanehisa, M.; Positive correlation between alternative splicing events and exon structure conservations in human-mouse orthologs. IBSB 2005 Poster Abstracts, P37 (2005). [pdf]

GIW 2004

• Tamada, Y., Bannai, H., Imoto, H., Katayama, T., Kanehisa, M., and Miyano, S.; Modeling gene networks utilizing evolutionary information using Bayesian network models. GIW 2004 Poster Abstracts, P020 (2004). [pdf]
• Sakai, H., Horimoto, K., and Kanehisa, M.; Systematic identification of weak connections between clusters in biological network. GIW 2004 Poster Abstracts, P024 (2004). [pdf]
• Ota, K., Goto, S., and Kanehisa, M.; Comparative analysis of conditional regulation across the yeast genomes. GIW 2004 Poster Abstracts, P033 (2004). [pdf]
• Miyama, T., Kawano, S., and Kanehisa, M.; Expression analysis of glycosyltransferase genes in human, mouse, and rat. GIW 2004 Poster Abstracts, P045 (2004). [pdf]
• Moriya, Y., Katayama, T., Nakaya, A., Itoh, M., Yoshizawa, A.C., Okuda, S., and Kanehisa, M.; Automatic generation of KEGG OC (Ortholog Cluster) and its assignment to draft genomes. GIW 2004 Poster Abstracts, P049 (2004). [pdf]
• Okuda, S., Yoshizawa, A.C., Moriya, Y., Itoh, M., Katayama, T., Goto, S., and Kanehisa, M.; Functional categorization of multiple genomes using KEGG OC in the genome indices. GIW 2004 Poster Abstracts, P050 (2004). [pdf]
• Okamoto, S., Kawashima, S., Narikawa, R., and Kanehisa, M.; Correlation between signal transduction domains and habitats in cyanobacteria. GIW 2004 Poster Abstracts, P054 (2004). [pdf]
• Tanaka, N., Goto, S., and Kanehisa, M.; An algorithm for graph isomorphism and its application to KEGG Compound Search. GIW 2004 Poster Abstracts, P061 (2004). [pdf]
• Kotera, M., Hattori, M., Oh, M.-A., Yamamoto, R., Komeno, T., Yabuzaki, J., Tonomura, K., Goto, S., and Kanehisa, M.; RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. GIW 2004 Poster Abstracts, P062 (2004). [pdf]
• Aoki, K.F., Mamitsuka, H., and Kanehisa, M.; Glycan linkage substitution matrix rooted on tree alignments. GIW 2004 Poster Abstracts, P063 (2004). [pdf]
• Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., and Kanehisa, M.; Classification and motif extraction of glycans in bloods. GIW 2004 Poster Abstracts, P064 (2004). [pdf]
• Lo, E., Yamada, T., Tanaka, M., Hattori, M., Goto, S., Chang,C.-H., and Kanehisa, M.; A method for customized cross-species metabolic pathway comparison. GIW 2004 Poster Abstracts, P068 (2004). [pdf]
• Schwartz, J.-M. and Kanehisa, M.; Decomposition of kinetically feasible metabolic flux distributions onto elementary modes. GIW 2004 Poster Abstracts, P069 (2004). [pdf]
• Hashimoto, K., Kawano, S., Okuno, Y., and Kanehisa, M.; Global tree of known carbohydrate structures to analyze biosynthetic pathways. GIW 2004 Poster Abstracts, P070 (2004). [pdf]
• Tanaka, M., Nariai, N., Handorf, T., Ebenhoeh, O., Miyano, S., Kanehisa, M., and Heinrich, H.; Comparative analysis of enzymatic reactions reveals phylogenic evolution of metabolic pathways. GIW 2004 Poster Abstracts, P071 (2004). [pdf]
• Fujita, M., Itoh, M., and Kanehisa, M.; Conservation of physicochemical properties during protein evolution. GIW 2004 Poster Abstracts, P076 (2004). [pdf]
• Muto, A., Yoshizawa, A.C., Okuda, S., Itoh, M., Hattori, M., and Kanehisa, M.; Analysis of the bacterial sequences recognized by RNA-binding proteins and compounds. GIW 2004 Poster Abstracts, P093 (2004). [pdf]
• Masoudi-Nejad, A., Jauregui, R., Kawashima, S., Goto, S., Kanehisa, M., and Endo, T.R.; The kingdom of plantae EST indices: a resource for plant genomics community. GIW 2004 Poster Abstracts, P102 (2004). [pdf]
• Sato, T., Yamanishi, Y., Kanehisa, M., and Toh, H.; Prediction of protein-protein interactions based on real-valued phylogenetic profiles using partial correlation coefficient. GIW 2004 Poster Abstracts, P122 (2004). [pdf]
• Limviphuvadh, V., Tanaka, S., Goto, S., Ueda, K., and Kanehisa, M.; Analysis of protein interaction networks in neurodegenerative disorders. GIW 2004 Poster Abstracts, P125 (2004). [pdf]
• Yoshizawa, A.C., Okuda, S., Moriya, Y., Itoh, M., Katayama, T., Kawano, S., Okamoto, S., Kawashima, S., and Kanehisa, M.; Functional classification of coiled-coil proteins in multiple genomes. GIW 2004 Poster Abstracts, P157 (2004). [pdf]

IBSB 2004

• Araki, M., Katayama, T., Matsuura, Y., and Kanehisa, M.; KEGG PEPTIDE: a database for peptide structures. IBSB 2004 Poster Abstracts, 1-2 (2004). [pdf]
• Fujita, M., Toh, H., and Kanehisa, M.; Protein sequence-structure alignment using 3D-HMM. IBSB 2004 Poster Abstracts, 7-8 (2004). [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Peptide variation governing identity of organisms. IBSB 2004 Poster Abstracts, 16-17 (2004). [pdf]
• Igarashi, Y., Kawano, S., Goto, S., and Kanehisa, M.; Comparative genome analysis of glycan transporters. IBSB 2004 Poster Abstracts, 18-19 (2004). [pdf]
• Jauregui, R., Itoh, M., and Kanehisa, M.; Genomic analysis of regulatory regions in organelle DNA. IBSB 2004 Poster Abstracts, 20-21 (2004). [pdf]
• Kawano, S., Okuno, Y., Hashimoto, K., Miyama, T., Goto, S., and Kanehisa, M.; Prediction of glycan structures from the glycan related microarray expression profiles. IBSB 2004 Poster Abstracts, 22-23 (2004). [pdf]
• Ota, K., Goto, S., and Kanehisa, M.; Comparative analysis of transcriptional regulation in eukaryotic cell cycles. IBSB 2004 Poster Abstracts, 26-27 (2004). [pdf]
• Limviphuvadh, V., Hattori, M., and Kanehisa, M.; Reconstruction of metabolic pathways for malaria parasite Plasmodium falciparum. IBSB 2004 Poster Abstracts, 30-31 (2004). [pdf]
• Nacher, J.C., Ueda, N., Yamada, T., Kanehisa, M., and Akutsu, T.; Study on the clustering coefficients in metabolic network using a hierarchical framework. IBSB 2004 Poster Abstracts, 34-35 (2004). [pdf]
• Okamoto, S., Ohmori, M., and Kanehisa, M.; Genome-wide distribution of bilin-binding GAF domains. IBSB 2004 Poster Abstracts, 38-39 (2004). [pdf]
• Okuda, S., Yoshizawa, A.C., Moriya, Y., Itoh, M., Goto, S., and Kanehisa, M.; Integration of biological features of multiple genomes: the construction of "Genome Indices" database. IBSB 2004 Poster Abstracts, 40-41 (2004). [pdf]
• Perret, J.-L., Igarashi, Y., and Kanehisa, M.; Modeling biological activities of chemical compounds: kernel methods for structure activity relationship. IBSB 2004 Poster Abstracts, 42-43 (2004). [pdf]
• Sakai, H., Maruyama, O., Murakami, H., Sugaya, N., Imaizumi, A., Sato, M., Aburatani, S., Horimoto, K., and Kanehisa, M.; Finding characteristic sequence patterns for alternative splicing in human genomic DNA. IBSB 2004 Poster Abstracts, 48-49 (2004). [pdf]
• Schwartz, J.-M. and Kanehisa, M.; Combining kinetics and network-based pathway analysis. IBSB 2004 Poster Abstracts, 59-60 (2004). [pdf]
• Tanaka, M., Goto, S., and Kanehisa, M.; Application of standard Gibbs free energy changes of reactions to metabolic pathway computation. IBSB 2004 Poster Abstracts, 63-64 (2004). [pdf]
• Tanaka, N., Goto, S., and Kanehisa, M.; ChemRuby: an open source library for integrating bioinformatics and cheminformatics. IBSB 2004 Poster Abstracts, 65-66 (2004). [pdf]
• Ueda, N., Aoki, K.F., Yamaguchi, A., Kanehisa, M., Akutsu, T., and Mamitsuka, H.; A new probabilistic model for glycans. IBSB 2004 Poster Abstracts, 67-68 (2004). [pdf]
• Yamanishi, Y., Sato, T., Vert, J.-P., Goto, S., and Kanehisa, M.; Prediction of protein network and functions for yeast using multiple types of genomic data. IBSB 2004 Poster Abstracts, 75-76 (2004). [pdf]
• Yoshizawa, A.C., Okuda, S., Itoh, M., Katayama, T., Kawashima, S., and Kanehisa, M.; Prediction and Comparison of Coiled-Coil Proteins in Multiple Genomes. IBSB 2004 Poster Abstracts, 77-78 (2004). [pdf]

GIW 2003

• Ota, K., Yamada, T., Yamanishi, Y., Goto, S., and Kanehisa, M.; Comprehensive analysis of delay in transcriptional regulation using expression profiles. Genome Informatics 14, 302-303 (2003). [doi]
• Kawano, S., Okuno, Y., Hashimoto, K., Yamamoto, H., Takematsu, H., Kozutsumi, Y., Goto, S., and Kanehisa, M.; Prediction of glycan structures from glycosyltransferase expression profiles. Genome Informatics 14, 304-305 (2003). [doi]
• Kotera, M., Hattori, M., Goto, S., and Kanehisa, M.; Analysis of reactive modules in the metabolic pathways. Genome Informatics 14, 366-367 (2003). [doi]
• Limviphuvadh, V., Okuno, Y., Katayama, T., Goto, S., Yoshizawa, A.C., and Kanehisa, M.; Metabolic pathway reconstruction for malaria parasite Plasmodium falciparum. Genome Informatics 14, 368-369 (2003). [doi]
• Tanaka, M., Okuno, Y., Yamada, T., Goto, S., Uemura, S., and Kanehisa, M.; Extraction of a thermodynamic property for biochemical reactions in the metabolic pathway. Genome Informatics 14, 370-371 (2003). [doi]
• Honda, W., Kawashima, S., and Kanehisa, M.; Self-nonself discrimination based on incompatibility of amino acid sequences of human and viruses. Genome Informatics 14, 432-433 (2003). [doi]
• Itoh, M., Yoshizawa, A.C., Okuda, S., Goto, S., and Kanehisa, M.; Analysis of domain combinations in eukaryotic genomes. Genome Informatics 14, 434-435 (2003). [doi]
• Yoshizawa, A.C., Itoh, M., Okuda, S., Limviphuvadh, V., Sakiyama, T., Kawashima, S., and Kanehisa, M.; Comprehensive survey of intracellular transport system-related proteins in complete genomes and draft genomes. Genome Informatics 14, 436-437 (2003). [doi]
• Yamanishi, Y., Yoshizawa, A.C., Itoh, M., Katayama, T., and Kanehisa, M.; Extraction of organism groups from whole genome comparisons. Genome Informatics 14, 438-439 (2003). [doi]
• Sato, T., Yamanishi, Y., Horimoto, K., Toh, H., and Kanehisa, M.; Prediction of protein-protein interactions from phylogenetic trees using partial correlation coefficient. Genome Informatics 14, 496-497 (2003). [doi]
• Minowa, Y., Katayama, T., Nakaya, A., Goto, S., and Kanehisa, M.; Classification of protein sequences into paralog and ortholog clusters using sequence similarity profiles of KEGG/SSDB. Genome Informatics 14, 528-530 (2003). [doi]
• Park, K.-J., Kanehisa, M., and Akiyama, Y.; PLOC: prediction of subcellular location of proteins. Genome Informatics 14, 559-560 (2003). [doi]
• Aoki, K.F., Yamaguchi, A., Okuno, Y., Akutsu, T., Ueda, N., Kanehisa, M., and Mamitsuka, H.; Statistical siginficance of tree similarity scores. Genome Informatics 14, 579-580 (2003). [doi]
• Igarashi, Y., Okuno, Y., Hattori, M., Goto, S., and Kanehisa, M.; Common features in substrates of multidrug resistance transporters. Genome Informatics 14, 601-602 (2003). [doi]
• Goto, N., Nakao, M.C., Kawashima, S., Katayama, T., and Kanehisa, M.; BioRuby: open-source bioinformatics library. Genome Informatics 14, 629-630 (2003). [doi]
• Hashimoto, K., Hamajima, M., Goto, S., Masumoto, S., Kawasima, M., and Kanehisa, M.; GLYCAN: the database of carbohydrate structures. Genome Informatics 14, 649-650 (2003). [doi]
• Sakiyama, T., Kawashima, S., Yoshizawa, A.C., and Kanehisa, M.; The construction of a database for ubiquitin signaling cascade. Genome Informatics 14, 653-654 (2003). [doi]
• Furumichi, M., Sato, Y., Katayama, T., Kawashima, S., and Kanehisa, M.; Development of community annotation databases for linking genomes to cellular functions. Genome Informatics 14, 657-658 (2003). [doi]
• Kawashima, S., Katayama, T., Sato, Y., and Kanehisa, M.; KEGG API: a web service using SOAP/WSDL to access the KEGG system. Genome Informatics 14, 673-674 (2003). [doi]
• Kanehisa, M.; Integration of bioinformatics and cheminformatics in KEGG. Genome Informatics 14, 715-716 (2003).

GIW 2002

• Katayama, T., Kawashima, S., Goto, N., Nakao, M.C., Okuji, Y.K., and Kanehisa, M.; BioRuby: object oriented open source library for bioinformatics. Genome Informatics 13, 248-249 (2002). [doi]
• Nakaya, A., Yoshizawa, A.C., Goto, S., and Kanehisa, M.; Indirect relations in yeast protein interactome. Genome Informatics 13, 328-329 (2002). [doi]
• Limviphuvadh, V., Goto, S., Tanaka, S., Ueda, K., and Kanehisa, M.; Searching for common protein networks in neurodegenerative disorders. Genome Informatics 13, 330-331 (2002). [doi]
• Itoh, M., Nakaya, A., and Kanehisa, M.; Identification of ortholog groups in KEGG/SSDB by considering domain structures. Genome Informatics 13, 342-343 (2002). [doi]
• Yamada, T., Yamanishi, Y., Goto, S., and Kanehisa, M.; Extraction of modules from the metabolic pathways with phylogenetic profile. Genome Informatics 13, 353-354 (2002). [doi]
• Okuno, Y., Hattori, M., Kotera, M., Igarashi, Y., Goto, S., and Kanehisa, M.; Vzyme: a template-based method to predict reactions between two chemical compounds. Genome Informatics 13, 355-356 (2002). [doi]
• Minowa, Y., Goto, S., and Kanehisa, M.; An analysis of cancer microarrays in the pathway context using Bayesian networks. Genome Informatics 13, 373-374 (2002). [doi]
• Katayama, T., Okamoto, S., Narikawa, R., Fujisawa, T., Kawashima, S., Itoh, M., Ohmori, M., and Kanehisa, M.; Comprehensive analysis of tandem repeat sequences in cyanobacteria genome. Genome Informatics 13, 400-401 (2002). [doi]
• Furumichi, M., Sato, Y., Omata, T., Ikeuchi, M., and Kanehisa, M.; CYORF: community annotation of cyanobacteria genes. Genome Informatics 13, 402-403 (2002). [doi]
• Yoshizawa, A.C., Kawashima, S., and Kanehisa, M.; Comparative analysis of Rab GTPases and SNAREs in eukaryotic genomes. Genome Informatics 13, 404-405 (2002). [doi]
• Fujita, M., Akutsu, T., Goto, S., and Kanehisa, M.; Weak homology detection by profile-profile comparison. Genome Informatics 13, 438-439 (2002). [doi]
• Yamada, R. and Kanehisa, M.; Bifurcation diagram analyzer for differential equations of biological models. Genome Informatics 13, 474-475 (2002). [doi]
• Kotera, M., Okuno, Y., Hattori, M., Goto, S., and Kanehisa, M.; Classification and analysis of KEGG/REACTION database. Genome Informatics 13, 490-491 (2002). [doi]
• Yamamoto, R., Komeno, T., Goto, S., Okuno, Y., Hattori, M., and Kanehisa, M.; Improvement of the LIGAND chemical database. Genome Informatics 13, 492-493 (2002). [doi]
• Igarashi, Y., Okuno, Y., Goto, S., and Kanehisa, M.; The construction and analysis of the multidrug resistance transporter knowledge-base. Genome Informatics 13, 494-495 (2002). [doi]
• Okuda, S., Kawashima, S., and Kanehisa, M.; Database of operons in Bacillus subtilis. Genome Informatics 13, 496-497 (2002). [doi]

GIW 2001

• Sato, Y., Nakaya, A., Shiraishi, K., Kawashima, S., Goto, S., and Kanehisa, M.; SSDB: sequence similarity database in KEGG. Genome Informatics 12, 230-231 (2001). [doi]
• Igarashi, Y., Okuno, Y., Vert, J.-P., and Kanehisa, M.; Detecting transcriptional cis-regulation from gene expression data. Genome Informatics 12, 241-242 (2001). [doi]
• Yoshizawa, A.C., Nakaya, A., Goto, S., and Kanehisa, M.; Extraction of related genes in the vesicular transport by simultaneous comparison of two-hybrid and microarray data. Genome Informatics 12, 243-244 (2001). [doi]
• Levchenko, M.E., Katayama, T., and Kanehisa, M.; Discovery and classification of peptide family G-protein coupled receptors in the human genome sequence. Genome Informatics 12, 352-353 (2001). [doi]
• Kawashima, S., Kawashima, T., Nakaya, A., Makabe, K.W., Goto, S., and Kanehisa, M.; Analysis of the maternal mRNAs encoding DNA-binding motifs in the ascidian egg using SSDB. Genome Informatics 12, 386-387 (2001). [doi]
• Itoh, M., Okuji, Y.K., Goto, S., Urushihara, H., Maeda, M., Tanaka, Y., and Kanehisa, M.; Analysis of Dictyostelium discoideum cDNA obtained from multicellular and unicellular stages. Genome Informatics 12, 400-401 (2001). [doi]

GIW 2000

• Goto, S., Kawashima, S., Okuji, Y., Kamiya, T., Miyazaki, S., Numata, Y., and Kanehisa, M.; KEGG/EXPRESSION: a database for browsing and analysing microarray expression data. Genome Informatics 11, 222-223 (2000). [doi]
• Nakao, M., Okuji, Y., and Kanehisa, M.; Quantitative estimation of cross-hybridization in DNA microarrays based on a linear model. Genome Informatics 11, 231-232 (2000). [doi]
• Okuji, Y., Hihara, Y., Kamei, A., Ikeuchi, M., Suzuki, I., Murata, N., and Kanehisa, M.; Gene expression analysis of orthologs in Synechocystis sp. with operons in Escherichia coli. Genome Informatics 11, 233-234 (2000). [doi]
• Uchiyama, I., Miwa, T., Nishide, H., Suzuki, I., Omata, T., Ikeuchi, M., Murata, N., and Kanehisa, M.; Data submission system for Cyanobacterial DNA Chip Consortium. Genome Informatics 11, 235-236 (2000). [doi]
• Katayama, T. and Kanehisa, M.; The role of gene expression regulation in yeast cell cycle pathway. Genome Informatics 11, 268-269 (2000). [doi]
• Nakaya, A., Goto, S., and Kanehisa, M.; Extraction of correlated gene clusters from multiple graph structures: theory. Genome Informatics 11, 270-271 (2000). [doi]
• Kawashima, S., Nakaya, A., Okuji, Y., Goto, S., and Kanehisa, M.; Extraction of correlated gene clusters from multiple graph structures: application. Genome Informatics 11, 272-273 (2000). [doi]
• Igarashi, Y., Kihara, D., and Kanehisa, M.; Classification and analysis of eukaryotic ABC transporters in complete eukarya genomes. Genome Informatics 11, 274-275 (2000). [doi]
• Yoshizawa, A.C., Kawashima, S., and Kanehisa, M.; The construction of a database on the intracellular vesicular transport. Genome Informatics 11, 276-277 (2000). [doi]

GIW 1999

• Goto, S., Shiraishi, K., Okamoto, K., Ishida, H., Nakatani, T., Deno, T., and Kanehisa, M.; Ortholog identifiers for integration of genomic and pathway information in KEGG. Genome Informatics 10, 204-205 (1999). [doi]
• Park, K.-J. and Kanehisa, M.; Prediction of nuclear localization signals by HMM. Genome Informatics 10, 261-262 (1999). [doi]
• Hattori, M. and Kanehisa, M.; Detection of apoptotic domains against KEGG database by the HMM search. Genome Informatics 10, 267-268 (1999). [doi]
• Kawashima, S., Kawashima, T., Nishida, H., Makabe, K.W., and Kanehisa, M.; MAGEST: ESTs and gene expression pattern database for Halocynthia roretzi maternal cDNA. Genome Informatics 10, 274-275 (1999). [doi]
• Sato, K.X., Goto, S., and Kanehisa, M.; Unit-based de novo drug design using a library of protein-ligand interaction sites. Genome Informatics 10, 320-321 (1999). [doi]

GIW 1998

• Goto, S., Shiraishi, K., Okamoto, K., Ishida, H., Asanuma, S., Bono, H., Ogata, H., Fujibuchi, W., and Kanehisa, M.; Constructing and annotating GENES database in KEGG. Genome Informatics 9, 226-227 (1998). [doi]
• Nakao, M., Sato, K., Kamiya, T., Kimura, Y., and Kanehisa, M.; Genome-scale gene expression profiles mapped onto the pathway and genome maps in KEGG. Genome Informatics 9, 230-231 (1998). [doi]
• Taniguchi, T. and Kanehisa, M.; Construction of ortholog/paralog group table for PTS. Genome Informatics 9, 296-297 (1998). [doi]
• Sato, K. and Kanehisa, M.; A Library of protein-ligand interaction sites for de novo ligand design. Genome Informatics 9, 298-299 (1998). [doi]
• Fujibuchi, W., Ogata, H., Matsuda, H., and Kanehisa, M.; Automatic detection of gene clusters by P-quasi complete linkage grouping. Genome Informatics 9, 300-301 (1998). [doi]
• Igarashi, Y. and Kanehisa, M.; The construction of the knowledge base of immune system. Genome Informatics 9, 302-303 (1998). [doi]
• Ogata, H., Fujibuchi, W., and Kanehisa, M.; Detection of co-regulated genes by comparative analysis of microbial genomes. Genome Informatics 9, 304-305 (1998). [doi]
• Kawashima, S., Ogata, H., and Kanehisa, M.; Extracting regulatory signals from the upstream region of co-expressed genes derived from DNA microarray experiments. Genome Informatics 9, 306-307 (1998). [doi]
• Takazawa, F., Sasai, M., Kanehisa, M.; Protein folding simulation and self-consistent potential functions. Genome Informatics 9, 308-309 (1998). [doi]

GIW 1997

• Bono, H., Goto, S., Ogata, H., and Kanehisa, M.; Genome scale prediction of two-component signal transducers from the knowledge of regulatory interactions. Genome Informatics 8, 260-261 (1997). [doi]
• Hattori, M. and Kanehisa, M.; The construction of the knowledge base on apoptotic molecular interactions. Genome Informatics 8, 276-277 (1997). [doi]
• Kawashima, S., Katayama, T., and Kanehisa, M.; Construction of molecular interaction database and searching for similar pathways. Genome Informatics 8, 298-299 (1997). [doi]
• Kihara, D. and Kanehisa, M.; Detection of membrane proteins in the whole genome sequences. Genome Informatics 8, 300-301 (1997). [doi]
• Nishioka, T., Goto, S., and Kanehisa, M.; Present status of LIGAND chemical database for enzyme reactions. Genome Informatics 8, 316-317 (1997). [doi]
• Sato, K., Katsurada, T., Kimura, Y., and Kanehisa, M.; Integrated GENES database in KEGG. Genome Informatics 8, 334-335 (1997). [doi]
• Suzuki, K. and Kanehisa, M.; Database and prediction of sequence motifs on protein molecular interactions. Genome Informatics 8, 344-345 (1997). [doi]
• Takazawa, F., Kanehisa, M., and Mitaku, S.; Analysis of amphiphilic periodicity of a-helices: detection of edges of helices and functional residues in proteins. Genome Informatics 8, 348-349 (1997). [doi]

GIW 1996

• Kihara, D., Shimizu, T., and Kanehisa, M.; A prediction method for transmembrane segments in proteins utilizing multiple discrimination functions. Genome Informatics 7, 244-245 (1996). [doi]
• Tomii, K. and Kanehisa, M.; A statistical analysis of gene arrangement patterns in bacterial and yeast genomes. Genome Informatics 7, 246-247 (1996). [doi]
• Goto, S., Fukushima, N., and Kanehisa, M.; Standard Gibbs free energy changes of enzyme reactions in metabolic pathway computation. Genome Informatics 7, 248-249 (1996). [doi]
• Fujibuchi, W., Goto, S., and Kanehisa, M.; Deductive calculation library for KEGG pathway simulation. Genome Informatics 7, 250-251 (1996). [doi]
• Bono, H., Ogata, H., Goto, S., and Kanehisa, M.; Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions. Genome Informatics 7, 252-253 (1996). [doi]
• Sato, K., Katsurada, T., Kamiya, T., Egoshi, M., and Kanehisa, M.; Java applets for handling genome maps in KEGG. Genome Informatics 7, 254-255 (1996). [doi]

GIW 1995

• Ogata, H., Fujibuchi, W., and Kanehisa, M.; Statistical features identified from comparison of homologous introns. Genome Informatics 6, 96-97 (1995). [doi]
• Fujibuchi, W. and Kanehisa, M.; Prediction of promoter expression specificity by conserved sequence patterns. Genome Informatics 6, 106-107 (1995). [doi]
• Uchiyama, I., Ogiwara, A., Takagi, T., and Kanehisa, M.; Protein Sequence Grouping by Peptide Word Motifs. Genome Informatics 6, 116-117 (1995). [doi]
• Suzuki, K., Akiyama, Y., and Kanehisa, M.; Multiple Sequence Alignment by Combining Incomplete Blocks of Similar Segments. Genome Informatics 6, 120-121 (1995). [doi]
• Fukushima, N. and Kanehisa, M.; A study of molecular recognition between DNA and metal ions. Genome Informatics 6, 136-137 (1995). [doi]
• Nishioka, T., Suyama, M., Goto, S., Akiyama, Y., and Kanehisa, M.; LIGAND chemical database for enzymatic reactions: A link between enzyme structures and chemical reactions. Genome Informatics 6, 138-139 (1995). [doi]
• Tomii, K. and Kanehisa, M.; AAindex: A database of amino acid indices and mutation matrices. Genome Informatics 6, 142-143 (1995). [doi]
• Tsukamoto, N. and Kanehisa, M.; A WWW tool for organizing knowledge of biomolecular reaction pathways. Genome Informatics 6, 158-159 (1995). [doi]
• Tateishi, N., Shiotari, H., Kuhara, S., Takagi, T., and Kanehisa, M.; An integrated database SPAD (Signaling PAthway Database) for signal transduction and genetic information. Genome Informatics 6, 160-161 (1995). [doi]

GIW 1994

• Suzuki, K., Goto, S., Akiyama, Y., and Kanehisa, M.; A signal transduction database. Genome Informatics 5, 144-145 (1994). [doi]
• Goto, S., Kuhara, S., Takagi, T., and Kanehisa, M.; Extension of the integrated database "HyperGenome" for genome maps and sequence information. Genome Informatics 5, 204-205 (1994). [doi]
• Ogiwara, A., Uchiyama, I., Takagi, T., and Kanehisa, M.; Further improvements on SMART: Sequence Motif Analysis and Retrieval Tool. Genome Informatics 5, 206-207 (1994). [doi]
• Oda, A., Yano, J., and Kanehisa, M.; A DNA/protein sequence retrieval system: an Xtpanel application. Genome Informatics 5, 220-221 (1994). [doi]
• Goto, S. and Kanehisa, M.; A knowledge base for searching and browsing metabolic pathways. Genome Informatics 5, 234-235 (1994). [doi]

GIW 1993 (oral)

• Araki, S., Goshima, M., Mori, S., Nakashima, H., Tomita, S., Akiyama, Y., and Kanehisa, M.; Application of parallelized DP and A* algorithm to multiple sequence alignment. Genome Informatics 4, 94-102 (1993). [doi]
• Ohkubo, Z. and Kanehisa, M.; A method for extracting spatially close peptide segments in proteins. Genome Informatics 4, 167-174 (1993). [doi]

GIW 1993

• Uchiyama, I., Ogiwara, A., Ohkubo, Z. and Kanehisa, M.; Automatic procedure to extract signature pentapeptides from the protein sequence database, Genome Informatics 4, 255-263 (1993). [doi]
• Ogata, H., Akiyama, Y. and Kanehisa, M.; A computer modeling method for the three-dimensional structure of RNA. Genome Informatics 4, 270-274 (1993). [doi]
• Fujibuchi, W. and Kanehisa, M.; Construction of a functional word dictionary for primate promoter sequences. Genome Informatics 4, 275-282 (1993). [doi]
• Suzuki, T., Nakashima, S., Takagi, T., Kuhara, S., and Kanehisa, M.; Enhancement of the integrated database "HyperGenome" for genome maps and sequence information. Genome Informatics 4, 362-369 (1993). [doi]
• Ogiwara, A., Uchiyama, I. and Kanehisa, M.; Sequence Motif Analysis and Retrieval Tool. Genome Informatics 4, 402-410 (1993). [doi]

GIW 1992 (oral)

• Seto, Y., Ikeuchi, Y., Kawakita, S., Nishikawa, K., and Kanehisa, M.; Trial to determine identity of proteins by motifs. Genome Informatics 3, 73-76 (1992). [doi]

GIW 1992

• Fujibuchi, W. and Kanehisa, M.; Integrated characterization of transcriptional upstream sequences by statistical consensus patterns and experimental data. Genome Informatics 3, 143-146 (1992). [doi]
• Ohkubo, Z. and Kanehisa, M.; A new method for finding packing patterns of protein C alpha segments. Genome Informatics 3, 163-166 (1992). [doi]
• Mizuno, M. and Kanehisa, M.; The distribution profiles of GC content surrounding the translation initiation site in different species. Genome Informatics 3, 183-186 (1992). [doi]
• Ogiwara, A., Uchiyama, I., Akiyama, Y., and Kanehisa, M.; Introduction to the GenomeNet. Genome Informatics 3, 191-194 (1992). [doi]
• Akiyama, Y. and Kanehisa, M.; NeuroFold: an RNA secondary structure prediction system using a Hopfield neural network. Genome Informatics 3, 199-202 (1992). [doi]
• Kuhara, S., Takagi, T., and Kanehisa, M.; HyperGenome: an integrated system for mapping data. Genome Informatics 3, 219-222 (1992). [doi]

GIW 1991 (oral)

• Ogiwara, A. and Kanehisa, M.: Wide-area network 'GenomeNet' and distributed genetic information processing. Genome Informatics 2, 20-23 (1991). [doi]
• Seto Y., Isoyama, M., Ikeuti, Y., Nishikawa, K., Kawakita, Y., and Kanehisa, M.; Fragment peptide library (FRAP) and analysis of motifs. Genome Informatics 2, 54-57 (1991). [doi]
• Ogiwara, A. and Kanehisa, M.; Automatic construcution of a dictionary of sequence motifs that characterize groups of similar proteins. Genome Informatics 2, 58-61 (1991). [doi]
• Ogiwara, A. and Kanehisa, M.; Automatic construcution of a dictionary of sequence motifs that characterize groups of similar proteins. Genome Informatics 2, 58-61 (1991). [doi]
• Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A., and Kanehisa, M.; Multiple alignment by parallel simulated annealing. Genome Informatics 2, 112-115 (1991). [doi]
• Matsuo, Y. and Kanehisa, M.; An approach to systematic detection of protein structural motifs. Genome Informatics 2, 154-157 (1991). [doi]