Kanehisa Laboratories

List of ISMB/ECCB/GIW/IBSB Oral Presentations

GIW 2011

• Kotera, M., Tokimatsu, T., Kanehisa, M., and Goto, S.; MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. GIW 2011, Busan.

IBSB 2011

• Moriya, Y., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; Application of the PathPred metabolic pathway prediction tool to finding enzyme genes in A. thaliana secondary metabolism. IBSB 2011, Berlin.
• Muto, A., Kotera, M., Tokimatsu, T., Nakagawa, Z., Goto, S., and Kanehisa, M.; Extraction of Tandem Reaction Patterns from Metabolic Pathways. IBSB 2011, Berlin.

IBSB 2010

• Erguner, B., Hattori, M., Goto, S., and Kanehisa, M.; Characterizing Common Substructures of Ligands for GPCR Protein Subfamilies. IBSB 2010, Kyoto.
• Kotera, M., Kobayashi, T., Hattori, M., Tokimatsu, T., Goto, S., Mihara, H., and Kanehisa, M.; Comprehensive Genomic Analysis of Sulfur-relay Pathway Genes. IBSB 2010, Kyoto.
• Mizutani, S., Tanaka, M., Wheelock, C.E., Kanehisa, M., and Goto, S.; Phylogenetic Analysis of Lipid Mediator GPCRs. IBSB 2010, Kyoto.
• Nishimura, Y., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; Genome-wide Analysis of Plant UGT Family Based on Sequence and Substrate Information. IBSB 2010, Kyoto.
• 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. IBSB 2010, Kyoto.

ISMB 2010

• Yamanishi, Y., Kotera, M., Kanehisa, M., and Goto, S.; Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. ISMB 2010, Boston.

GIW 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. GIW 2009, Yokohama. [pdf]

IBSB 2009

• Onuki, R., Shibuya, T., and Kanehisa, M.; New kernel methods for phenotype prediction from genotype data. IBSB 2009, Boston. [pdf]
• Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., and Kanehisa, M.; Characterization and classification of adverse drug interactions. IBSB 2009, Boston. [pdf]
• Tanaka, M., Moriya, Y., Goto, S., and Kanehisa, M.; Analysis of a lipid biosynthesis protein family and phospholipid structural variations. IBSB 2009, Boston. [pdf]

ISMB/ECCB 2009

• 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. ISMB/ECCB 2009, Stockholm. [pdf]

IBSB 2008

• Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.; Generalized reaction patterns for prediction of unknown enzymatic reactions. IBSB 2008, Berlin. [pdf]
• Takarabe, M., Okuda, S., Itoh, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; Network analysis of adverse drug interactions. IBSB 2008, Berlin. [pdf]

ISMB 2008

• Hashimoto, K., Takigawa, I., Shiga, M., Kanehisa, M., and Mamitsuka, H.; Mining significant tree patterns in carbohydrate sugar chains. ISMB 2008, Toronto. [pdf]
• 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. ISMB 2008, Toronto. [pdf]

GIW 2007

• Huang, J., Honda, W., and Kanehisa, M.; Predicting B cell epitope residues with network topology based amino acid indices. GIW 2007, Singapore. [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. GIW 2007, Singapore. [pdf]

IBSB 2007

• Huang, J., Kawashima, S., and Kanehisa, M.; New amino acid indices based on residue network topology. IBSB 2007, Tokyo. [pdf]
• Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.; An improved scoring scheme for predicting glycan structures from gene expressison data. IBSB 2007, Tokyo. [pdf]
• Muto, A., Hattori, M., and Kanehisa, M.; Analysis of common substructures of metabolic compounds within the different organism groups. IBSB 2007, Tokyo. [pdf]

IBSB 2006

• Hashimoto, K., Yoshizawa, A.C., Saito, K., Yamada, T., and Kanehisa, M.; The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes. IBSB 2006, Boston. [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Metabolite antigens and pathway incompatibility. IBSB 2006, Boston. [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. IBSB 2006, Boston. [pdf]

ISMB 2006

• Aoki-Kinoshita, K., Ueda, N., Mamitsuka, H., and Kanehisa, M.; ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. ISMB 2006, Fortaleza, Brazil. [pdf]
• Nacher, J., Schwartz, J.-M., Kanehisa, M., and Akutsu, T.; Identification of metabolic units induced by environmental signals. ISMB 2006, Fortaleza, Brazil. [pdf]

ECCB 2005

• Schwartz, J.M. and Kanehisa, M.; A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. ECCB 2005, Madrid. [pdf]

IBSB 2005

• Okuda, S., Kawashima, S., Goto, S., and Kanehisa, M.; Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli. IBSB 2005, Berlin. [pdf]
• Yamada, T., Kawashima, S., Mamitsuka, H., Goto, S., and Kanehisa, M.; Comprehensive analysis and prediction of synthetic lethality using subcellular locations. IBSB 2005, Berlin. [pdf]
• Fujita, M. and Kanehisa, M.; Comparative analysis of DNA-binding proteins between thermophilic and mesophilic bacteria. IBSB 2005, Berlin. [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. IBSB 2005, Berlin. [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Autoimmune diseases and peptide variations. IBSB 2005, Berlin. [pdf]

ISMB 2005

• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Supervised enzyme network inference from the integration of genomic data and chemical information. ISMB 2005, Detroit. [pdf]

GIW 2004

• Nikitin, F., Rance, B., Itoh, M., Kanehisa, M., and Lisacek, F.; Using protein motif combinations to update KEGG pathway maps and orthologue tables. GIW 2004, Yokohama. [pdf]

ISMB 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. ISMB 2004, Glasgow. [pdf]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Protein network inference from multiple genomic data: a supervised approach. ISMB 2004, Glasgow. [pdf]

IBSB 2004

• Hizukuri, Y., Yamanishi, Y., Hashimoto, K., and Kanehisa, M.; Extraction of species-specific glycan substructures. IBSB 2004, Kyoto. [pdf]
• Itoh, M., Akutsu, T., and Kanehisa, M.; Clustering of database sequences for fast homology search using upper bounds on alignment score. ISMB 2004, Glasgow. [pdf]
• Yamada, T., Goto, S., and Kanehisa, M.; Extraction of phylogenetic network modules from prokayrote metabolic pathways. ISMB 2004, Glasgow

GIW 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. GIW 2003, Yokohama. [pdf]
• Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M.; Heuristics for chemical compound matching. GIW 2003, Yokohama. [pdf]

ECCB 2003

• Vert, J.-P. and Kanehisa, M.; Extracting active pathways from gene expression data. ECCB 2003, Paris. [pdf]

ISMB 2003

• 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. ISMB 2003, Brisbane. [pdf]

GIW 2002

• Yamanishi, Y., Itoh, M., and Kanehisa, M.; Extraction of organism groups from phylogenetic profiles using independent component analysis. GIW 2002, Yokohama. [pdf]

GIW 2001

• Nakaya, A., Goto, S., and Kanehisa, M.; Extraction of correlated gene clusters by multiple graph comparison. GIW 2001, Yokohama. [pdf]

GIW 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. GIW 1999, Yokohama. [pdf]

GIW 1998

• Bono, H., Goto, S., Fujibuchi, W., Ogata, H., and Kanehisa, M.; Systematic prediction of orthologous units of genes in the complete genomes. GIW 1998, Yokohama. [pdf]

PSB 1998

• Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an Integrated Database Retrieval System. PSB 1998, Hawaii. [pdf]

PSB 1997

• 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. PSB 1997, Hawaii. [pdf]

GIW 1996

• Ogata, H., Bono, H., Fujibuchi, W., Goto, S., and Kanehisa, M.; Analysis of binary relations and hierarchies of enzymes in the metabolic pathways. GIW 1996, Yokohama. [pdf]

GIW 1994

• Mizuno, M. and Kanehisa, M.; Distribution of base composition around the splice sites in different species. GIW 1994, Yokohama.