Publication List

Papers Reviews Posters

Research Papers (Peer Reviewed)

  1. 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]

  2. Nishimura, Y., Yoshida, T., Kuronishi, M., Uehara, H., Ogata, H. and Goto, S.;
    ViPTree: the viral proteomic tree server.
    Bioinformatics, in press (2017). [PubMed]

  3. Shimizu, Y., Ogata, H. and Goto, S.;
    Discriminating the reaction types of plant type III polyketide synthases.
    Bioinformatics, 33:1937-1943 (2017). [PubMed]

  4. Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., Sullivan, M. B., Goto, S., Ogata, H. and Yoshida, T.;
    Environmental viral genomes shed new light on virus-host interactions in the ocean.
    mSphere 2:e00359-16 (2017). [PubMed]

  5. Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S. and Ishihama, Y.;
    jPOSTrepo: an international standard data repository for proteomes.
    Nucleic Acids Res. 45:D1107-D1111 (2017). [PubMed]

  6. Takami, H., Taniguchi, T., Arai, W., Takemoto, K., Moriya, Y. and Goto, S.;
    An automated system for evaluation of the potential functionome: MAPLE version 2.1.0.
    DNA Res. 23:467-475 (2016). [PubMed]

  7. Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S. and Ogata, H.;
    Linking virus genomes with host taxonomy.
    Viruses 8:66 (2016). [PubMed]

  8. 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]

  9. Suzuki, M., Nakabayashi, R., Ogata, Y., Sakurai, N., Tokimatsu, T., Goto, S., Suzuki, M., Jasinski, M., Martinoia, E., Otagaki, S., Matsumoto, S., Saito, K. and Shiratake, K.;
    Multi omics in grape berry skin revealed specific induction of stilbene synthetic pathway by UV-C irradiation.
    Plant Physiol. 168:47-59 (2015). [PubMed] [Plant Physiology]

  10. 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]

  11. Jin, Z., Kotera, M. and Goto, S.;
    Virus proteins similar to human proteins as possible disturbance on human pathways.
    Syst. Synth. Biol. 8:283-295 (2014). [PubMed]

  12. 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]

  13. Kotera, M., Tabei, Y., Yamanishi, Y., Muto, A., Moriya, Y., Tokimatsu, T. and Goto, S.;
    Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach.
    Bioinformatics 30:i165-i174 (2014). [PubMed]

  14. Mizutani, S., Noro, Y., Kotera, M. and Goto, S.;
    Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms.
    Comput. Biol. Chem. 50:50-59 (2014). [PubMed]

  15. Ingale, A. G. and Goto, S.;
    Prediction of CTL epitope, in silico modeling and functional analysis of cytolethal distending toxin (CDT) protein of Campylobacter jejuni.
    BMC Res. Notes 7:92 (2014). [PubMed]

  16. 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]

  17. 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(S6):S2 (2013). [PubMed]

  18. Iwata, H., Mizutani, S., Tabei, Y., Kotera, M., Goto, S. and Yamanishi, Y.;
    Inferring protein domains associated with drug side effects based on drug-target interaction network.
    BMC Syst. Biol. 7(S6):S18 (2013). [PubMed]

  19. Kotera, M., Tabei, Y., Yamanishi, Y., Tokimatsu, T. and Goto, S.;
    Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets.
    Bioinformatics 29:i135-i144 (2013). [PubMed] [PDF]

  20. Kirwan, G. M., Hancock, T., Hassell, K., Niere, J. O., Nugegoda, D., Goto, S. and Adams, M. J.;
    Nuclear magnetic resonance metabonomic profiling using tO2PLS.
    Anal. Chim. Acta 781:33-40 (2013). [PubMed]

  21. 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]

  22. 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] [PDF]

  23. Frost, K., Johansson, E., Shanks, R., Goto, S. and Kirwan, G. M.;
    Thermoplastic starch films: DOE and O2PLS methodology for optimization and increased understanding of polymer processing.
    Polymer Testing 32:343-352 (2013). [DOI]

  24. Takami, H., Taniguchi, T., Moriya, Y., Kuwahara, T., Kanehisa, M. and Goto, S.;
    Evaluation method for the potential functionome harbored in the genome and metagenome.
    BMC Genomics 13:699 (2012). [PubMed] [BMC]

  25. Godel, C., Kumar, S., Koutsovoulos, G., Ludin, P., Nilsson, D., Comandatore, F., Wrobel, N., Thompson, M., Schmid, C. D., Goto, S., Bringaud, F., Wolstenholme, A., Bandi, C., Epe, C., Kaminsky, R., Blaxter, M. and Mäser, P.;
    The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets.
    FASEB J. 26:4650-4661 (2012). [PubMed]

  26. Kirwan, G. M., Johansson, E., Kleemann, R., Verheij, E. R., Wheelock, A. M., Goto, S., Trygg, J. and Wheelock, C. E.;
    Building multivariate systems biology models.
    Anal. Chem. 84:7064-7071 (2012). [PubMed]

  27. Mizutani, S., Pauwels, E., Stoven, V., Goto, S. and Yamanishi, Y.;
    Relating drug-protein interaction network with drug side-effects.
    Bioinformatics 28:i522-i528 (2012). [PubMed]

  28. Takarabe, M., Kotera, M., Nishimura, Y., Goto, S. and Yamanishi, Y.;
    Drug target prediction using adversed event report systems: a pharmacogenomic approach.
    Bioinformatics 28:i611-i618 (2012). [PubMed]

  29. Diez, D., Goto, S., Fahy, J. V., Erle, D. J., Woodruff, P. G., Wheelock, A. M. and Wheelock, C. E.;
    Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics.
    BMC Med. Genomics 5:27 (2012). [PubMed] [BMC]

  30. 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] [PDF]

  31. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M.;
    KEGG for integration and interpretation of large-scale molecular data sets.
    Nucleic Acids Res. 40:D109-114 (2012). [PubMed] [PDF]

  32. 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:S1 (2011). [PubMed]

  33. 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]

  34. Tamura, T., Yamanishi, Y., Tanabe, M., Goto, S., Kanehisa, M., Horimoto, K. and Akutsu, T.;
    Integer programming-based method for computing signaling pathways and its application to colorecal cancer.
    Genome Informatics 24:193-203 (2010). [PubMed]

  35. Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Ruebenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Le Novère, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. and Bader, G. D.;
    The BioPAX community standard for pathway data sharing.
    Nat. Biotechnol. 28:935-942 (2010). [PubMed]

  36. 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]

  37. Mizutani, S., Tanaka, M., Wheelock, C. E., Kanehisa, M. and Goto, S.;
    Phylogenetic analysis of lipid mediator GPCRs.
    Genome Informatics 24:116-126 (2010). [PubMed]

  38. 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]

  39. Erguner, B., Hattori, M., Goto, S. and Kanehisa, M.;
    Characterizing common substructures of ligands for GPCR protein subfamilies.
    Genome Informatics 24:31-40 (2010). [PubMed]

  40. 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]

  41. 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]

  42. 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]

  43. 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]

  44. 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]

  45. 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]

  46. 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]

  47. Folkersen, L., Diez, D., Wheelock, C. E., Haeggstrom, J. Z., Goto, S., Eriksson, P. and Gabrielsen, A.;
    GeneRegionScan: a Bioconductor package for probe level analysis of specific, small regions of the genome.
    Bioinformatics 25:1978-1979 (2009). [PubMed]

  48. 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:i179-i186 (2009). [PubMed]

  49. 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]

  50. 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]

  51. 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]

  52. 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]

  53. 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]

  54. 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]

  55. Wheelock, C. E., Forshed, J., Goto, S., Hammock, B. and Newman, J.;
    Effects of pyridine exposure upon structural lipid metabolism in Swiss Webster mice.
    Chem. Res. Toxicol. 21:583-590 (2008). [PubMed]

  56. 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]

  57. 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]

  58. 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]

  59. Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S. and Kanehisa, M.;
    An improved scoring scheme for predicting glycan structures from gene expression data.
    Genome Informatics 18:237-246 (2007). [PubMed]

  60. Wheelock, C. E., Goto, S., Hammock, B. D. and Newman, J. W.;
    Clofibrate-induced changes in the liver, heart, brain and white adipose lipid metabolome of Swiss-Webster mice.
    Metabolomics 3:137-145 (2007). [PubMed]

  61. Fujita, M., Mihara, M., 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]

  62. Itoh, M., Nacher, J. C., Kuma, K., Goto, S. and Kanehisa, M.;
    Evolutionary history and functional implication of protein domains and their combinations in eukaryotes.
    Genome Biology 8:R121 (2007). [PubMed]

  63. 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]

  64. 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]

  65. Masoudi-Nejad, A., Goto, S., Jauregui, R., Ito, M., Kawashima, S., Moriya, Y., Endo, T. and Kanehisa, M.;
    EGENES: Transcriptome-based plant database of genes with metabolic pathway information and EST indices in KEGG.
    Plant Physiol. 44:857-866 (2007). [PubMed]

  66. 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 Journal 274:2262-2273 (2007). [PubMed]

  67. Gutteridge, A., Kanehisa, M. and Goto, S.;
    Regulation of metabolic networks by small molecule metabolites.
    BMC Bioinformatics 8:88 (2007). [PubMed]

  68. 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]

  69. 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]

  70. 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]

  71. Azuma, Y., Hirakawa, H., Yamashita, A., Cai, Y., Rahman, M. A., Suzuki, H., Mitaku, S., Toh, H., Goto, S., Murakami, T., Sugi, K., Hayashi, H., Fukushi, H., Hattori, M., Kuhara, S. and Shirai, M.;
    Genome sequence of the cat pathogen, Chlamydophila felis.
    DNA Res. 13:15-23 (2006). [PubMed]

  72. Yamada, T., Kanehisa, M. and Goto, S.;
    Extraction of phylogenetic network modules from the metabolic network.
    BMC Bioinformatics 7:130 (2006). [PubMed]

  73. Wheelock, A. M., Morin, D., Goto, S. and Buckpitt, A. R.;
    Sources of variance in gel-based quantitative proteomics studies.
    Proc. SIPZOO: From Genome to Proteome in Animal Science 40:74-90 (2006).

  74. 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-D357 (2006). [PubMed]

  75. 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]

  76. 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]

  77. 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]

  78. 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]

  79. 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):140-158 (2005). [PubMed]

  80. Hashimoto, K., Kawano, S., Goto, S., Aoki-Kinoshita, K. F., 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]

  81. 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]

  82. Itoh, M., Goto, S., Akutsu, T. and Kanehisa, M.;
    Fast and accurate database homology search using upper bounds of local alignment.
    Bioinformatics 21:912-921 (2005). [PubMed]

  83. 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).

  84. 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]

  85. 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]

  86. Yamada, T., Goto, S. and Kanehisa, M.;
    Extraction of phylogenetic network modules from prokaryote metabolic pathways.
    Genome Informatics 15(1):249-259 (2004). [PubMed]

  87. 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]

  88. Hattori, M., Okuno, Y., Goto, S. and Kanehisa, M.;
    Heuristics for chemical compound matching.
    Genome Informatics 14:144-153 (2003). [PubMed]

  89. 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]

  90. Kanehisa, M., Goto, S., Kawashima, S. and Nakaya, A.;
    The KEGG databases at GenomeNet.
    Nucleic Acids Res. 30:42-46 (2002). [PubMed]

  91. 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]

  92. 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]

  93. Nakaya, A., Goto, S. and Kanehisa, M.;
    Extraction of correlated gene clusters by multiple graph comparison.
    Genome Informatics 12:44-53 (2001). [PubMed]

  94. 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]

  95. 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]

  96. Kanehisa, M. and Goto, S.;
    KEGG: Kyoto Encyclopedia of Genes and Genomes.
    Nucleic Acids Res. 28:27-30 (2000). [PubMed]

  97. Goto, S., Nishioka, T. and Kanehisa, M.;
    LIGAND: chemical database of enzyme reactions.
    Nucleic Acids Res. 28:380-382 (2000). [PubMed]

  98. Nakao, M., Bono, H., Kawashima, S., Sato, K., Goto, S. and Kanehisa, M;
    Genome-scale gene expression analysis and pathway reconstruction in KEGG.
    Genome Informatics 10:94-103 (1999). [PubMed]

  99. 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]

  100. Goto, S., Nishioka, T. and Kanehisa, M.;
    LIGAND: chemical database for enzyme reactions.
    Nucleic Acids Res. 27:377-379 (1999). [PubMed]

  101. Goto, S., Nishioka, T. and Kanehisa, M.;
    LIGAND: chemical database for enzyme reactions.
    Bioinformatics 14:591-599 (1998). [PubMed]

  102. 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]

  103. Ogata, H., Goto, S., Fujibuchi, W. and Kanehisa, M.;
    Computation with the KEGG pathway database.
    BioSystems 47:119-128 (1998). [PubMed]

  104. Bono, H., Goto, S., Fujibuchi, W., Ogata, H. and Kanehisa, M.;
    Systematic prediction of orthologous units of genes in the complete genomes.
    Genome Informatics 1998 pp. 32-40 (1998). [PubMed]

  105. 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).

  106. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y. and Kanehisa, M.;
    DBGET/LinkDB: an Integrated Database Retrieval System.
    Pacific Symp. Biocomputing 3:683-694 (1997). [PubMed]

  107. 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 Symp. Biocomputing 2:75-186 (1996). [PubMed] [pdf]

  108. 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 1996 pp. 128-136 (1996). [GIW96014] [pdf]

  109. Sakamoto, N., Goto, S. and Takagi, T.;
    A Deductive Database System for Analyzing Human Nucleotide Sequence Data.
    Int. J. Biomed. Comput. 36:171-179 (1994). [PubMed]

  110. Goto, S., Sakamoto, N., Takagi, T. and Ushijima, K.;
    A Deductive Language in Object-Oriented Database for Genome Analysis.
    Proc. Int. Symp. Next Generation Database Systems and Their Applications pp. 123-129 (1993).

  111. Goto, S., Sakamoto, N. and Takagi, T.;
    Object-Oriented Database with Rule-Based Query Interface for Genomic Computation.
    Proc. 3rd Int. Symp. Database Systems for Advanced Applications pp. 65-72 (1993).

  112. Takagi, T., Suzuki, T., Goto, S. and Ushijima, K.;
    Applicability of a Deductive Database to CAD Systems.
    Proc. Suppl. 7th Int. Conf. Data Engineering pp. 51-58 (1991).
Papers Reviews Posters

Review Articles (peer reviewed) and Book Chapters

  1. Shimizu, Y., Ogata, H. and Goto, S.;
    Type III polyketide synthases: functional classification and phylogenomics.
    ChemBioChem 18:50-65 (2017). [PubMed] [ChemBioChem]

  2. Kotera, M. and Goto, S.;
    Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis.
    Biophysics and Physicobiology 13:195-205 (2016). [J-STAGE]

  3. Kotera, M., Goto, S. and Kanehisa, M.;
    Predictive genomic and metabolic analysis for the standardization of enzyme data.
    Perspectives in Science 1:24-32 (2014). [ScienceDirect]

  4. 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). [SpringerReference]

  5. 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.
    Methods Mol. Biol. 802:19-39 (2012). [PubMed]

  6. Kirwan, G. M., Diez, D., Haeggstrom, J. Z., Goto, S. and Wheelock, C. E.;
    Systems biology approaches for investigating the relationships between lipids and cardiovascular disease.
    Curr. Cardiovasc. Risk Rep. 5:52-61 (2011). [Springer]

  7. 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., Hawkins, T., Luban, S., Li, B., Ramani, K. and Agrawal, M., eds), pp. 271-288, Springer (2011). [Springer]

  8. Diez, D., Hayes, C. 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. 114:144-151 (2010). [PubMed]

  9. Diez, D., Wheelock, A. M., Goto, S., Haeggstrom, J. Z., Paulsson-Berne, G., Hansson, G. K., Hedin, U., Gabrielsen, A. and Wheelock, C. E.;
    The use of network analyses for elucidating mechanisms in cardiovascular disease.
    Mol. Biosyst. 6:289-304 (2010). [PubMed]

  10. Wheelock, C. E., Goto, S., Yetukuri, L., D'Alexandri, F. L., Klukas, C., Schreiber, F. and Orešič, M.;
    Bioinformatics strategies for the analysis of lipids.
    Methods Mol. Biol. 580:339-368 (2009). [PubMed]

  11. 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 tools for investigating cardiovascular disease.
    Mol. Biosyst. 5:588-602 (2009). [PubMed]

  12. Masoudi-Nejad, A., Goto, S., Endo, T. R. and Kanehisa, M.;
    KEGG bioinformatics resource for plant genomics research.
    Methods Mol. Biol. 406:437-458 (2007). [PubMed]

  13. Hayes, C. N., Wheelock, A. M., Normark, J., Wahlgren, M., Goto, S. and Wheelock, C. E.;
    Enlistment of omics technologies in the fight against malaria: Panacea or Pandra's Box?
    J. Pestic. Sci. 31:263-272 (2006).

  14. Kadowaki, T., Wheelock, C. E., Hattori, M. Goto, S. and Kanehisa, M.;
    Strucutre-activity relationships and pathway analysis of biological degradation processes.
    J. Pestic. Sci. 31:273-281 (2006).

  15. 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]

  16. Wheelock, A. M. and Goto, S.;
    Effects of post-electrophoretic analysis on variance in gel-based proteomics.
    Expert Rev. Proteomics. 3:129-142 (2006). [PubMed]

  17. Futaki, S., Goto, S. and Sugiura, Y.;
    Membrane permeability commonly shared among arginine-rich peptides.
    J. Mol. Regognit. 16:260-264 (2003). [PubMed]

  18. Futaki, S., Goto, S., Suzuki, T., Nakase, I. and Sugiura, Y.;
    Structural variety of membrane permeable peptides.
    Curr. Protein and Pept. Sci. 4:87-96 (2003). [PubMed]

  19. 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).

  20. 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 Press (1997).
Papers Reviews Posters

Symposium, Workshop and Seminar Presentations

  1. *Moriya, Y., Kawano, S., Watanabe, Y., Okuda, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S. and Ishihama, Y.;
    jPOST: Current status in 2016.
    HUPO 15th Annual World Congress (HUPO 2016), Taipei, Taiwan, 18-21 September 2016.

  2. *Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S. and Ishihama, Y.;
    jPOST: repository opened.
    HUPO 15th Annual World Congress (HUPO 2016), Taipei, Taiwan, 18-21 September 2016.

  3. *Yoshizawa, A. C., Tabata, T., Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Sugiyama, N., Goto, S. and Ishihama, Y.;
    jPOST: Re-analysis Protocol.
    HUPO 15th Annual World Congress (HUPO 2016), Taipei, Taiwan, 18-21 September 2016.

  4. Mihara, T., Nishimura, Y., Nishiyama, H., Goto, S. and *Ogata, H.;
    Virus-Host Database: A manually curated resource for viral host prediction.
    8th Aquatic Virus Workshop, Plymouth, UK, 10-13 July 2016.

  5. *Nishimura, Y., Watai, H., Roux, S., Hingamp, P., Sako, Y., Sullivan, M. B., Goto, S., Ogata, H. and Yoshida, T.;
    Metagenomic whole genomes of marine DNA viruses.
    8th Aquatic Virus Workshop, Plymouth, UK, 10-13 July 2016.

  6. *Ishihama, Y., Tabata, T., Sugiyama, N., Goto, S., Araki, N., Matsumoto, M., Okuda, S. and Kawano, S.;
    Proteomics data analysis workflow for accumulated LCMS files in public database.
    HUPO 14th Annual World Congress (HUPO 2015), Vancouver, Canada, 27-30 September 2015.

  7. *Kawano, S., Moriya, Y., Okuda, S., Yamamoto, T., Matsumoto, M., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S. and Ishihama, Y.;
    jPOST: Development of Japan ProteOme STandard repository/database.
    HUPO 14th Annual World Congress (HUPO 2015), Vancouver, Canada, 27-30 September 2015.

  8. *Shiratake, K., Suzuki, M., Nakabayashi, R., Ogata, Y., Sakurai, N., Tokimatsu, T., Goto, S. and Saito, K.;
    Update of the KEGG database and the KaPPA-View 4 KEGG system of grape and multi-omics study of grape berry skin.
    The 2nd Plant Genomics Congress: Asia, Kuala Lumpur, Malaysia, 19-20 March 2015.

  9. *Goto, S.;
    KEGG for functional annotation of metagenomes.
    International Symposium for Frontier of Bioinformatics, Tokyo, Japan, 16 April 2015.

  10. *Goto, S.;
    Annotation and comparison of genome and metagenome data: an application of functionome evalutator MAPLE.
    IGS Seminar, Marseille, France, 29 January 2015.

  11. *Goto, S.;
    KEGG, OSD, metagenome BLAST.
    MicroB3 WP6 meeting, Marseille, France, 28-29 January 2015.

  12. *Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M. and Goto, S.;
    DINIES: A web-based application for predicting drug-target interaction networks.
    APBC 2015, HsinChu, Taiwan, 21-23 January 2015.

  13. *Taniguchi, T., Kato, Y., Goto, S. and Fujibuchi, W.;
    Development of a pipeline for meta- and single genome sequence analysis.
    GIW / ISCB-Asia 2014, Tokyo, Japan, 15-17 December 2014.

  14. *Arai, W., Taniguchi, T., Moriya, Y., Goto, S. and Takami, H.;
    MAPLE system for evaluation of metabolic and physiological potential harbored in gneome and metagenome.
    15th International Symposium on Microbial Ecology, Seol, South-Korea, 24-29 August 2014.

  15. *Takami, H., Taniguchi, T., Arai, W., Moriya, Y., Goto, S.;
    Metabolic and physiological potential evaluator (MAPLE) to characterize comprehensive functions harbored by an individual organism or an entire microbial community.
    EMBO Conference on Microbiology after the genomics evolution: Genomes 2014, Paris, France, 24-27 June 2014.

Poster Presentations before 2007

  1. Küntzer, J., Lenhof, H.-P., Goto, S. and Kanehisa, M.;
    Network analysis using the biochemical network library.
    IBSB 2007 P001 (2007).

  2. 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).

  3. 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).

  4. Gutteridge, A., Kanehisa, M. and Goto, S.;
    Regulation of metabolic networks by small molecule metabolites.
    GIW 2006 Poster Abstracts P014 (2006).

  5. 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).

  6. 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).

  7. 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).

  8. Oh, M., Hattori, M., Yamada, T., Goto, S. and Kanehisa M.;
    Analysis of characteristic biochemical transformation patterns in metabolic pathways.
    IBSB 2006 Boston (2006).

  9. 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).

  10. 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).

  11. 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).

  12. Oh, M., Hattori, M., Goto, S. and Kanehisa, M.;
    Characteristic chemical transformation patterns in biodegradation pathways.
    GIW 2005 Poster Abstracts P167 (2005).

  13. Itoh, M., Goto, S. and Kanehisa, M.;
    Phylogenetic analysis of domain combinations in eukaryotic genomes.
    IBSB 2005 Poster Abstracts P7 (2005).

  14. Ota, K., Goto, S. and Kanehisa, M.;
    Comparative analysis of conditional regulation across the yeast genomes.
    GIW 2004 Poster Abstracts P033 (2004).

  15. 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).

  16. 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).

  17. 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).

  18. 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).

  19. 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).

  20. 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).

  21. 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).

  22. Igarashi, Y., Kawano, S., Goto, S. and Kanehisa, M.;
    Comparative genome analysis of glycan transporters.
    IBSB 2004 Poster Abstracts 18-19 (2004).

  23. 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).

  24. Ota, K., Goto, S. and Kanehisa, M.;
    Comparative analysis of transcriptional regulation in eukaryotic cell cycles.
    IBSB 2004 Poster Abstracts 26-27 (2004).

  25. 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).

  26. 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).

  27. Tanaka, N., Goto, S. and Kanehisa, M.;
    ChemRuby: an open source library for integrating bioinformatics and cheminformatics.
    IBSB 2004 Poster Abstracts 65-66 (2004).

  28. 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).

  29. 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).

  30. 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).

  31. Kotera, M., Hattori, M., Goto, S. and Kanehisa, M.;
    Analysis of reactive modules in the metabolic pathways.
    Genome Informatics 14:366-367 (2003).

  32. 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).

  33. 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).

  34. 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).

  35. 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 14:528-529 (2003).

  36. 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).

  37. 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).

  38. Nakaya, A., Yoshizawa, A.C., Goto, S. and Kanehisa, M.;
    Indirect relations in yeast protein interactome.
    Genome Informatics 13:328-329 (2002).

  39. 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).

  40. 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).

  41. 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 13:355-35 (2002).

  42. 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).

  43. Fujita, M., Akutsu, T., Goto, S. and Kanehisa, M.;
    Weak homology detection by profile-profile comparison.
    Genome Informatics 13:438-439 (2002).

  44. Kotera, M., Okuno, Y., Hattori, M., Goto, S. and Kanehisa, M.;
    Classification and analysis of KEGG/REACTION database.
    Genome Informatics 13:490-491 (2002).

  45. 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).

  46. 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).

  47. 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).

  48. 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).

  49. 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).

  50. 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).

  51. 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).

  52. Nakaya, A., Goto, S. and Kanehisa, M.;
    Extraction of correlated gene clusters from multiple graph structures: Theory.
    Genome Informatics 11:270-271 (2000).

  53. 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).

  54. Goto, S., Shiraishi, K., Okamoto, K., Ishida, H., Nakatani, T., Deno, T. and Kanehisa, M.;
    Ortholog Identifier for Integration of Genomic and Pathway Information in KEGG.
    Genome Informatics 1999 pp.204-205 (1999).

  55. Sato, K. X., Goto, S. and Kanehisa, M.;
    Unit-Based de novo Drug Design Using a Library of Protein-Ligand Interaction Sites.
    Genome Informatics 1999 pp.320-321 (1999).

  56. 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 1998 pp.226-227 (1998).

  57. 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 1997 pp.260-261 (1997).

  58. Nishioka, T., Goto, S. and Kanehisa, M.;
    Present Status of LIGAND Chemical Database for Enzyme Reactions.
    Genome Informatics 1997 pp.316-317 (1997).

  59. Goto, S., Fukushima, N. and Kanehisa, M.;
    Standard Gibbs free energy changes of enzyme reactions in metabolic pathway computation.
    Genome Informatics 1996 pp.248-249 (1996).

  60. Fujibuchi, W., Goto, S. and Kanehisa, M.;
    Deductive calculation library for KEGG pathway simulation.
    Genome Informatics 1996 pp.250-251 (1996).

  61. Bono, H., Ogata, H., Goto, S. and Kanehisa, M.;
    Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions.
    Genome Informatics 1996 pp.252-253 (1996).

  62. 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 Workshop 1995 pp.138-139 (1995).

  63. Akiyama, Y., Goto, S., Uchiyama, I. and Kanehisa, M.;
    WebDBGET: an integrated database retrieval system which provides hyper-links among related entries.
    MIMBD'95: Second Meeting on the Interconnection of Molecular Biology Databases (1995). [pdf] [ps]

  64. Goto, S., Akiyama, Y. and Kanehisa, M.;
    LinkDB: a database of cross links between molecular biology databases.
    MIMBD'95: Second Meeting on the Interconnection of Molecular Biology Databases (1995). [pdf] [ps]

  65. Suzuki, K., Goto, S., Akiyama, Y. and Kanehisa, M.;
    A Signal Transduction Database.
    Genome Informatics Workshop 1994 pp.144-145 (1994).

  66. Goto, S., Kuhara, S., Takagi, T. and Kanehisa, M.;
    Extension of the Integrated Database ``HyperGenome'' for Genome Maps and Sequence Information.
    Genome Informatics Workshop 1994 pp.204-205 (1994).

  67. Goto, S. and Kanehisa, M.;
    A Knowledge Base for Searching and Browsing Metabolic Pathways.
    Genome Informatics Workshop 1994 pp.234-235 (1994).

  68. Goto, S., Sakamoto, N. and Takagi, T.;
    Integration of Genome Databases Using a Deductive Object-Oriented Database.
    Genome Informatics IV pp.352-361 (1993).

  69. Goto, S., Sakamoto, N. and Takagi, T.;
    Object-Oriented Database with Logical Query Interface for Genomic Computation.
    Genome Informatics III pp.223-226 (1992).
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Last updated: June 25, 2017