Faculty Information, Institute for Chemical Research, Kyoto University   [ English | Japanese ]


GOTO, Susumu

Bioinformatics Center - Chemical Life Science -
(Laboratory in the Science / Pharmaceutical Sciences)
Associate Professor
D. Eng
URL:http://goto.kuicr.kyoto-u.ac.jp/
E-mail: goto@kuicr.kyoto-u.ac.jp
Tel: 0774-38-3271
Fax: 0774-38-3269

Academic career
    1994.3 Graduated from Dr. Course, Kyushu University
    1994.3 D. Eng., Kyushu University
    1994.4-1999.9 Research Associate, Kyoto University
    1999.10- Associate Professor, Kyoto University
Research field
    Bioinformatics
Current research
  1. Development of a database for chemical compounds and reactions in biological pathways
  2. Development of a database for link information among databases
  3. Prediction of molecular interaction and functional association networks
  4. Development of a database of antigenic variations for the elucidation of their evolutionary and functional mechanisms
Selected publications
  1. Shimizu, Y.; Ogata, H.; Goto, S., Type III polyketide synthases: functional classification and phylogenomics Chembiochem in press, (2016)  [pubmed]
  2. Kotera, M.; Goto, S., Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis Biophysics and Physicobiology 13, 195-205 (2016)
  3. 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.; Ishihama, Y., jPOSTrepo: an international standard data repository for proteomes Nucleic Acids Res. in press, (2016)
  4. Takami, H.; Taniguchi, T.; Arai, W.; Takemoto, K.; Moriya, Y.; Goto, S., An automated system for evaluation of the potential functionome: MAPLE version 2.1.0 DNA Res. 23, 467-475 (2016)  [pubmed]
  5. Mihara, T.; Nishimura, Y.; Shimizu, Y.; Nishiyama, H.; Yoshikawa, G.; Uehara, H.; Hingamp, P.; Goto, S.; Ogata, H., Linking virus genomes with host taxonomy Viruses 8, 66 (2016)  [pubmed]
  6. Moriya, Y.; Yamada, T.; Okuda, S.; Nakagawa, Z.; Kotera, M.; Tokimatsu, T.; Kanehisa, M.; Goto, S., Identification of enzyme genes using chemical structure alignments of substrate-product pairs J Chem. Inf. Model. 56, 510-516 (2016)  [pubmed]
  7. Suzuki, M.; Nakabayashi, R.; Ogata, Y.; Sakurai, N.; Tokimatsu, T.; Goto, S.; Suzuki, M.; Jasinski, M.; Martinoia, E.; Otagaki, S.; Matsumoto, S.; Saito, K.; 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]
  8. Kotera, M.; Nishimura, Y.; Nakagawa, Z.; Muto, A.; Moriya, Y.; Okamoto, S.; Kawashima, S.; Katayama, T.; Tokimatsu, T.; Kanehisa, M.; 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]
  9. Jin, Z.; Kotera, M.; Goto, S., Virus proteins similar to human proteins as possible disturbance on human pathways Syst. Synth. Biol. 8, 283-295 (2014)  [pubmed]
  10. Yamanishi, Y.; Kotera, M.; Moriya, Y.; Sawada, R.; Kanehisa, M.; Goto, S., DINIES: Drug-Target Interaction Network Inference Engine Based on Supervised Analysis Nucleic Acids Res. 42, W39-W45 (2014)  [pubmed]
  11. Kotera, M.; Tabei, Y.; Yamanishi, Y.; Muto, A.; Moriya, Y.; Tokimatsu, T.; Goto, S., Metabolome-Scale Prediction of Intermediate Compounds in Multistep Metabolic Pathways with a Recursive Supervised Approach Bioinformatics 30, i165-i174 (2014)  [pubmed]
  12. Mizutani, S.; Noro, Y.; Kotera, M.; Goto, S. , Pharmacoepidemiological Characterization of Drug-Induced Adverse Reaction Clusters towards Understanding of Their Mechanisms Comput. Biol. Chem. 50, 50-59 (2014)  [pubmed]
  13. Ingale, A. G.; 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]
  14. Kanehisa, M.; Goto, S.; Sato, Y.; Kawashima, M.; Furumichi, M.; Tanabe, M., Data, Information, Knowledge and Principle: Back to Metabolism in KEGG Nucleic Acids Res. 42, D199-D205 (2014)  [pubmed]
  15. Kotera, M.; Tabei, Y.; Yamanishi, Y.; Moriya, Y.; Tokimatsu, T.; Kanehisa, M.; Goto, S., KCF-S: KEGG Chemical Function and Substructure for Improved Interpretability and Prediction in Chemical Bioinformatics BMC Syst. Biol. 7, S2 (2013)  [pubmed]
  16. Iwata, H.; Mizutani, S.; Tabei, Y.; Kotera, M.; Goto, S.; Yamanishi, Y., Inferring Protein Domains Associated with Drug Side Effects Based on Drug-Target Interaction Network. BMC Syst. Biol. 7, S18 (2013)  [pubmed]
  17. Kotera M, Tabei Y, Yamanishi Y, Tokimatsu T, Goto S., Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. Bioinformatics 29, i135-44 (2013)  [pubmed]
  18. Muto A, Kotera M, Tokimatsu T, Nakagawa Z, Goto S, Kanehisa M., Modular Architecture of Metabolic Pathways Revealed by Conserved Sequences of Reactions. J Chem Inf Model 53, 613-22 (2013)  [pubmed]
  19. Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S., KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res 41, D353-7 (2013)  [pubmed]
  20. Takami H, Taniguchi T, Moriya Y, Kuwahara T, Kanehisa M, Goto S., Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics 13, 699 (2012)  [pubmed]
  21. Kotera M, Yamanishi Y, Moriya Y, Kanehisa M, Goto S., GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res 40, W162-7 (2012)  [pubmed]
  22. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M., KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40, D109-14 (2012)  [pubmed]
  23. Kotera M, Tokimatsu T, Kanehisa M, Goto S., MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. BMC Bioinformatics 12 Suppl 14, S1 (2011)  [pubmed]
  24. Diez D, Hayes N, Joannin N, Normark J, Kanehisa M, Wahlgren M, Wheelock CE, Goto S., varDB: a database of antigenic variant sequences--current status and future prospects. Acta Trop 114, 144-51 (2010)  [pubmed]
  25. Hattori M, Tanaka N, Kanehisa M, Goto S., SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res 38, W652-6 (2010)  [pubmed]
  26. Yamanishi Y, Kotera M, Kanehisa M, Goto S., Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics 26, i246-54 (2010)  [pubmed]
  27. Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggstrom JZ, Goto S., Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol Biosyst 5, 588-602 (2009).  [pubmed]
  28. Hayes CN, Diez D, Joannin N, Honda W, Kanehisa M, Wahlgren M, Wheelock CE, Goto S., varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 24, 2564-5 (2008)  [pubmed]
  29. Gutteridge A, Kanehisa M, Goto S., Regulation of metabolic networks by small molecule metabolites. BMC Bioinformatics 8, 88 (2007)  [pubmed]
  30. Okuda S, Kawashima S, Kobayashi K, Ogasawara N, Kanehisa M, Goto S., Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics 8, 48 (2007)  [pubmed]
  31. Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S., EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 34, W459-62 (2006)  [pubmed]
  32. Yamada T, Kanehisa M, Goto S., Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics 7, 130 (2006).  [pubmed]
  33. Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M, LIGAND: database of chemical compounds and reactions in biological pathways Nucleic Acids Res 30, 402-404 (2002).  [pubmed]
  34. Kanehisa M, Goto S., KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28, 27-30 (2000).  [pubmed]
  35. Goto S, Nishioka T, Kanehisa M., LIGAND: chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998).  [pubmed]
  36. Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M., Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput 2, 175-86 (1997).  [pubmed]


Update: Nov 28,2016