[ English | Japanese ]

Masaaki KOTERA

Assistant Professor, Ph.D. Science.
Bioknowledge Systems Laboratory (Minoru Kanehisa Laboratory)

Research Interests

Enzyme reactions, drug metabolism, xenobiotic degradation, phytochemical compounds, comparative genomics, microarray analysis, playing GO and drinking whiskey.

Related Webprograms

Brief Biography

  • Ph.D.Science (Kyoto University), 2005 (H17) Mar 23
  • Class I Information Technology Engineer, 1997 (H9) Jul 08
  • Class II Information Technology Engineer, 1996 (H8) Jun 06

Journal Publications

  1. Characterization and Classification of Adverse Drug Interactions.
    Masataka Takarabe, Daichi Shigemizu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa. Genome Informatics 2009, Vol 22, 167-175. [Genome Informatics 2009]

  2. E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
    Yoshihiro Yamanishi, Masahiro Hattori, Masaaki Kotera, Susumu Goto, Minoru Kanehisa. Bioinformatics 2009 June 15; 25(12): i179-i186. [PMID:2687977] (Cited by 4 articles)

  3. Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites.
    Masaaki Kotera, Andrew G. McDonald, Sinéad Boyce, Keith F. Tipton. J. Chem. Inf. Model. 2008, 48(12):2335-2349. [PMID: 19053521] (Cited by 5 articles)

  4. Functional Group and Substructure Searching as a Tool in Metabolomics.
    Masaaki Kotera, Andrew G. McDonald, Sinéad Boyce, Keith F. Tipton. PLoS ONE 2008, 3(2): e1537. doi:10.1371 / journal.pone.0001537. [PMID: 18253485] (Cited by 3 articles)

  5. Maize Phosphoenolpyruvate Carboxylase. Mutations at the Putative Binding Site for Glucose 6-phosphate Caused Desensitization and Abolished Responsiveness to Regulatory Phosphorylation.
    Akiko Takahashi-Terada, Masaaki Kotera, Kenta Ohshima, Tsuyoshi Furumoto, Hiroyoshi Matsumura, Yasushi Kai, Katsura Izui. J. Biol. Chem. 2005, 280, 11798-11806. [PMID: 15665330] (Cited by 14 articles)

  6. Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
    Masaaki Kotera, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Minoru Kanehisa. J. Am. Chem. Soc. 2004, 126, 16487-16498. [PMID: 15600352] (Cited by 53 articles)

Book Chapter

  1. Chemoinformatics on metabolic pathways: attaching biochemical information on putative enzymatic reactions.
    Masahiro Hattori and Masaaki Kotera. In "Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques" (Editors: Huma Lodhi and Yoshihiro Yamanishi), in press.

Proceedings

  1. Reclassification of oxidoreductase subclasses based on the relationships of reductants and oxidants.
    Masaaki Kotera, Toshiaki Tokimatsu, Zen-ichi Nakagawa, Yuki Moriya, Masahiro Hattori, Susumu Goto and Minoru Kanehisa. Genome Informatics, 2009, P124. [Genome Informatics 2009]

  2. Structural clustering of plant secondary metabolite to estimate compound classes reflecting their biosynthetic pathway.
    Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Shigehiko Kanaya and Minoru Kanehisa. Genome Informatics, 2009, P127. [Genome Informatics 2009]

  3. Chemical continuity of reaction centers along successive metabolic reactions.
    Masahiro Hattori, Masaaki Kotera, Ai Muto, Susumu Goto and Minoru Kanehisa. Genome Informatics, 2009, P135. [Genome Informatics 2009]

  4. Comprehensive analysis of polyketide synthase families.
    Yugo Shimizu, Masaaki Kotera, Toshiaki Tokimatsu, Masahiro Hattori, Susumu Goto and Minoru Kanehisa. Genome Informatics, 2009, P022. [Genome Informatics 2009]

  5. Analysis of plant UGT family sequences and substrate specificity.
    Yosuke Nishimura, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto and Minoru Kanehisa. Genome Informatics, 2009, P027. [Genome Informatics 2009]

  6. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions.
    Masaaki Kotera, Masahiro Hattori, Min-A Oh, Rumiko Yamamoto, Tomoko Komeno, Junko Yabuzaki, Koichiro Tonomura, Susumu Goto, Minoru Kanehisa. Genome Informatics, 2004, 15, P062. [Genome Informatics 2004] (Cited by 7 articles)

  7. Analysis of Reactive Modules in the Metabolic Pathways.
    Masaaki Kotera, Masahiro Hattori, Susumu Goto, Minoru Kanehisa. Genome Informatics, 2003, 14, 366-367. [Genome Informatics 2003]

  8. Vzyme: a Template-Based Method to Predict Reactions between Two Chemical Compounds.
    Yasushi Okuno, Masahiro Hattori, Masaaki Kotera, Yoshinobu Igarashi, Susumu Goto, Minoru Kanehisa. Genome Informatics, 2002, 13, 355-356. [Genome Informatics 2002] (Cited by 3 articles)

  9. Classification and analysis of KEGG/REACTION database.
    Masaaki Kotera, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Minoru Kanehisa. Genome Informatics, 2002, 13, 490-491. [Genome Informatics 2002] (Cited by 4 articles)

Talks

  1. E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
    Yoshihiro Yamanishi, Masahiro Hattori, Masaaki Kotera, Susumu Goto, Minoru Kanehisa.
    17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology in Stockholm, Sweden, 2009 [ISMB ECCB 2009].

  2. [The title and presentation in Japanese]
    Susumu Goto, Masahiro Hattori, Toshiaki Tokimatsu, Masaaki Kotera, Yuki Moriya, Zen-ichi Nakagawa, Minoru Kanehisa. Biochemistry and Molecular Biology (BMB), Kobe, 2008.

  3. Substructure searching and tracing as a tool in metabolomics.
    Masaaki Kotera. Chemical Annotation Workshop, Kyoto, Japan, 2007.

  4. Systematic Classification of Enzymatic Reactions and Its Application to Analysis of Ortholog Candidates.
    Masaaki Kotera. International Workshop of Bioinformatics and Systems Biology, Dresden, Germany, 2003. [IBSB 2003]

Posters

  1. Prediction of reactant pairs from enzyme reaction formula.
    Masaaki Kotera, Masahiro Hattori, Toshiaki Tokimatsu, Zen-ichi Nakagawa, Susumu Goto and Minoru Kanehisa. The 32nd Annual Meeting of the Molecular Biology Society of Japan, Yokohama, Japan, 2009.

  2. Reclassification of oxidoreductase subclasses based on the relationships of reductants and oxidants.
    Masaaki Kotera, Toshiaki Tokimatsu, Zen-ichi Nakagawa, Yuki Moriya, Masahiro Hattori, Susumu Goto and Minoru Kanehisa. The 20th International Conference on Genome Informatics, Yokohama, Japan, 2009.

  3. Chemical continuity of reaction centers along successive metabolic reactions.
    Masahiro Hattori, Masaaki Kotera, Ai Muto, Susumu Goto and Minoru Kanehisa. The 20th International Conference on Genome Informatics, Yokohama, Japan, 2009.

  4. Structural clustering of plant secondary metabolite to estimate compound classes reflecting their biosynthetic pathway.
    Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Shigehiko Kanaya and Minoru Kanehisa. The 20th International Conference on Genome Informatics, Yokohama, Japan, 2009.

  5. Comprehensive analysis of polyketide synthase families.
    Yugo Shimizu, Masaaki Kotera, Toshiaki Tokimatsu, Masahiro Hattori, Susumu Goto and Minoru Kanehisa. The 20th International Conference on Genome Informatics, Yokohama, Japan, 2009.

  6. Analysis of plant UGT family sequences and substrate specificity.
    Yosuke Nishimura, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto and Minoru Kanehisa. The 20th International Conference on Genome Informatics, Yokohama, Japan, 2009.

  7. GenomeNet Chemical Compound Database and Tools for Metabolomics Research.
    Toshiaki Tokimatsu, Masahiro Hattori, Masaaki Kotera, Yuki Moriya, Zen-ichi Nakagawa, Susumu Goto and Minoru Kanehisa. The 4th Metabolome Symposium, Yokohama, Japan, Nov18-19, 2009.

  8. Structural clustering of secondary metabolites based on their substructures.
    Masaaki Kotera, Toshiaki Tokimatsu, Susumu Goto and Minoru Kanehisa. The 9th Annual International Workshop on Bioinformatics and Systems Biology, Boston, USA, Jul27-29, 2009. [IBSB2009]

  9. Estimating the connectivity in secondary metabolite groups based on the structural clustering.
    Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto and Minoru Kanehisa. The 9th Annual International Workshop on Bioinformatics and Systems Biology, Boston, USA, Jul27-29, 2009. [IBSB2009]

  10. Analysis of conserved pattern in enzymatic reactions and its application to EC prediction.
    Masahiro Hattori, Masaaki Kotera, Susumu Goto and Minoru Kanehisa. The 9th Annual International Workshop on Bioinformatics and Systems Biology, Boston, USA, Jul27-29, 2009. [IBSB2009]

  11. Co-occurrence Analysis in Differentially Expressed Genes in Adenoma Using Frequent Itemset Mining.
    Sayaka Mizutani, Wataru Honda, Masaaki Kotera, Hiroshi Mamitsuka and Minoru Kanehisa. Annual Conference of the Japanese Society for Bioinformatics (JSBi), Osaka, Japan, Dec15-56, 2008. [JSBi2008]

  12. Computational characterization of enzyme-specific substrate substructures.
    Masaaki Kotera, Andrew G. McDonald, Sinéad Boyce, Keith F. Tipton. Bioinformatics Research and Development 2007, Berlin, Germany. [BIRD2007]

  13. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions.
    Masaaki Kotera, Masahiro Hattori, Min-A Oh, Rumiko Yamamoto, Tomoko Komeno, Junko Yabuzaki, Koichiro Tonomura, Susumu Goto, Minoru Kanehisa. The 15th International Conference on Genome Informatics, Yokohama, Japan, 2004. [GIW 2004]

  14. [The title and presentation in Japanese]
    Masaaki Kotera, Masahiro Hattori, Susumu Goto, Minoru Kanehisa. Annual Conference of the Molecular Biology Society of Japan, Kobe, 2004.

  15. Analysis of Reactive Modules in the Metabolic Pathways.
    Masaaki Kotera, Masahiro Hattori, Susumu Goto, Minoru Kanehisa. The 14th International Conference on Genome Informatics, Yokohama, Japan, 2003. [GIW 2003]

  16. Vzyme: a Template-Based Method to Predict Reactions between Two Chemical Compounds.
    Yasushi Okuno, Masahiro Hattori, Masaaki Kotera, Yoshinobu Igarashi, Susumu Goto, Minoru Kanehisa. The 13th International Conference on Genome Informatics, Yokohama, Japan, 2002. [GIW 2002]

  17. Classification and analysis of KEGG/REACTION database.
    Masaaki Kotera, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Minoru Kanehisa. The 13th International Conference on Genome Informatics, Yokohama, Japan, 2002. [GIW 2002]

  18. [The title and presentation in Japanese]
    Yasushi Okuno, Masahiro Hattori, Masaaki Kotera, Susumu Goto, Minoru Kanehisa. Annual Conference of the Molecular Biology Society of Japan, Yohohama, 2002.

  19. [The title and presentation in Japanese]
    Masaaki Kotera, Masahiro Hattori, Yasushi Okuno, Susumu Goto, Minoru Kanehisa. Annual Conference of the Molecular Biology Society of Japan, Yohohama, 2002.

Reports

  1. Classification of pharmacological and side effects of drugs based on the package insert.
    Masaaki Kotera. Kyoto University Super Computer Laboratory Annual Report, 2009, 44-47. [PDF]

  2. Development of Classification Algorithm for Enzymatic Reactions and Its Application to Genomic-Scale Analyses.
    Masaaki Kotera. Kyoto University Super Computer Laboratory Annual Report, 2005, 74-75. [Abstract]

  3. Analysis of the Reaction Classification and the EC number.
    Masaaki Kotera. Kyoto University Super Computer Laboratory Annual Report, 2004, 79-81. [Abstract]

  4. General Description and Systematic Classification of Enzymatic Reactions.
    Masaaki Kotera. Kyoto University Super Computer Laboratory Annual Report, 2003, 74. [Abstract]

Lectures

  1. Medicinal Information (KEGG DRUG, JAPIC) + KegDraw.
    Masaaki Kotera. KEGG/GenomeNet Database Tutorials, Human Genome Center, University of Tokyo, Feb 4-5, 2010.

  2. Metabolic Network Analysis.
    Masaaki Kotera. Joint Bioinformatics Education Program, Kyoto University and University of Tokyo, Nov10, 2009.

  3. Medicinal Information (KEGG DRUG, JAPIC, KegDraw).
    Masaaki Kotera. KEGG/GenomeNet Database Tutorials, Human Genome Center, University of Tokyo, Jan29-30, 2009.

Education and Carrer

2008 (H20) Aug 01 - : Assistant Professor, Ph.D.
Bioknowledge Systems Laboratory (Minoru Kanehisa Laboratory),
2005 (H17) Apr 01 - 2008 (H20) Jul 31: Ph.D. Research Fellow
Laboratory of Neurochemistry, Enzymology and Systems Biology (Keith Tipton Laboratory),
School of Biochemistry and Immunology, Faculty of Engineering, Mathematics and Science, Trinity College Dublin, IRELAND.
2004 (H16) Apr 01 - 2005 (H17) Mar 31:Associate Instructor
Bioknowledge Systems Laboratory (Minoru Kanehisa Laboratory),
Bioinformatics Centre, Institute for Chemical Research, Kyoto University.
2001 (H13) Apr 01 - 2004 (H16) Mar 31: Graduate student (Ph.D course)
Bioknowledge Systems Laboratory (Minoru Kanehisa Laboratory),
Department of Biophysics, Division of Biological Science, Graduate School of Science, Kyoto University.
1999 (H11) Apr 01 - 2001 (H13) Mar 31: Graduate student (Master course)
Laboratory of Plant Physiology (Katsura Izui Laboratory),
Department of Responses to Environmental Signals and Stresses, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University.
1995 (H7) Apr 01 - 1999 (H11) Mar 31:Undergraduate student
Graduation thesis in: Bio-Organic Chemistry Laboratory (Hitoshi Tamiaki Laboratory),
Department of Bioscience and Biotechnology, Section of Applied Chemistry, The Institute of Science and Engineering, Ritsumeikan University.