Life Science and Technology News

Labs spotlight #9 - Kotera Laboratory -

Massive omics data analysis using bioinformatics

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October 31, 2016

The Department has a variety of laboratories for Life Science and Technology, in which cutting-edge innovative research is being undertaken not only in basic science and engineering but also in the areas of medicine, pharmacy, agriculture, and multidisciplinary sciences.

This "Spotlight" series features a laboratory from the Department and introduces you to the laboratory's research projects and outcomes. This time we focus on Kotera Laboratory.

Associate Professor Masaaki Kotera

Life Science and Technology
Associate Professor Masaaki Koteraouter

Degree PhD 2004, Kyoto University
Areas of Research Bioinformatics, Cheminformatics
Keywords Metabolic pathway, enzymatic reaction, chemical ecology

Research interest

Omics studies are becoming increasingly important in life sciences to collect and analyze comprehensive biomolecular data. Information technologies are requisite to deal with the vast amount of omics data and to discover the underlying biological rules. To date, however, the challenging issue remains in integrating two kinds of omics, i.e., gene-related omics (genomics, transcriptomics and proteomics) and chemical-related omics (metabolomics and glycomics).

We focus on the analyses of biochemical interactions as the following two perspectives: (1) Integration of genomic and chemical information on metabolic pathways. Recent development of metabolomics studies unveiled the increasing number of chemical compound for which the metabolic pathways are not known yet. We research on the automated method to predict and analyze such metabolic pathways and to link the genomic information. (2) Integration of genomic and chemical information on inter-species interaction. The relationship between insects and edible plants is mediated by a variety of chemical compounds produced by the plants and the receptor proteins in the insects. We research on the fundamental infrastructure to computationally analyze such interactions in the view of systems biology.

Research findings

Selected publications

  1. 1.Yasuo Tabei, Yoshihiro Yamanishi, Masaaki Kotera. Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction., Oxford Journals, Vol. 32, No. 12, pp. i278-i287, Jun. 2016.
  2. 2.Yuki Moriya, Takuji Yamada, Shujiro Okuda, Masaaki Kotera, Zenichi Nakagawa, Toshiaki Tokimatsu, Susumu Goto, Minoru Kanehisa. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs, Journal of Chemical Information and Modeling, Vol. 56, No. 3, pp. 510-516, Feb. 2016.
  3. 3.Iwata Hiroaki, Sawada Ryusuke, Mizutani Sayaka, Kotera Masaaki, Yamanishi Yoshihiro. Large-Scale Prediction of Beneficial Drug Combinations Using Drug Efficacy and Target Profiles, Journal of Chemical Information and Modeling, Vol. 55, No. 12, pp. 2705-2716, Dec. 2015.
  4. 4.Yoshihiro Yamanishi, Yasuo Tabei, Masaaki Kotera. Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments, Bioinformatics, Vol. 31, No. 12, pp. i161-i170, Jun. 2015.
  5. 5.Masaaki Kotera, Yosuke Nishimura, Zen-ichi Nakagawa, Ai Muto, Yuki Moriya, Shinobu Okamoto, Shuichi Kawashima, Toshiaki Katayama, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto. PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB Enzyme List, J Bioinform Comput Biol.12(6):1442001, Dec. 2014.
  6. 6.Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach, Bioinformatics, Vol. 30, No. 12, pp. i165-174, Jun. 2014.
  7. 7.Zhao Jin, Masaaki Kotera, Susumu Goto. Virus proteins similar to human proteins as possible disturbance on human pathways., Syst Synth Biol, Vol. 8, No. 4, pp. 283-295, May. 2014.
  8. 8.Masaaki Kotera. Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction., The 24th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2016), 2016.
  9. 9.Masaaki Kotera. Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments, 23rd Annual International Conference on Intelligent Systems for Molecular Biology, Jun. 2015.
  10. 10.Masaaki Kotera. PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB Enzyme List, GIW / ISCB-Asia 2014, Nov. 2014.
  11. 11.Masaaki Kotera. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach, The 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2014), Jun. 2014.
  12. 12.Masaaki Kotera, Susumu Goto. Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis, Biophysics and Physicobiology, Vol. 13, 195-205, Jul. 2016.
  13. 13.Ryusuke Sawada, Masaaki Kotera, Yoshihiro Yamanishi. Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach., Molecular Informatics, Vol. 33, No. 11-12, pp. 719-731, Nov. 2014.

Contact

Associate Professor Masaaki Kotera
Room 202A, M6 building, Ookayama campus
E-mail : maskot@bio.titech.ac.jp

*Please contact the laboratory for more information.

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