English

【NAME】

Michihiro Araki

Ph.D. (Pharmaceutical Sciences, Kyoto University)

【HISTORY】

2017.4 ~ present

Professor, Graduate School of Medicine, Kyoto University

Visiting Professor, Graduate School of Science, Technology and Innovation, Kobe University

2013.3 ~ 2017.3

Organization of Science and Technology, Kobe University (Prof. Akihiko Kondo)

Associate Professor

2008.9 ~ 2013.2

Graduate School of Pharmaceutical Sciences, Kyoto University

Associate Professor

2003.11 ~ 2008.8

Human Genome Center, The University of Tokyo (Prof. Minoru Kanehisa)

Assistant Professor

2001.4 ~ 2003.10

Department of Biomedical Engineering, Boston University (Prof. James J. Collins)

Research Associate

1996.4 ~ 2001.3

Institute for Chemical Research, Kyoto University (Prof. Yukio Sugiura)

Graduate Student, JSPS fellow

【RESEARCH】

  • Computational design of an artificial metabolic pathway: M-path
  • Web server for designing metabolic pathway: M-path Server
  • Designed metabolic pathway database:M-path DB
  • Metabolic pathway editor:PathPod

【INTERESTS】

  • Clinical genome informatics
  • Synthetic biology/Metabolic engineering
  • Bioinformatics/Chemoinformatics

【PUBLICATIONS】Google Scholar

  1. Hara, K.Y., Kobayashi, J., Yamada, R., Sasaki, D., Kuriya, Y., Hara, Y.H., Ishii, J., Araki, M., Kondo, A. “Transporter Engineering in Biomass Utilization by Yeast” FEMS Yeast Research fox061 (2017).
  2. Vavricka, C.J., Muto, C., Hasunuma, T., Kimura, Y., Araki, M., Wu, Y., Gao, G.F., Ohrui, H., Izumi, M. and Kiyota, H. “Synthesis of Sulfo-Sialic Acid Analogues: Potent Neuraminidase Inhibitors in Regards to Anomeric Functionality” Scientific Reports, 7:8239 (2017).
  3. Hsu, HH., Araki, M., Mochizuki, M., Hori, Y., Murata, M., Kahar, P., Yoshida, T., Hasunuma, T. and Kondo A. “A Systematic Approach to Time-series Metabolite Profiling and RNA-seq Analysis of Chinese Hamster Ovary Cell Culture” Scientific Reports, 7:43518 (2017).
  4. Hsu, H.H., Hasunuma, T., Araki, M., Yoshida, T., Hori, Y., Murata, M., Kondo, A. “Application of LC-MS/MS analysis for time-lapse amino acid metabolomics analysis in CHO cell culture” Shimadzu Journal, 5 (1), 17-21 (2017).
  5. Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, KY., Shimatani, Z. and Kondo, A. “Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems” Science (2016).
  6. Hara, K.Y., Aoki, N., Kobayashi, J., Kiriyama, K., Nishida, K., Araki, M., Kondo, A. “Improvement of oxidized glutathione fermentation by thiol redox metabolism engineering in Saccharomyces cerevisiaeAppl. Microbiol. Biotechnol. 99: 9771-9778 (2015).
  7. Ye, X., Morikawa, K., Ho, SH., Nishida, K., Araki, M., Hasunuma, T., Hara, K.Y., Kondo, A. "Evaluation of genes involved in oxidative phosphorylation in yeast by developing a simple and rapid method to measure mitochondrial ATP synthetic activity " Microbial Cell Factories, 14 (1), 56.
  8. *Araki, M., Cox III, RS., Makiguchi, H., Ogawa, T., Taniguchi, T., Miyaoku, K., Nakatsui M., Hara, KY., Kondo, A. "M-path: A Compass for Navigating Potential Metabolic Pathways" Bioinformatics, 31(6) 905-911 (2015).
  9. Hara, K.Y., Morita, K., Mochizuki, M., Yamamoto, K., Ogino, C., Araki, M., Kondo, A. “Development of a multi-gene expression system in Xanthophyllomyces dendrorhousMicrobial Cell Factories, 13: 175 (2014).
  10. Hara, K.Y., Araki, M., Okai, N., Wakai, S., Hasunuma, T., Kondo, A. “Development of bio-based fine chemical production through synthetic bioengineering” Microbial Cell Factories, 13: 173 (2014).
  11. Hara, K.Y., Morita, K., Endo, Y., Mochizuki, M., Araki, M., Kondo, A. “Evaluation and screening of efficient promoters to improve astaxanthin production inXanthophyllomyces dendrorhousAppl. Microbiol. Biotechnol. 98: 6787-6793 (2014).
  12. Nakatsui, M., *Araki, M., *Kondo, A.,“An Approach for Dynamical Network Reconstruction of Simple Network Motifs” BMC Systems Biology, 7(Suppl 6), S4 (2013).
  13. Araki, M., Taniguchi, T., Miyaoku, K., Makiguchi H., “A Computational Platform for Designing Natural Products" INCOB2012, P66 (2012.10 Bangkok, Thailand).
  14. Adachi, K., Fukumorita, K., Araki, M., Zaima, N., Yang, Z-H., Chiba, S., Kishimura, H., Saeki, H. “Transcriptome analysis of the Duodenum, Pancreas, Liver, and Muscle from Diabetic Goto-Kakizaki Rats Fed a Trypsin Inhibitor Derived from Squid Viscera” Journal of Agricultural and Food Chemistry. 60, 5540-5546 (2012).
  15. Araki, M., Taniguchi, T., Miyaoku, K., “A Computational Method for Exploring Extensive Biosynthetic Pathways" Metabolic Engineering IX, P46 (2012.6 Biarritz, France).
  16. Adachi, K., Fukumorita, K., Araki, M., Zaima, N., Chiba, S., Kishimura, H., Saeki, H. “Transcriptome analysis of the duodenum in Wistar rats fed a trypsin inhibitor derived from squid viscera.” Journal of Agricultural and Food Chemistry. 59, 9001-9010 (2011).
  17. Doi, M., Ishida, A., Miyake, A., Sato, M., Komatsu, R., Yamazaki, F., Kimura, I., Tsuchiya, S., Kori, H., Seo, K., Yamaguchi, Y., Matsuo, M., Fustin. J. M., Tanaka, R., Santo, Y., Yamada, H., Takahashi, Y., Araki, M., Nakao, K., Aizawa, S., Kobayashi, M., Obrietan, K., Tsujimoto, G., Okamura, H. “Circadian regulation of intracellular G- protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus.” Nature Communications. 2, 327 (2011).
  18. Feng, C., Araki, M., Kunimoto, R., Tamon, A., Makiguchi, A., Niijima, S., Tsujimoto, G., Okuno, Y., “A Web Tool for Expression Pattern-Based Data Retrieval and Relevant Network Discovery from vast Public Microarray Database” Genome Informatics Workshop(GIW) 2009, P056, Yokohama (2009).
  19. Feng, C., Araki, M., Kunimoto, R., Tamon, A., Makiguchi, H., Niijima, S., Tsujimoto, G., Okuno, Y., “GEM-TREND: a web tool for gene expression data mining toward relevant network discovery”, BMC Genomics, 10, 411 (2009).
  20. Shigemizu, D., Araki, M., Okuda, S., Goto, S., Kanehisa, M. “Extraction and analysis of chemical modification patterns in drug development”, Journal of Chemical Information and Modeling, 49 (4), 1122-1129 (2009).
  21. Shigemizu, D., Araki, M., Okuda, S., Goto, S., Kanehisa, M., “Analysis of Chemical Modification Patterns Extracted from KEGG Drug Structure Maps” International Workshop on Bioinformatics and Systems Biology (IBSB) 2009, Boston (2009).
  22. Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., Kanehisa, M., “Prediction of drug-target interaction networks from the integration of chemical and genomic spaces”, Bioinformatics (ISMB2008), 24, i232-i240 (2008).
  23. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y., “KEGG for linking genomes to life and the environment”, Nucleic Acids Research, 36, D480-484, (2008).
  24. Minowa, Y., Araki, M., Kanehisa, M., “Comprehensive Analysis of Distinctive Polyketide and Nonribosomal Peptide Structural Motifs Encoded in Microbial Genomes”, Journal of Molecular Biology, 368, 1500-1517, (2007).
  25. Suematsu, K., Araki, M., Shibuya, T., “Graph Tiling Algorithm for Molecular Synthesis Analysis” IPSJ, 49 (AL-106), 25-32 (2006).
  26. Shigemizu, D., Okuda, S., Araki, M., Goto, S., Kanehisa, M., “Construction of the drug substructure library from the KEGG DRUG database” International Workshop on Bioinformatics and Systems Biology (IBSB) 2006, Boston (2006).
  27. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M., “From Genomics to Chemical Genomics: New Developments in KEGG”, Nucleic Acids Research, 34, D354-357 (2006).
  28. Araki, M., Katayama, T., Matsuura, Y., Kanehisa, M., “KEGG PEPTIDE: a database for peptide structures”International Workshop on Bioinformatics and Systems Biology (IBSB) 2004, 1-2 (2004).
  29. Kobayashi, H., Kaern, M., Araki, M., Chung, K., Gardner, T.S., Cantor, C.R., Collins, J.J., “Programmable cells: interfacing natural and engineered gene networks”, Proc. Natl. Acad. Sci. U. S. A., 101(22), 8414-8419 (2004).
  30. Hori, Y., Bichenkova, E.V., Wilton, A.N., El-Attug, M.N., Sadat-Ebrahimi, S., Tanaka, T., Kikuchi, Y., Araki, M., Sugiura, Y., Douglas, K.T., “The transfer RNA-like binding domain of the ribonuclease P ribozyme as a basis for the design and discovery of inhibitors of the processing of pre-transfer RNA”, 5th Australia/Japan DDD, 24-26 (2002.10).
  31. Hori, Y., Bichenkova, E.V., Wilton, A.N., El-Attug, M.N., Sadat-Ebrahimi, S., Tanaka, T., Kikuchi, Y., Araki, M., Sugiura, Y., Douglas, K.T., “The first synthetic chemical inhibitors of the ribonuclease P ribozyme”, RNA as Therapeutic and Genomics Target, 37 (2001.9).
  32. Futaki, S., Araki, M., Kiwada, T., Nakase, I., Sugiura, Y., “A Cassette Ribonuclease: Site Selective Cleavage of RNA by a Ribonuclease S-Bearing RNA-Recognition Segment”, Peptides-American Synposium, 17, 452-453 (2001.6).
  33. Araki, M., Hashima, M., Okuno, Y., Sugiura, Y., “Coupling between substrate binding and allosteric regulation in ribozyme catalysis”, Bioorganic & Medicinal Chemistry, 9, 1155-1163, (2001).
  34. Futaki, S., Araki, M., Kiwada, T., Nakase, I., Sugiura, Y., “A 'cassette' RNase: site-selective cleavage of RNA by RNase S equipped with RNA-recognition segment”, Bioorg. Med. Chem. Lett. , 11(9), 1165-1168 (2001).
  35. Hori, Y., Bichenkova, E.V., Wilton, A.N., El-Attug, M.N., Sadat-Ebrahimi, S., Tanaka, T., Kikuchi, Y., Araki, M., Sugiura, Y., Douglas, K.T., “Synthetic inhibitors of the processing of pre-transfer RNA by the ribonuclease P ribozyme: enzyme inhibitors which act by binding to substrate”, Biochemistry, 40, 603-608 (2001).
  36. Sadat-Ebrahimi, S., Hori, Y., Tanaka, T., Kikuchi, Y., Wilton, A.N., El-Attug, M.N., Araki, M., Sugiura, Y., Douglas, K.T., “The first synthetic inhibitor classes for ribonuclease P, the ribozyme maturing pre-transfer RNA”, Journal of Pharmacy and Pharmacology, 52, 125 (2000).
  37. Araki, M., Okuno, Y., Sugiura, Y., “Expression mechanism of the allosteric interactions in a ribozyme catalysis” Nucleic Acids Symposium Series, 44, 205-206 (2000).
  38. Araki, M., Okuno, Y., Hara, Y., Sugiura, Y., “Allosteric regulation of a ribozyme activity through ligand-induced conformational change”, Nucleic Acids Research, 26, 3379-3384, (1998).
  39. Sugiura, Y., Totsuka, R., Araki, M., Okuno, Y., “Selective cleavages of tRNAphe with secondary and tertiary structures by enediyne antitumor antibiotics”, Bioorganic & Medicinal Chemistry, 5, 1229-1234, (1997).

【PATENTS】

  1. Araki M, Miyaoku K, Taniguchi T, Yoda N, Yumura S (Patent Application 2011-281442, 2011)
  2. Araki M, Miyaoku K, Taniguchi T(Patent Application 2011-179573 , 2011)
  3. Araki M, Miyaoku K, Taniguchi T(Patent Application 2010-281794 , 2010)
  4. Collins JJ, Kobayashi H, Kaern M, Araki M, Friedland A, Kuan-Ta Lu T, “Engineered Enzymatically Active Bacteriphages and Methods of Uses Thereof”, US Provisional Application No. 11/662, 551 (Filed: Dec 21, 2007)
  5. Collins JJ, Kobayashi H, Kaern M, Araki M, Friedland A, Kuan-Ta Lu T, “Enter and Destroy the Biofilm Matrix: Dispersing Bacterial Biofilms with Engineered, Enzymatically Active Bacteriophage”, US Provisional Application No. 60/609, 400 (Filed: Sep 13, 2004)