English

【NAME】

Michihiro Araki

Ph.D. (Pharmaceutical Sciences,  Kyoto University)

【HISTORY】

2025.4 ~ present

Professor, College of Pharmaceutical Sciences, Ritsumeikan University

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

Visiting Researcher, Graduate School of Medicine, Kyoto University

Visiting Researcher, National Cerebral and Cardiovascular Center 

Visiting Researcher, National Institutes of Biomedical Innovation, Health and Nutrition

2020.4 ~ 2025.3

Chief Reseracher, Project leader, AI nutrition project, National Institutes of Biomedical Innovation, Health and Nutrition

Deputy director, AI Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition

Visiting Researcher, Graduate School of Medicine, Kyoto University

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

Visiting Researcher, National Cerebral and Cardiovascular Center 

2017.4 ~ 2020.3

Professor, Graduate School of Medicine, Kyoto University

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

Invited Researcher, National Institutes of Biomedical Innovation, Health and Nutrition (2019.4 ~)

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

【INTERESTS】

• Health, Medicine and Nutrition

• Metabolism

• Bioinformatics

【PUBLICATIONS】Google Scholar

1. Tanemura, N., Kakizaki, M., Kusumi, T., Onodera, R., Tominaga, Y. and Araki, M. "Feature extraction contributing to risk-acceptance prediction by machine learning models in food benefit-risk communication in Japan" Food and Humanity, 3(100427) (2024).

2. Kubota, T., Todoroki-Mori, K., Iwamoto, M., Kobori, T., Kikuchi, T., Tahara, T., Onishi, Y., Araki, M., Kasuga, M. and Yoshida, Y. "Thirty-Year Trends in the Prevalence and Severity of Diabetic Retinopathy at the First Visit in Patients with Untreated Type 2 Diabetes Mellitus" Ophthalmic Epidemiology, 1-8 (2024).

3. Takenaka, M., Kamasaka, K., Daryong,K., Tsuchikane, K., Miyazawa, S., Fujihana, S., Hori, Y., Vavricka, CJ., Hosoyama, A., Kawasaki, H., Shirai, T., Araki, M., Nakagawa, A., Minami, H., Kondo, A., Hasunuma, T.  “Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis”, Microbial Cell Factories, 23 (1), 178 (2024).

4. Vu, T., Kokubo, Y., Inoue, M., Yamamoto, M., Mohsen, A., Martin-Morales, A., Inoue, T. and *Araki, M. “Machine Learning Approaches for Stroke Risk Prediction: Findings from the Suita Study”, Journal of Cardiovascular Development and Disease, 11(7), 207(2024).

5. Vu, T., Kokubo, Y., Inoue, M., Yamamoto, M., Mohsen, A., Martin-Morales, A., Inoue, T., Jie Ting, T., Yoshizaki, M., Watanabe, N., Kuriya, Y., Matsumoto, C., Arafa, A., Nakao, Y., Kato, Y., Teramoto, M. and *Araki, M. “Unveiling Coronary Heart Disease Prediction through Machine Learning Techniques: Insights from the Suita Population-Based Cohort Study”, preprint, (2024).

6. Yoshizaki, M., Kuriya, Y., Yamamoto, M., Watanabe, N., and *Araki, M. “Development of method using language processing techniques for extracting information on drug–health food product interactions”, British Journal of Clinical Pharmacology, 90(6) (2024).

7. Yamaguchi, M., Araki, M., Hamada, K., Nojiri, T., Nishi, N. “Development of a Machine Learning Model for Classifying Cooking Recipes According to Dietary Styles”, Foods, 13(5), 667 (2024).

8. Tanemura, N., Kashino, I. and Araki, M. “A first survey of the public’s colour preferences for four processed foods as major sources of salt intake in Japan”, Food and Humanity, 100330 (2024).

9. Vu, T., Inoue, M., Yamamoto, M., Martin-Morales, A., Mohsen, A., Inoue, T., Dawadi, R., Kokubo, Y. and Araki, M. "Prediction of Stroke Incidence Using Machine Learning: The Suita Study", Stroke, 55 (Suppl_1), AWP266, (2024). 

10. Watanabe, N., Kuriya, Y., Murata, M., Yamamoto, M. and *Araki, M. “EnzymeNet: Residual Neural Networks model for Enzyme Commission number prediction”, Bioinformatics Advances, 3 (1), vbad173 (2023).

11. Tanemura, N., Sasaki, T., Miyamoto, R., Watanabe, J., Araki, M., Sato, J. and Chiba, T.  “Extracting the latent needs of dementia patients and caregivers from transcribed interviews in japanese: an initial assessment of the availability of morpheme selection as input data with Z-scores in machine learning” BMC Medical Information and Decision Making 23(203), (2023).

12. Martin-Morales, A., Yamamoto, M., Inoue, M., Vu, T., Dawadi, R., *Araki, M. “Predicting Cardiovascular Disease Mortality: Leveraging Machine Learning for Comprehensive Assessment of Health and Nutrition Variables.”, Nutrients, 15(18), 3937 (2023).

13. Mohsen, A., Yamamoto, M., Martin-Morales, A., Watanabe, D., Nishi, N., Nakagata, T., Yoshida, T., Miyachi, M., Mizuguchi, K., Araki, M. "Using Explainable AI to understand frailty indicators", medRxiv, 2023.05. 30.23290760.

14. Park, J., Bushita, H., Nakano, A., Hara, A., Ueno, H., Ozato, N., Hosomi, K., Kawashima, H., Chen, Y., Mohsen, A., Ohno, H., Konishi, K., Tanisawa, K., Nanri, H., Murakami, H., Miyachi, M., Kunisawa, J., Mizuguchi, K., *Araki, M. "Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study", Microorganisms, 11(8), 1892 (2023).

15. Watanabe, N, Kuriya, Y., Murata, M.,  Yamamoto, M., Shimizu, M, and *Araki, M. “Different Recognition of Protein Features Depending on Deep Learning Models: A Case Study of Aromatic Decarboxylase UbiD .”, Biology, 12(6), 795 (2023).

16. Kuriya, Y., Murata, M.,  Yamamoto, M., Watanabe, N, and *Araki, M. “Dynamic Flux Balance Analysis to Evaluate the Strain Production Performance on Shikimic Acid Production in Escherichia coli.”, Bioengineering, 10(6), 636 (2023).

17. Tanemura, N., Kakizaki, M., Kusumi, T., Onodera, R., Tominaga, Y., Araki, M., and Chiba, T. "The initial assessment of single/multiple scales in public risk perception in food safety research: a scoping review" Nutrire, 48(1)  (2023).

18. Tanemura, N., Kakizaki, M., Kusumi, T., Onodera, R., Tominaga, Y., Araki, M., and Chiba, T. "Information integration through benefit-risk messages on food with quality-adjusted life years from the public agency in Japan: a randomized control study" Nutrire, 48(1)  (2023).

19. Tanemura, N., Kakizaki, M., Kusumi, T., Onodera, R., Tominaga, Y., Araki, M., and Chiba, T. "Differences in consumers' perceptions based on the description order/amount of benefit–risk information on foods: a randomized comparative survey in Japan" British Food Journal, in press (2023).

20. Wong, JE., Yamaguchi, M., Nishi, N., Araki, M., Wee, LM. "Predicting Overweight and Obesity Status among Malaysian Adults using Supervised Machine Learning" JMIR Formative Research, in press (2022).

21. Watanabe, N., Yamamoto, M., Murata, M., Vavricka, C.J., Kondo, A., Ogino, C., *Araki, M. “Comprehensive Machine Learning Prediction of Extensive Enzymatic Reactions.”, The Journal of Physical Chemistry B, 126 (36) (2022).

22. Tanemura, N., Kakizaki, M., Kusumi, T., Onodera, R., Tominaga, Y., Araki, M., and Chiba, T. "Usefulness of integrated vs separated information on food safety with quality-adjusted life year indicators: A randomized control study" Nutrire, 47(11) (2022).

23. Vavricka, C.J., Takahashi, S., Watanabe, N., Takenaka, M., Matsuda, M., Yoshida, T., Suzuki、R., Kiyota, H., Li, J., Ishii, J., Tsuge, K., Minami, H., *Araki, M., Kondo, A., *Hasunuma, T. “Machine learning discovery of missing links that mediate alternative branches to plant alkaloids” Nature Communications. 13 (1) (2022).

24. Tongununui, P., Kuriya Y., Murata M., Sawada H., Araki M., Nomura M., Morioka K.,Ichie T., Ikejima K., Adachi K. "Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling." PLOS One, 16(12), (2021)

25. Kuriya, Y., Inoue, M., Yamamoto, M., Murata, M., *Araki, M. "Knowledge extraction from literatures and enzyme sequences complements FBA analysis in metabolic engineering.", Biotechnology Journal, 16(12) , (2021).

26. Nakazawa, S., Imaichi, O., Kogure, T., Kubota, T., Toyoda, K., Suda, M., Inui, M., Ito, K., Shirai, T., and Araki, M. "History-Driven Genetic Modification Design Technique Using a Domain-Specific Lexical Model for the Acceleration of DBTL Cycles for Microbial Cell Factories.", ACS Synthetic Biology, 10(9), (2021).

27. Takemura, M., Kubo, A., Watanabe, A., Sakuno, H., Minobe, Y., Sahara, T., Murata, M., Araki, M., Harada, H., Terada, Y., Yaoi, K., Ohdan, K., Misawa, N. "Pathway engineering for high-yield production of lutein in Escherichia coli.", Synthetic Biology, ysab012 (2021).

28. Kuriya, Y. and *Araki, M. “Dynamic Flux Balance Analysis to Evaluate the Strain Production Performance on Shikimic Acid Production in Escherichia coli”, Metabolites, 10(5), 198 (2020).

29. Watanabe, N., Murata, M., Ogawa, T., Vavricka, C.J., Kondo, A., Ogino, C., *Araki, M. “Exploration and Evaluation of Machine Learning-Based Models for Predicting Enzymatic Reactions”, Journal of Chemical Information and Modeling, 60(3), 1833-1843 (2020).

30. Aburatani, S., Kokabu, Y., Teshima, R., Ogawa, T., Araki, M., Shirai, T. "Application of Graphs Theory to Evaluate the Chemical Reactions in Living Cells." IC-MSQUARE 2019 (2019) 

31. Noda, S., Mori, Y., Oyama, S. Kondo, A., Araki, M., Shirai, T. "Reconstruction of metabolic pathway for isobutanol production in Escherichia coli." Microb Cell Fact 18, 124 (2019) 

32. Vavricka, C.J., Yoshida, T., Kuriya, Y., Takahashi, S., Ogawa, T., Ono, F., Agari, K., Kiyota, H., Li, J., Ishii, J., Tsuge, K., Minami, H., *Araki, M., *Hasunuma, T., Kondo, A. “Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids” Nature Communications. 10(1):2015 (2019).

33. 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).

34. 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).

35. 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).

36. 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).

37. 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).

38. 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 cerevisiae” Appl. Microbiol. Biotechnol. 99: 9771-9778 (2015).

39. 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.

40. *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).

41. Hara, K.Y., Morita, K., Mochizuki, M., Yamamoto, K., Ogino, C., Araki, M., Kondo, A. “Development of a multi-gene expression system in Xanthophyllomyces dendrorhous” Microbial Cell Factories, 13: 175 (2014).

42. 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).

43. Hara, K.Y., Morita, K., Endo, Y., Mochizuki, M., Araki, M., Kondo, A. “Evaluation and screening of efficient promoters to improve astaxanthin production inXanthophyllomyces dendrorhous” Appl. Microbiol. Biotechnol. 98: 6787-6793 (2014).

44. Nakatsui, M., *Araki, M., *Kondo, A.,“An Approach for Dynamical Network Reconstruction of Simple Network Motifs” BMC Systems Biology, 7(Suppl 6), S4  (2013).

45. Araki, M., Taniguchi, T., Miyaoku, K., Makiguchi H., “A Computational Platform for Designing Natural Products" INCOB2012,  P66 (2012.10 Bangkok, Thailand).

46. 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).

47. Araki, M., Taniguchi, T., Miyaoku, K., “A Computational Method for Exploring Extensive Biosynthetic Pathways" Metabolic Engineering IX, P46 (2012.6 Biarritz, France).

48. 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).

49. 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).

50. 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).

51. 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).

52. 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).

53. 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).

54. 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).

55. 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).

56. 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).

57. Suematsu, K., Araki, M., Shibuya, T., “Graph Tiling Algorithm for Molecular Synthesis Analysis” IPSJ, 49 (AL-106), 25-32 (2006).

58. 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).

59. 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).

60. 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).

61. 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).

62. 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).

63. 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).

64. 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).

65. 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).

66. 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).

67. 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).

68. 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).

69. Araki, M., Okuno, Y., Sugiura, Y., “Expression mechanism of the allosteric interactions in a ribozyme catalysis” Nucleic Acids Symposium Series, 44, 205-206 (2000).

70. 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).

71. 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).