論文・著書・特許

【論文】Google Scholar

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).
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).
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).
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.
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).
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).
Kuriya, Y., Murata, M., Yamamoto, M., Watanabe, N, and *Araki, M. “Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli.”, Bioengineering, 10(6), 636 (2023).
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).
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).
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).
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, 6(12) (2022).
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).
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).
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).
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).
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).
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).
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, 6(1), ysab012 (2021).
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).
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).
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)
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)
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).
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).
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).
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).
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).
Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., Shimatani, Z. and Kondo, A. “Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems” Science, 353(6305), aaf8729 (2016).
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).
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 (2015).
*Araki, M., Cox III, R.S., Makiguchi, H., Ogawa, T., Taniguchi, T., Miyaoku, K., Nakatsui M., Hara, K.Y., Kondo, A. "M-path: A Compass for Navigating Potential Metabolic Pathways" Bioinformatics, 31(6) 905-911 (2015).
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).
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).
Hara, K.Y., Morita, K., Endo, Y., Mochizuki, M., Araki, M., Kondo, A. “Evaluation and screening of efficient promoters to improve astaxanthin production in Xanthophyllomyces dendrorhous” Appl. Microbiol. Biotechnol. 98: 6787-6793 (2014).
Nakatsui, M., *Araki, M., *Kondo, A. “An Approach for Dynamical Network Reconstruction of Simple Network Motifs” BMC Systems Biology, 7(Suppl 6), S4 (2013).
Araki, M., Taniguchi, T., Miyaoku, K., Makiguchi H. “A Computational Platform for Designing Natural Products" INCOB2012, P66 (2012.10 Bangkok, Thailand).
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).
Araki, M., Taniguchi, T., Miyaoku, K. “A Computational Method for Exploring Extensive Biosynthetic Pathways" Metabolic Engineering IX, P46 (2012.6 Biarritz, France).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Suematsu, K., Araki, M., Shibuya, T. “Graph Tiling Algorithm for Molecular Synthesis Analysis” IPSJ, 49 (AL-106), 25-32 (2006).
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).
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).
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).
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).
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).
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).
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 Symposium, 17, 452-453 (2001.6).
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).
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).
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).
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).
Araki, M., Okuno, Y., Sugiura, Y. “Expression mechanism of the allosteric interactions in a ribozyme catalysis” Nucleic Acids Symposium Series, 44, 205-206 (2000).
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).
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).

【著書】

荒木通啓、伊藤眞里「疾患予測モデル開発に向けたデジタルヘルス推進の意義と期待される効果」新医療 (2023)
荒木通啓「食・栄養の理解に向けた代謝インフォマティクス」実験医学 (2023)
渡邉直暉、荒木通啓「スマートセルの効率的創製に向けた情報解析技術とAI活用」微生物を活用した有用物質の製造技術（シーエムシー出版） (2023)
荒木通啓、奥野恭史「AI創薬」日経BPテクノロジーロードマップ 2023-2032 (2023)
荒木通啓、奥野恭史「AI創薬」日経BPテクノロジーロードマップ 2021-2030 (2021)
厨祐喜, 伊藤潔人, 荒木通啓「スマートセルの動向と効率的創製に向けたAI活用第2節スマートセルの効率的創製に向けた情報解析技術とAI活用」バイオリアクターのスケールアップと物質生産事例集、技術情報協会 (2021)
厨祐喜、荒木通啓「代謝パスウェイ・酵素反応改変における情報解析技術の活用」ファルマシア (2020)
蓮沼誠久, Christopher Vavricka Jr., 荒木通啓「新たに設計した代謝経路を用いた大腸菌によるアルカロイド高生産」バイオサイエンスとインダストリー (2020)
荒木通啓、奥野恭史「AI創薬」日経BPテクノロジーロードマップ 2019-2028 (2019)
浅野泰久、荒木通啓「構造に着想する酵素工学」生物工学会誌 Vol.96, 10 (2018)
荒木通啓「バイオロジクス・製剤・ロボティクス」医薬ジャーナル Vol.54, 9（2018）
内野詠一郎、荒木通啓、奥野恭史「ビッグデータ時代のゲノム創薬」分子精神医学 Vol.18, 3（2018）
荒木通啓、伊藤潔人、武田志津「バイオ生産に資するAI基盤技術」スマートセルインダストリー（シーエムシー出版）T1080 (2018)
荒木通啓「代謝設計に向けた酵素選択」スマートセルインダストリー（シーエムシー出版）T1080 (2018)
厨祐喜、白井智量、荒木通啓「代謝モデル構築と代謝経路設計」スマートセルインダストリー（シーエムシー出版）T1080 (2018)
荒木通啓、白井智量「新規代謝経路の設計」スマートセルインダストリー（シーエムシー出版）T1080 (2018)
荒木通啓、中津井雅彦、奥野恭史「集合知によるAI創薬の展開 ―ライフインテリジェンスコンソーシアム（LINC）―」国際医薬品情報 1106号（2018）
柘植謙爾、石井純、荒木通啓、近藤昭彦「ゲノム合成の潮流のインパクト：微生物による物質生産」現代化学 No.562, 36 (2018)
荒木通啓「インシリコ代謝モデルの可能性」実験医学（羊土社）Vol.35 No.9 (2017)
石井純、荒木通啓、中津井雅彦、崎濱由梨、柘植陽太、蓮沼誠久、近藤昭彦「合成生物工学によるモノづくり微生物のデザインに向けて」生物工学会誌 Vol.93, 9 (2015)
荒木通啓「合成生物学をデザインするデータベースについて」H26環境対応技術開発等報告書（一般財団法人バイオインダストリー協会） (2015)
荒木通啓「データベースからの再発見」生物工学会誌（バイオミディア） Vol.92, 6 (2014)
石川文洋、荒木通啓、掛谷秀昭「創薬を牽引する有機化学：天然物創薬とケモインフォマティクス」ファルマシア (2012)
荒木通啓「創薬に役立つケミカル・バイオデータベース」最新創薬インフォマティクス活用マニュアル (2011)
荒木通啓「ケモインフォマティクス」バイオインフォマティクス事典 (2006)
荒木通啓、金久實「創薬科学のためのKEGG」化学工業 Vol.57 No.3, 42-46 (2006)
荒木通啓、服部正泰、金久實「バイオインフォマティクスとケモインフォマティクスの融合」現代医療 Vol.36 No.5, 86-92 (2004)

【特許】

「Δ１５脂肪酸デサチュラーゼ発現カセットを含む酵母」 JP2022047741A, 2020
「Recombinant host cell for producing benzylisoquinoline alkaloid (bia) and novel method for producing benzylisoquinoline alkaloid (bia)」 US20210395717A1, 2019
「情報解析システム、方法、およびプログラム」 JP2021016325A, 2019
「計算機システム、及び、その方法」 JP2022103706A, 2019
「機能性配列選択方法及び機能性配列選択システム」 JP2020150919A, 2019
「テレフタル酸の製造方法」 JP2013128460A, 2011
「Synthetic pathway generating apparatus, synthesis pathway generating method, synthesis pathway generating program, and method of producing 3-hydroxypropionic acid, crotonyl alcohol and butadiene」 WO2012081723A1, 2011
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)
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)