AI Systems Medicine

34  articles.  
* There may be some overlapped articles listed due to the difference of format.

  1. Tomoya Sakuma , Yuki Otani , Hideyuki Shimizu: Geometric-Evolutionary Deep Learning Decodes the Human GPCR-Metabolome Interactome and Enables Systematic De-Orphanization bioRxiv. 2026.02; ( DOI )

  1. Takumi Ito, Kohei Ota, Hidekazu Hishinuma, Hideyuki Shimizu: A Functional Atlas of the Tardigrade Resistome Reveals a Diverse Molecular Toolkit for Extremotolerance bioRxiv. 2025.06; ( DOI )

  2. Takumi Ito, Satoshi Ohno, Yiran Wang, Saori Uematsu, Shinya Kuroda, Hideyuki Shimizu: MetDeeCINE: Deciphering Metabolic Regulation through Deep Learning and Multi-Omics 2025.03; ( DOI )

  1. Molecular characteristic analysis of single-nucleotide polymorphisms in SLC16A9/hMCT9. 2023.12; 334 122205. ( PubMed , DOI )

  2. DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle 2023.11; 13 (1): ( DOI )

  3. Atorvastatin Exerts More Selective Inhibitory Effects on hMCT2 than on hMCT1 and hMCT4. 2023.07; 43 (7): 3015-3022. ( PubMed , DOI )

  4. Monocarboxylate transporter 4 involves in energy metabolism and drug sensitivity in hypoxia. 2023.01; 13 (1): 1501. ( PubMed , DOI )

  1. Involvement of SLC16A1/MCT1 and SLC16A3/MCT4 in l-lactate transport in the hepatocellular carcinoma cell line. 2022.10; 43 (5): 183-191. ( PubMed , DOI )

  2. Toshiya Kokaji, Miki Eto, Atsushi Hatano, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-Ichi Hironaka, Yuki Ito, Riku Egami, Saori Uematsu, Akira Terakawa, Yifei Pan, Hideki Maehara, Dongzi Li, Yunfan Bai, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Hiroyuki Kubota, Yutaka Suzuki, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states. Sci Rep. 2022.08; 12 (1): 13719. ( PubMed , DOI )

  3. Akira Terakawa, Yanhui Hu, Toshiya Kokaji, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Yifei Pan, Yunfan Bai, Andrey A Parkhitko, Xiaochun Ni, John M Asara, Martha L Bulyk, Norbert Perrimon, Shinya Kuroda: Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes. iScience. 2022.05; 25 (5): 104231. ( PubMed , DOI )

  4. Satoshi Ohno, Saori Uematsu, Shinya Kuroda: Quantitative metabolic fluxes regulated by trans-omic networks. Biochem J. 2022.03; 479 (6): 787-804. ( PubMed , DOI )

  5. Saori Uematsu, Satoshi Ohno, Kaori Y Tanaka, Atsushi Hatano, Toshiya Kokaji, Yuki Ito, Hiroyuki Kubota, Ken-Ichi Hironaka, Yutaka Suzuki, Masaki Matsumoto, Keiichi I Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. iScience. 2022.02; 25 (2): 103787. ( PubMed , DOI )

  1. Riku Egami, Toshiya Kokaji, Atsushi Hatano, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-Ichi Hironaka, Saori Uematsu, Akira Terakawa, Yunfan Bai, Yifei Pan, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Masaki Matsumoto, Keiichi I Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle. iScience. 2021.03; 24 (3): 102217. ( PubMed , DOI )

  1. Toshiya Kokaji, Atsushi Hatano, Yuki Ito, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-Ichi Hironaka, Riku Egami, Akira Terakawa, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Kazutaka Ikeda, Makoto Arita, Masaki Matsumoto, Keiichi I Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity. Sci Signal. 2020.12; 13 (660): ( PubMed , DOI )

  2. Satoshi Ohno, Lake-Ee Quek, James R Krycer, Katsuyuki Yugi, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Tomoyoshi Soga, David E James, Shinya Kuroda: Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes. iScience. 2020.09; 23 (9): 101479. ( PubMed , DOI )

  3. Lake-Ee Quek, James R Krycer, Satoshi Ohno, Katsuyuki Yugi, Daniel J Fazakerley, Richard Scalzo, Sarah D Elkington, Ziwei Dai, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Jason W Locasale, Tomoyoshi Soga, David E James, Shinya Kuroda: Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin. iScience. 2020.02; 23 (2): 100855. ( PubMed , DOI )

  1. Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics 2019.06; 15 109-120.

  1. James R Krycer, Katsuyuki Yugi, Akiyoshi Hirayama, Daniel J Fazakerley, Lake-Ee Quek, Richard Scalzo, Satoshi Ohno, Mark P Hodson, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Westa Domanova, Benjamin L Parker, Marin E Nelson, Sean J Humphrey, Nigel Turner, Kyle L Hoehn, Gregory J Cooney, Tomoyoshi Soga, Shinya Kuroda, David E James: Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism. Cell Rep. 2017.12; 21 (12): 3536-3547. ( PubMed , DOI )

  1. Takanori Sano, Kentaro Kawata, Satoshi Ohno, Katsuyuki Yugi, Hiroaki Kakuda, Hiroyuki Kubota, Shinsuke Uda, Masashi Fujii, Katsuyuki Kunida, Daisuke Hoshino, Atsushi Hatano, Yuki Ito, Miharu Sato, Yutaka Suzuki, Shinya Kuroda: Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. Sci Signal. 2016.11; 9 (455): ra112. ( PubMed , DOI )

  1. Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa, Hiroshi Shimizu: Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli. Microbial Cell Factories. 2014.05; 13 64. ( PubMed , DOI )

  2. Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa: FastPros: screening of reaction knockout strategies for metabolic engineering. Bioinformatics. 2014.04; 30 (7): 981-987. ( PubMed , DOI )

  3. Nobutaka Nakashima, Satoshi Ohno, Katsunori Yoshikawa, Hiroshi Shimizu, Tomohiro Tamura: A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli. Applied and Environmental Microbiology. 2014.01; 80 (2): 564-573. ( PubMed , DOI )

  1. Satoshi Ohno, Chikara Furusawa, Hiroshi Shimizu: In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites. J Biosci Bioeng. 2013.02; 115 (2): 221-228. ( PubMed , DOI )

  1. 大野聡: 代謝フラックスの定量によるトランスオミクスネットワークの理解 生物工学会誌. 2022;

  1. 柚木 克之, Krycer James R, 平山 明由, Fazakerley Daniel J, Quek Lake-Ee, Scalzo Richard, 大野 聡, Hodson Mark P, 池田 五月, 庄司 二葉, 鈴木 久美, Domanova Westa, Parker Benjamin L, Nelson Marin E, Humphrey Sean J, Turner Nigel, Hoehn Kyle L, Cooney Gregory J, 曽我 朋義, 黒田 真也, James David E: 動的13C-メタボロミクスおよびリン酸化プロテオミクスの統合解析により明らかとなった脂肪細胞の代謝プライミング機構 JSBMS Letters. 2017.08; 42 (Suppl.): 108. ( ichushi )

  1. 大野, others: 大腸菌による有用物質生産に向けた 3 重反応破壊の in silico スクリーニング (2014 生物工学論文賞) 生物工学会誌: Seibutsu-kogaku Kaishi. 2015;

  1. Akinori Kawaharada, Takumi Ito, Hideyuki Shimizu: Pan–Pharmacological Drug–Target Interaction Prediction with 3D–Informed Protein Encoding at Scale bioRxiv. 2026.04;

  1. Tomoya Sakuma, Yuki Otani, Hideyuki Shimizu: High-Resolution Mapping of the Human E3-Substrate Interactome using Ubicon Uncovers Network Architecture and Cancer Vulnerabilities bioRxiv. 2025.04; ( DOI )

  2. Keigo Morita, Atsushi Hatano, Toshiya Kokaji, Hikaru Sugimoto, Takaho Tsuchiya, Haruka Ozaki, Riku Egami, Dongzi Li, Akira Terakawa, Satoshi Ohno, Hiroshi Inoue, Yuka Inaba, Yutaka Suzuki, Masaki Matsumoto, Masatomo Takahashi, Yoshihiro Izumi, Takeshi Bamba, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: Structural robustness and temporal vulnerability of the starvation-responsive metabolic network in liver of healthy and obese mice Science Signaling. 2025.04; ( DOI )

  3. Yuki Otani, Daisuke Koga, Yasunari Wakizaka, Hideyuki Shimizu: BaCNet: Deep Learning Accelerates Novel Antibiotic Discovery Against Resistant Pathogens bioRxiv. 2025.03; ( DOI )

  4. Yuki Otani, Daisuke Koga, Yasunari Wakizaka, Hideyuki Shimizu: AMP-Atlas: Comprehensive Atlas of Antimicrobial Peptides to Combat Multidrug-resistant Bacteria bioRxiv. 2025.03; ( DOI )

  1. Yifei Pan, Atsushi Hatano, Satoshi Ohno, Keigo Morita, Toshiya Kokaji, Yunfan Bai, Hikaru Sugimoto, Riku Egami, Akira Terakawa, Dongzi Li, Saori Uematsu, Hideki Maehara, Suguru Fujita, Hiroshi Inoue, Yuka Inaba, Atsushi J. Nagano, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver npj Systems Biology and Applications. 2024.09; 10 (1): ( DOI )

  2. Tomoya Sakuma, Yuto Mukai, Atsushi Yamaguchi, Yudai Suganuma, Keisuke Okamoto, Ayako Furugen, Katsuya Narumi, Shuhei Ishikawa, Yoshitaka Saito, Masaki Kobayashi: Monocarboxylate Transporters 1 and 2 Are Responsible for L-Lactate Uptake in Differentiated Human Neuroblastoma SH-SY5Y Cells Biological and Pharmaceutical Bulletin. 2024.04; 47 (4): 764-770. ( DOI )

  3. Yunfan Bai, Keigo Morita, Toshiya Kokaji, Atsushi Hatano, Satoshi Ohno, Riku Egami, Yifei Pan, Dongzi Li, Katsuyuki Yugi, Saori Uematsu, Hiroshi Inoue, Yuka Inaba, Yutaka Suzuki, Masaki Matsumoto, Masatomo Takahashi, Yoshihiro Izumi, Takeshi Bamba, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda: Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity iScience. 2024.03; 27 (3): 109121. ( DOI )

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