国立研究開発法人 医薬基盤・健康・栄養研究所 AI健康・医薬研究センター

センター長Director

夏目 やよいYayoi Natsume-Kitatani, PhD

• 2025年10月10日インフォメーション/Infomation

  ArCHERのウェブサイトをリニューアルしました。

  ArCHER website has been renewed!

2025

• Natsume-Kitatani Y., Kobiyama K., Igarashi Y., Aoshi T., Nakatsu N., Tripathi LP., et al. An adjuvant database for preclinical evaluation of vaccines and immunotherapeutics. Cell Chem Biol. 2025, doi: 10.1016/j.chembiol.202507005.

• Yoshimura E., Hamada Y., Hatamoto Y., Nakagata T., Nanri H., Nakayama Y., et al. Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis. Gut Microbes. 2025;17(1):2514137, doi: 10.1080/19490976.2025.2514137.

• Doi K., Numasaki H., Anetai Y., Natsume-Kitatani Y. Homology-feature-assisted quantification of fibrotic lesions in computed tomography images: a proof of concept for CT image feature-based prediction for gene-expression-distribution. Int J Comput Assist Radiol Surg. 2025, doi: 10.1007/s11548-025-03428-8.

• Dawadi R., Vu T., Tay JT., Tran Ngoc Hoang P., Oya A., Yamamoto M., et al. Large language models and questions from older adults: a human and machine-based evaluation study. Discov Artif Intell. 2025;5(1):42, doi: 10.1007/s44163-025-00267-z.

• Vu T., Kokubo Y., Inoue M., Yamamoto M., Mohsen A., Martin-Morales A., et al. Machine Learning Model for Predicting Coronary Heart Disease Risk: Development and Validation Using Insights From a Japanese Population–Based Study. JMIR Cardio. 2025;9(1):e68066, doi: 10.2196/68066.

• Chen Y-A., Kawashima H., Park J., Mohsen A., Hosomi K., Nakagata T., et al. NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health. Sci Rep. 2025;15(1):19640, doi: 10.1038/s41598-025-04339-z.

• Higuchi C., Irie M., Ide T., Kushida T. (Preprint) Adapting bioinformatics data systems in the era of foundational models: leveraging retrieval-augmented generation and low-resource large language models. 2025, doi: 10.21203/rs.3.rs-7360068/v1.

• Nishitsu T., Tsutsui Y., Kataoka T., Fukushima K., Motooka D., Shichino S., et al. Spatial transcriptomics identifies SPARC as a prognostic marker in interstitial lung diseases. J Pathol. 2025;267(1):79-91, doi: 10.1002/path.6451.

• Maharani R., Muhajir MI., Dirgantara JM., Rasyid H., Kusumawati Y., Kartikowati CW., et al. Synthesis, antimicrobial activity, and in silico mechanistic study of linear bacicylin analogs. Arab J Chem. --;0(0):1-9, doi: 10.25259/AJC_328_2024.

• Anetai Y., Tsutsui Y., Kinami S., Yokoi M., Tomita Y., Koike Y., et al. Visualization and evaluation of the quality variations of EBT4 Gafchromic film using multidimensional scaling and Lie derivative image analysis. Phys Eng Sci Med. 2025, doi: 10.1007/s13246-025-01545-x.

2024

• Allendes Osorio RS., Kosugi Y., Nyström-Persson JT., Mizuguchi K., Natsume-Kitatani Y. A modern multi-omics data exploration experience with Panomicon. Bioinforma Adv. 2024:vbae147, doi: 10.1093/bioadv/vbae147.

• Kageyama S., Inoue R., Hosomi K., Park J., Yumioka H., Doi M., et al. Association Between Gut Microbiome Composition and Physical Characteristics in Patients with Severe Motor and Intellectual Disabilities: Perspectives from Microbial Diversity. Nutrients. 2024;16(20):3546, doi: 10.3390/nu16203546.

• Ishikawa T., Masuda T., Hachiya T., Dina C., Simonet F., Nagata Y., et al. Brugada syndrome in Japan and Europe: a genome-wide association study reveals shared genetic architecture and new risk loci. Eur Heart J. 2024:ehae251, doi: 10.1093/eurheartj/ehae251.

• Inoue R., Hosomi K., Park J., Sakaue H., Yumioka H., Kamitani H., et al. Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home. Nutrients. 2024;16(22):3839, doi: 10.3390/nu16223839.

• Kuroda M., Kasahara Y., Hirose M., Yamaguma H., Oda M., Nagao C., et al. Construction of a Tm-value prediction model and molecular dynamics study of AmNA-containing gapmer antisense oligonucleotide. Mol Ther - Nucleic Acids. 2024;35(3):102272, doi: 10.1016/j.omtn.2024.102272.

• Haga A., Iwasawa T., Misumi T., Okudela K., Oda T., Kitamura H., et al. Correlation of CT-based radiomics analysis with pathological cellular infiltration in fibrosing interstitial lung diseases. Jpn J Radiol. 2024;42(10):1157-67, doi: 10.1007/s11604-024-01607-2.

• Anetai Y., Doi K., Takegawa H., Koike Y., Yui M., Yoshida A., et al. (Doi-san affiliation Osaka Univ) Diffusion equation quantification: selective enhancement algorithm for bone metastasis lesions in CT images. Phys Med Biol. 2024, doi: 10.1088/1361-6560/ad965c.

• Uchida M., Park J., Fujie S., Hosomi K., Horii N., Watanabe K., et al. Effect of resistance training and chicken meat on muscle strength and mass and the gut microbiome of older women: A randomized controlled trial. Physiol Rep. 2024;12(12):e16100, doi: 10.14814/phy2.16100.

• Maruyama S., Matsuoka T., Hosomi K., Park J., Murakami H., Miyachi M., et al. High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study. Front Nutr. 2024;11, doi: 10.3389/fnut.2024.1434150.

• Wariishi T., Kataoka Y., Nakamura T., Kasahara Y., Kuroda M., Obika S., et al. Lantern-type G-quadruplex fluorescent sensors for detecting divalent metal ions. Anal Biochem. 2024;690:115525, doi: 10.1016/j.ab.2024.115525.

• Chyży P., Kulik M., Shinobu A., Re S., Sugita Y., Trylska J. Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proc Natl Acad Sci U S A. 2024;121:e2317197121, doi: 10.1073/pnas.2317197121.

• Momma K., Shimizu T., Hayashi T., Hirakawa Y., Kuroda M., Oda M. Monoclonal antibodies against jellyfish collagen. J Biomater Appl. 2025;39(7):807-15, doi: 10.1177/08853282241298354.

• Shoji H., Hirano H., Nojima Y., Gunji D., Shinkura A., Muraoka S., et al. Phosphoproteomic subtyping of gastric cancer reveals dynamic transformation with chemotherapy and guides targeted cancer treatment. Cell Rep. 2024;43(10):114774, doi: 10.1016/j.celrep.2024.114774.

• Tanjo T., Steinberg D., Crusoe MR., Bendiken A., Noisagul P., Yamamoto K., et al. (Preprint) DBCLS BioHackathon 2024 report: Everything about workflow and container. 2024, doi: 10.37044/osf.io/6qrau.

• Enomoto T., Shirai Y., Takeda Y., Edahiro R., Shichino S., Nakayama M., et al. SFTPB in serum extracellular vesicles as a biomarker of progressive pulmonary fibrosis. JCI Insight. 2024;9(11), doi: 10.1172/jci.insight.177937.

2023

• Nagano N., Tokunaga N., Ikeda M., Inoura H., Khoa D., Miwa M., Sohrab M., Topić G., Nogami-Itoh M., Takamura H. A novel corpus of molecular to higher-order events that facilitates the understanding of the pathogenic mechanisms of idiopathic pulmonary fibrosis Scientific Reports 13(1):5986, 2023

• Kawashima H., Watanabe R., Esaki T., Kuroda M., Nagao C., Natsume-Kitatani Y., Ohashi R., Komura H., Mizuguchi K., DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform, Journal of Medicinal Chemistry, 66(14): 9697-9709, 2023

• Kozawa S., Tejima K., Takagi S., Kuroda M., Nogami-Itoh M., Kitamura H., Niwa T., Ogura T., Natsume-Kitatani Y., Sato T. N., Latent inter-organ mechanism of idiopathic pulmonary fibrosis unveiled by a generative computational approach, Scientific Reports, 13(1):21981. 2023

• Sohrab M. G., Duong K., Topić G., Ikeda M., Nagano N., Natsume-Kitatani Y., Kuroda M., Nogami-Itoh M., Takamura H., Disease Network Constructor: a Pathway Extraction and Visualization, Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations) pp. 549-557. 2023

• Tomoto M., Mineharu Y., Sato N., Tamada Y., Nogami-Itoh M., Kuroda M., Adachi J., Takeda Y., Mizuguchi K., Kumanogoh A., Natsume-Kitatani Y., Okuno Y., Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information, Scientific Reports, 14(1): 1315. 2024

• Wariishi T., Kataoka Y., Nakamura T., Kasahara Y., Kuroda M., Obika S., Kuwahara M. Lantern-type G-quadruplex fluorescent sensors for detecting divalent metal ions, Analytical Biochemistry,

• Yoshimura H., Takeda Y., Shirai Y., Yamamoto M., Nakatsubo D., Amiya S., Enomoto T., Hara R., Adachi Y., Edahiro R., Yaga M., Masuhiro K., Koba T., Itoh-Takahashi M., Nakayama M., Takata S., Hosono Y., Obata S., Nishide M., Hata A., Yanagawa M., Namba S., Iwata M., Hamano M., Hirata H., Koyama S., Iwahori K., Nagatomo I., Suga Y., Miyake K., Shiroyama T., Fukushima K., Futami S., Naito Y., Kawasaki T., Mizuguchi K., Kawashima Y., Yamanishi Y., Adachi J., Nogami-Itoh M., Ueki S., Kumanogoh A., Galectin-10 in serum extracellular vesicles reflects asthma pathophysiology, Journal of Allergy and Clinical Immunology,

• Nojima Y., Aoki M., Re S., Hirano H., Abe Y., Narumi R., Muraoka S., Shoji H., Honda K., Tomonaga T., Mizuguchi K., Boku N., Adachi J. Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines, Computational and Structural Biotechnology Journal, 21, 2023

• Ikeda K., Maezawa Y., Yonezawa T., Shimizu Y., Tashiro T., Kanai S., Sugaya N., Masuda Y., Inoue N., Niimi T., Masuya K., Mizuguchi K., Furuya T., Osawa M. DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions. Front Chem. 10:1090643, 2023.

• Watanabe R., Kawata T., Ueda S., Shinbo T., Higashimori M., Natsume-Kitatani Y., Mizuguchi K., Prediction of the Contribution Ratio of a Target Metabolic Enzyme to Clearance from Chemical Structure Information, Molecular Pharmaceutics, 20(1): 419-426, 2023

2022

• Ikubo Y., Sanada T., Hosomi K., Park J., Naito A., Shoji H., Misawa T., Suda R., Sekine A., Sugiura T., Shigeta A., Nanri H., Sakao S., Tanabe N., Mizuguchi K., Kunisawa J., Suzuki T., Tatsumi K., Altered gut microbiota and its association with inflammation in patients with chronic thromboembolic pulmonary hypertension: a single-center observational study in Japan, BMC Pulmonary Medicine, 22(1):138, 2022

• Sawane K., Hosomi K., Park J., Ookoshi K., Nanri H., Nakagata T., Chen Y., Mohsen A., Kawashima H., Mizuguchi K., Miyachi M., Kunisawa J. Identification of Human Gut Microbiome Associated with Enterolignan Production, Microorganisms, 10(11):2169,2022

• Nagata Y., Watanabe R., Eichhorn C., Ohno S., Aiba T., Ishikawa T., Nakano Y., Aizawa Y., Hayashi K., Murakoshi N., Nakajima T., Yagihara N., Mishima H., Sudo T., Higuchi C., Takahashi A., Sekine A., Makiyama T., Tanaka Y., Watanabe A., Tachibana M., Morita H., Yoshiura K., Tsunoda T., Watanabe H., Kurabayashi M., Nogami A., Kihara Y., Horie M., Shimizu W., Makita N., Tanaka T. Targeted deep sequencing analyses of long QT syndrome in a Japanese population, PLOS ONE, 17(12):e0277242, 2022

• Murakami Y., Mizuguchi K. Recent developments of sequence-based prediction of protein–protein interactions, Biophysical Reviews, 14(6) :1393–1411, 2022

• Gupta S., Vundavilli H., Allendes Osorio R. S., Itoh M., Mohsen A., Datta A., Mizuguchi K., Tripathi L., Integrative Network Modeling Highlights the Crucial Roles of Rho-GDI Signaling Pathway in the Progression of Non-Small Cell Lung Cancer, IEEE Journal of Biomedical and Health Informatics, 26(9) :4785-4793, 2022

• Mohsen A., Chen Y., Allendes Osorio R. S., Higuchi C., Mizuguchi K., Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2, Frontiers in Bioinformatics, 2, 2022

• Chen Y., Allendes Osorio R. S., Mizuguchi K., TargetMine 2022: A new vision into drug target analysis, Bioinformatics, 38(18): 4454-4456, 2022

• Hosomi K., Saito M., Park J., Murakami H., Shibata N., Ando M., Nagatake T., Konishi K., Ohno H., Tanisawa K., Mohsen A., Chen Y., Kawashima H., Natsume-Kitatani Y., Oka Y., Shimizu H., Furuta M., Tojima Y., Sawane K., Saika A., Kondo S., Yonejima Y., Takeyama H., Matsutani A., Mizuguchi K., Miyachi M., Kunisawa J., Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota, Nature Communications, 13(1):4477, 2022

• Kuroda M., Watanabe R., Esaki T., Kawashima H., Ohashi R., Sato T., Honma T., Komura H., Mizuguchi K., Utilizing public and private sector data to build better machine learning models for the prediction of pharmacokinetic parameters, Drug Discovery Today, 27(11) :103339, 2022

• Futami Y., Takeda Y., Koba T., Narumi R., Nojima Y., Ito M., Nakayama M., Ishida M., Yoshimura H., Naito Y., Fukushima K., Takimoto T., Edahiro R., Matsuki T., Nojima S., Hirata H., Koyama S., Iwahori K., Nagatomo I., Shirai Y., Suga Y., Satoh S., Futami S., Miyake K., Shiroyama T., Inoue Y., Adachi J., Tomonaga T., Ueda K., Kumanogoh A. Identification of CD14 and lipopolysaccharide-binding protein as novel biomarkers for sarcoidosis using proteomics of serum extracellular vesicles, International Immunology, 34 (6): 327-340, 2022

• Hosoe Y., Miyanoiri Y., Re S., Ochi S., Asahina Y., Kawakami T., Kuroda M., Mizuguchi K., Oda M. Structural dynamics of the N-terminal SH2 domain of PI3K in its free and CD28-bound states, The FEBS Journal, Oct. 25, 2022

• Iiyama M., Hantani Y., Wink R., Kuroda M., Oda M. Role of Cys residues of C-terminal SH2 domain of phosphoinositide 3-kinase in its conformational stability and CD28-binding ability, Chemical Thermodynamics and Thermal Analysis, 8:100080, 2022

• Otaki M., Hirane N., Natsume-Kitatani Y., Nogami Itoh M., Shindo M., Kurebayashi Y., Nishimura S. Mouse tissue glycome atlas 2022 highlights inter-organ variation in major N-glycan profiles, Scientific Reports, 12(1):17804, 2022

• Kawasaki T., Takeda Y., Edahiro R., Shirai Y., Nogami-Itoh M., Matsuki T., Kida H., Enomoto T., Hara R., Noda Y., Adachi Y., Niitsu T., Amiya S., Yamaguchi Y., Murakami T., Kato Y., Morita T., Yoshimura H., Yamamoto M., Nakatsubo D., Miyake K., Shiroyama T., Hirata H., Adachi J., Okada Y., Kumanogoh A. Next-generation proteomics of serum extracellular vesicles combined with single-cell RNA sequencing identifies MACROH2A1 associated with refractory COVID-19, Inflammation and Regeneration, 42(1):53, 2022

• Hioki K., Hayashi T., Natsume-Kitatani Y., Kobiyama K., Temizoz B., Negishi H., Kawakami H., Fuchino H., Kuroda E., Coban C., Kawahara N,m Ishii H.J., Machine-learning-assisted screening of herbal medicine extracts as vaccine adjuvants, Frontiers in Immunology, 13, 2022

• Sohrab, M. G., Duong, K. N., Masami, I., Topić, G., Natsume-Kitatani, Y., Kuroda, M., Nogami-Itoh M., Takamura, H. (2022, November). BiomedCurator: Data Curation for Biomedical Literature, In Proceedings of the 2nd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics and the 12th International Joint Conference on Natural Language Processing: System Demonstrations, PP 63-71, 2022

• Yagi K., Re S., Mori T., Sugita Y., Weight average approaches for predicting dynamical properties of biomolecules, Current Opinion in Structural Biology. 72: 88-94, 2022

• Takegawa-Araki T., Kumagai S., Yasukawa K., Kuroda M., Sasaki T., Obika S., Structure–Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids, Journal of Medicinal Chemistry, 2022

• Miki Y., Taketomi Y., Kidoguchi Y., Yamamoto K., Muramatsu K., Nishito Y., Park J., Hosomi K., Mizuguchi K., Kunisawa J., Soga T., Boilard E., Gowda S., Ikeda K., Arita M., Murakami M., Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota, JCI Insight, 2(7),2022

• Arakawa M., Tabata K., Ishida K., Kobayashi M., Arai A., Ishikawa T., Suzuki R., Takeuchi H., Tripathi L., Mizuguchi K., Morita E., Flavivirus recruits the valosin-containing protein–NPL4 complex to induce stress granule disassembly for efficient viral genome replication, Journal of Biological Chemistry, 3(298):101597, 2022

• Matsuoka T., Hosomi K., Park J., Goto Y., Nishimura M., Maruyama S., Murakami H., Konishi K., Miyachi M., Kawashima H., Mizuguchi K., Kobayashi T., Yokomichi H., Kunisawa J., Yamagata Z., Relationships between barley consumption and gut microbiome characteristics in a healthy Japanese population: a cross-sectional study, BMC Nutrition, 8(1):23, 2022

• Tsuji T., Hashiguchi K., Yoshida M., Ikeda T., Koga Y., Honda Y., Tanaka T., Re S., Mizuguchi K., Takahashi D., Yazaki R., Ohshima T., α-Amino acid and peptide synthesis using catalytic cross-dehydrogenative coupling, Nature Synthesis, 2022

• Otoshi T., Nagano T., Park J., Hosomi K., Yamashita T., Tachihara M., Tabata T., Sekiya R., Tanaka Y., Kobayashi K., Mizuguchi K., Itoh T., Maniwa Y., Kunisawa J., Nishimura Y., The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma, Anticancer Research, 42(3),1589-1598 2022

• Hirano H., Abe Y., Nojima Y., Aoki M., Shoji H., Isoyama J., Honda K., Boku N., Mizuguchi K., Tomonaga T., Adachi J. Temporal dynamics from phosphoproteomics using endoscopic biopsy specimens provides new therapeutic targets in stage IV gastric cancer, Scientific Reports, 12(1):4419, 2022

• Maruyama S., Matsuoka T., Hosomi K., Park J., Nishimura M., Murakami H., Konishi K., Miyachi M., Kawashima H., Mizuguchi K., Kobayashi T., Ooka T., Yamagata Z., Kunisawa J., Classification of the Occurrence of Dyslipidemia Based on Gut Bacteria Related to Barley Intake, Frontiers in Nutrition, 9, 2022

• Dokainish H., Re S., Mori T., Kobayashi C., Jung J., Sugita Y., The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein, eLife, 11:e75720, 2022

• Yamane D., Onitsuka S., Re S., Isogai H., Hamada R., Hiramoto T., Kawanishi E., Mizuguchi K., Shindo N., Ojida A., Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide, Chemical Science, 13(10):3027-3034, 2022

• Shinobu A., Re S., Sugita Y., Practical Protocols for efficient sampling of kinase-inhibitor binding pathways using two-dimensional replica-exchange molecular dynamics, frontiers in Molecular Biosciences, 2022

• Hioki K., Hayashi T., Natsume-Kitatani Y., Kobiyama K., Temizoz B., Negishi H., Kawakami H., Fuchino H., Kuroda E., Coban C., Kawahara N,m Ishii H.J., Machine-learning-assisted screening of herbal medicine extracts as vaccine adjuvants, Frontiers in Immunology, 2022

• Alarabi A., Mohsen A., Mizuguchi K., Alshbool F., Khasawneh F., Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets, BMC Medical Genomics, 2022

2021

• Park J., Kato K., Murakami H., Hosomi K., Tanisawa K., Nakagata T., Ohno H., Konishi K., Kawashima H., Chen Y., Mohsen A., Xiao J., Odamaki T., Kunisawa J., Mizuguchi K., Miyachi M. Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts, BMC Microbiology, 21(1):151, 2021

• Kasahara K., Re S., Nawrocki G., Oshima H., Mishima-Tsumagari C., Miyata-Yabuki Y., Kukimoto-Niino M., Yu I., Shirouzu M., Feig M., Sugita Y. Reduced efficacy of a Src kinase inhibitor in crowded protein solution, Nature Communications, 12(1):4099, 2021

• Fujiyama K., Kato N., Re S., Kinugasa K., Watanabe K., Takita R., Nogawa T., Hino T., Osada H., Sugita Y., Takahashi S., Nagano S. Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons, Angewandte Chemie International Edition, 60: 2-12, 2021

• Tomizawa R., Park J., Hosomi K., Matsumoto N., Kawashima H., Mizuguchi K., Kunisawa J., Honda C. Relationship between Human Gut Microbiota and Nutrition Intake in Hypertensive Discordant Monozygotic Twins, Journal of Hypertension, 10(8), 2021

• Mohsen A., Lokesh P. Tripathi., Mizuguchi K. Deep Learning Prediction of Adverse Drug Reactions In Drug Discovery Using Open TG–GATEs and FAERS Databases, Frontiers in Drug Discovery, 1:768792, 2021

• Ueta M., Hosomi K., Park J., Mizuguchi K., Sotozono C., Kinoshita S., Kunisawa J. Categorization of the Ocular Microbiome in Japanese Stevens–Johnson Syndrome Patients With Severe Ocular Complications, Frontiers in Cellular and Infection Microbiology, 11:1130, 2021

• Kageyama S., Inoue R., Hosomi K., Park J., Yumioka H., Suka T., Kurohashi Y., Teramoto K., Syauki A., Doi M., Sakaue H., Mizuguchi K., Kunisawa J., Irie Y. Effects of Malted Rice Amazake on Constipation Symptoms and Gut Microbiota in Children and Adults with Severe Motor and Intellectual Disabilities: A Pilot Study, Nutrients, 13(12):4466, 2021

• Sakib S., Fouda M., Al-Mahdawi M., Mohsen A., Oogane M., Ando Y., Fadlullah Z. Deep Learning Models for Magnetic Cardiography Edge Sensors Implementing Noise Processing and Diagnostics, IEEE Access, 10:2656-2668, 2021

• Mori T., Jung J., Kobayashi C., Dokainish H., Re S., Sugita Y. Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein, Biophysical Journal 120(6):1060-1071, 2021

• Komura H., Watanabe R., Kawashima H., Ohashi R., Kuroda M., Sato T., Honma T., Mizuguchi K. A public–private partnership to enrich the development of in silico predictive models for pharmacokinetic and cardiotoxic properties, Drug Discovery Today, 2021

• Chyży P., Kulik M., Re S., Sugita Y., Trylska J. Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection, Frontiers in Molecular Biosciences 8, 2021

• Re S., Mizuguchi K. Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein, The Journal of Physical Chemistry B, 125 (8):2089-2097, 2021

• Watanabe R., Esaki T., Ohashi R., Kuroda M., Kawashima H., Komura H., Natsume-Kitatani Y., Mizuguchi K. Development of an In Silico Prediction Model for P-glycoprotein Efflux Potential in Brain Capillary Endothelial Cells toward the Prediction of Brain Penetration, Journal of Medicinal Chemistry, 2021

• Vundavilli H., Tripathi L., Datta A., Mizuguchi K. Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity, Journal of Theoretical Biology, 110647, 2021

• Matsumoto N., Park J., Tomizawa R., Kawashima H., Hosomi K., Mizuguchi K., Honda C., Ozaki R., Iwatani Y., Watanabe M., Kunisawa J. Relationship between nutrient intake and human gut microbiota in monozygotic twins, medicina, 57(3):275, 2021

• Lee J., Mohsen A., Banerjee A., McCullough L., Mizuguchi K., Shimaoka M., Kiyono H., Park E. Distinct Age-Specific miRegulome Profiling of Isolated Small and Large Intestinal Epithelial Cells in Mice, International Journal of Molecular Sciences, 7(22):3544, 2021

• Koba T., Takeda Y., Narumi R., Shiromizu T., Nojima Y., Ito M., Kuroyama M., Futami Y., Takimoto T., Matsuki T., Edahiro R., Nojima S., Hayama Y., Fukushima K., Hirata H., Koyama S., Iwahori K., Nagatomo I., Suzuki M., Shirai Y., Murakami T., Nakanishi K., Nakatani T., Suga Y., Miyake K., Shiroyama T., Kida H., Sasaki T., Ueda K., Mizuguchi K., Adachi J., Tomonaga T., Kumanogoh A. Proteomics of serum extracellular vesicles identifies a novel COPD biomarker, fibulin-3 from elastic fibres, ERJ open research, 7(1):00658-2020, 2021

2020

• Esaki T., Kumazawa K., Takahashi K., Watanabe R., Masuda T., Watanabe H., Shimizu Y., Okada A., Takimoto S., Shimada T., Ikeda K., Open Innovation Platform using Cloud-based Applications and Collaborative Space: A Case Study of Solubility Prediction Model Development,Chem-Bio Informatics Journal, 20:5-18, 2020

• Mohsen A., Alarabi A., The impact of community containment implementation timing on the spread of COVID-19: A simulation study, F1000Research l9:452, 2020

• Esaki T., Horinouchi T., Natsume-Kitatani Y., Nojima Y., Sakane I., Matsui H., Estimation of relationships between gene expression and chemical substructures: Adapting canonical correlation analysis for small sample data by gathered features using consensus clustering, Chem-Bio Informatics Journal 20:58-61, 2020

• Tabata T., Yamashita T., Hosomi K., Park J., Hayashi T., Yoshida N., Saito Y., Fukuzawa K., Konishi K., Murakami H., Kawashima H., Mizuguchi K., Miyachi M., Kunisawa J., Hirata K., Gut microbial composition in patients with atrial fibrillation: effects of diet and drugs, Heart and Vessels 36:105-114, 2020

• Allendes Osorio R., Nyström-Persson J., Nojima Y., Kosugi Y., Mizuguchi K., Natsume-Kitatani Y., Panomicon: A web-based environment for interactive, visual analysis of multi-omics data, Heliyon 6(8): e04618, 2020

• Jujo Sanada T., Hosomi K., Shoji H., Park J., Naito A., Ikubo Y., Yanagisawa A., Kobayashi T., Miwa H., Suda R., Sakao S., Mizuguchi K., Kunisawa J., Tanabe N., Tatsumi K., EXPRESS: Gut microbiota modification suppresses the development of pulmonary arterial hypertension in a Su/Hx rat model, Pulmonary Circulation 10(3):2045894020929147, 2020

• Nojima Y., Takeda Y., Maeda Y., Bamba T., Fukusaki E., Itoh M., Mizuguchi K., Kumanogoh A., Metabolomic analysis of fibrotic mice combined with public RNA-Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis, FEBS Open Bio 11(10):2427-2436, 2020

• Teranishi Y., Kuwahara H., Ueda M., Takemura T., Kusumoto M., Nakamura K., Sakai J., Kimura T., Furutani Y., Kawashima M., Imokawa G., Nogami-Itoh M., Sphingomyelin Deacylase, the Enzyme Involved in the Pathogenesis of Atopic Dermatitis, Is Identical to the β-Subunit of Acid Ceramidase, International Journal of Molecular Sciences 22(21):8789, 2020

• Afanasyeva A., Nagao C., Mizuguchi K., Developing a Kinase-Specific Target Selection Method Using a Structure-Based Machine Learning Approach, Advances and Applications in Bioinformatics and Chemistry 13:27-40, 2020

• Chen Y., Park J., Natsume-Kitatani Y., Kawashima H., Mohsen A., Hosomi K., Tanisawa K., Ohno H., Konishi K., Murakami H., Miyachi M., Kunisawa J., Mizuguchi K., MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data, PLOS ONE 15(12):e0243609, 2020

• Tripathi L., Itoh M., Takeda Y., Tsujino K., Kondo Y., Kumanogoh A., Mizuguchi K., Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema, Frontiers in Genetics 11:585998, 2020

• Iiyama M., Numoto N., Ogawa S., Kuroda M., Morii H., Abe R., Ito N., Oda M., Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains, Molecular Immunology 131:51-59, 2020

• Tokunaga M., Miyamoto Y., Suzuki T., Otani M., Inuki S., Esaki T., Nagao C., Mizuguchi K., Ohno H., Yoneda Y., Okamoto T., Oka M., Matsuura Y., Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein, Virology 541:41-51, 2020

2019

• Kataoka Y., Fujita H., Afanasyeva A., Nagao C., Mizuguchi K., Kasahara Y., Obika S., Kuwahara M. High Contrast facile Imaging with Target-Directing Fluorescent Molecular Rotors N3-Modified Thioflavin T Derivatives, Biochemistry, 58(6):493-498, 2019

• Chen Y.A., Yogo E., Kurihara N., Ohno T., Higuchi C., Rokushima M., Mizuguchi K. Assessing drug target suitability using TargetMine, F1000Research, 8:233, 2019

• Yamada T., Habara O., Yoshii Y., Matsushita R., Kubo H., Nojima Y., Nishimura T. Role of glycogen in development and adult fitness in Drosophila, Development, 2019

• Takahashi Y.*, Park J.*, Hosomi K., Yamada T., Kobayashi A., Yamaguchi Y., Iketani S., Kunisawa J., Mizuguchi K., Maeda N., Ohshima T. Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing, Journal of Oral Biosciences, 2019

• Ohashi R., Watanabe R., Esaki T., Taniguchi T., Torimoto-Katori N., Watanabe T., Ogasawara Y., Takahashi T., Tsukimoto M., Mizuguchi K. Development of a Simplified in Vitro P-glycoprotein Substrate Assay and in Silico Prediction Models to Evaluate Transport Potential of P-glycoprotein, Molecular Pharmaceutics, 2019

• Esaki T., Watanabe R., Kawashima H., Ohashi R., Natsume-Kitatani Y., Nagao C., Mizuguchi K. Data Curation can improve the Prediction Accuracy of Metabolic intrinsic Clearance, Mol Inform., 38(1-2):e1800086, 2019

• Yamada T., Habara O., Yoshii Y., Matsushita R., Kubo H., Nojima Y., Nishimura T. The role of glycogen in development and adult fitness in Drosophila, Development, 146 (8), dev176149, 2019

• Lee M.S.J., Natsume-Kitatani Y., Temizoz B., Fujita Y., Konishi A., Matsuda K., Igari Y., Tsukui T., Kobiyama K., Kuroda E., Onishi M., Marichal T., Ise W., Inoue T., Kurosaki T., Mizuguchi K., Akira S., Ishii K.J., Coban C. B cell‐intrinsic MyD88 signaling controls IFN‐γ‐mediated early IgG2c class switching in mice in response to a particulate adjuvant, European Journal of Immunology, 49(9), 1433-1440, 2019

• Ohashi R., Watanabe R., Esaki T., Taniguchi T., Torimoto-Katori N., Watanabe T., Ogasawara Y., Takahashi T., Tsukimoto M., Mizuguchi K. Development of Simplified in Vitro P-Glycoprotein Substrate Assay and in Silico Prediction Models To Evaluate Transport Potential of P-Glycoprotein., Mol Pharm., 16(5):1851-1863, 2019

• Miyake K., Sakane A., Tsuchiya Y., Sagawa I., Tomida Y., Kasahara J., Imoto I., Watanabe S., Higo D., Mizuguchi K., Sasaki T. Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Finetuned by Intramolecular Interaction between First LiM Zinc Finger and C-terminal Coiled-coil Domains, Scientific Reports, 9(1):12794, 2019

• Chen Y.A., Tripathi L.P., Fujiwara T., Kameyama T., Ito M., Mizuguchi K. The TargetMine data warehouse: enhancement and updates, Frontiers in Genetics - Bioinformatics and Computational Biology, 10:934, 2019

• Allendes O.R.S., Tripathi L.P., Mizuguchi K. CLINE: A web-tool for the Comparison of Biological Dendrogram Structures, BMC Bioinformatics, 20:528, 2019

2018

• Watanabe R., Esaki T., Kawashima H., Natsume-Kitatani Y., Nagao C., Ohashi R., Mizuguchi K., Predicting Fraction Unbound in Human Plasma from Chemical Structure: Improved Accuracy in the Low Value Ranges, Molecular Pharmaceutics, 5;15(11):5302-5311, 2018

• Tripathi L.P., Chen Y.A., Mizuguchi K., Morita E., Network-Based Analysis of Host-Pathogen Interactions, Encyclopedia of Bioinformatics and Computational Biology, 3(2019):932-937, 2018

• Afanasyeva A., Bockwoldt M., Cooney C.R., Heiland I., Gossmann T.I., Human long intrinsically disordered protein regions are frequent targets of positive selection, Genome Research, 28(7):975-982, 2018