Takadera K., Ramadhan D., Watanabe R., Mizuguchi K.. "In Silico Regression Modeling and Improved Interpretability To Predict the Transport Inhibitory Activity of Breast Cancer Resistance Protein". ACS Omega, 2026-04-21. DOI
Nasution M.A.F., Bekker G.J., Re S., Mizuguchi K.. "Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from MD Simulations". Computational and Structural Biotechnology Journal, 2026-04-16. DOI
Boonserm P., Sangtanoo P., Sutthibutpong T., Ariyawansa H., Re S., Mizuguchi K., Srimongkol P., Karnchanatat A.. "Modulation of the Keap1–Nrf2 Pathway Using a Peptide Derived from Edible Mushrooms: In Silico and In Vitro Studies". Journal of Agriculture and Food Research, 2026-03. DOI
Otoshi R., Kitamura H., Niwa T., Murohashi K., Oda T., Baba T., Hagiwara E., Iwasawa T., Takemura T., Okudela K., Nojima Y., Nakamura Y., Mizuguchi K., Kitatani Y.N., Ogura T.. "PPFE-like findings identify an IPF subgroup with shortened telomeres and poor prognosis". ERJ Open Research, 2026-02-20. DOI
Wang X., Mizuguchi K., Hashimoto K.. "Excitatory GABA receptors shape locomotor circuit organization in C. elegans". Scientific Reports, 2026-02-17. DOI
Akazawa N., Nakamura M., Eda N., Murakami H., Nakagata T., Nanri H., Park J., Hosomi K., Mizuguchi K., Kunisawa J., Miyachi M., Hoshikawa M.. "Relationship between gastrointestinal environment and physical conditions in elite athletes". The Journal of Physical Fitness and Sports Medicine, 2026-01-25. DOI
Miyamoto R., Sakane A., Morino H., Kume K., Matsubara T., Fukumoto T., Osaki Y., Oki R., Hanada K., Tachibana K., Nakataki M., Nishida Y., Takahashi Y., Mizuguchi K., Murayama S., Saito Y., Kawakami H., Takai Y., Sasaki T., Izumi Y.. "An R83W mutation in Rab3A causes autosomal-dominant cerebellar ataxia". Human Molecular Genetics, 2026-01-06. DOI
Allendes osorio R.S., Chen Y.A., Mizuguchi K.. "SEND: a suite of tools for the easy sharing of linked biological data". Database, 2025-10-29. DOI
Ito S., Koyama T., Matsumoto S., Kojima R., Okamoto Y., Kuroda M., Kawashima H., Watanabe R., Yonezawa T., Sumiyoshi T., Ikeda K., Mizuguchi K., Iwata H., Okuno Y.. "Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization". Journal of Chemical Information and Modeling, 2025-10-22. DOI
Shirai Y., Enomoto T., Takeda Y., Edahiro R., Itoh M.T., Noda Y., Adachi Y., Nakayama M., Kawasaki T., Koba T., Futami Y., Yoshimura H., Amiya S., Hara R., Yamamoto M., Nakatsubo D., Suga Y., Naito M., Masuhiro K., Matsuki T., Hirata H., Iwahori K., Nagatomo I., Miyake K., Koyama S., Fukushima K., Shiroyama T., Naito Y., Futami S., Kitatani Y.N., Ose N., Funaki S., Nojima S., Shichino S., Yanagawa M., Shintani Y., Itoh M.N., Adachi J., Inoue Y., Tomonaga T., Okada Y., Mizuguchi K., Kumanogoh A.. "Serum vesicle biomarkers reflect the disease activity of idiopathic pulmonary fibrosis". Journal of Translational Medicine, 2025-10-15. DOI
Ramadhan D., Watanabe R., Mizuguchi K.. "Optimizing Multi-Task Learning with Evolutionary Relatedness Metrics for Enhanced QSAR-Based Natural Product Activity Prediction". ACS Omega, 2025-09-11. DOI
Kitatani Y.N., Kobiyama K., Igarashi Y., Aoshi T., Nakatsu N., Tripathi L.P., Ito J., Persson J.N., Kosugi Y., Osorio R.S.A., Nagao C., Temizoz B., Kuroda E., Standley D.M., Kiyono H., Nakanishi K., Uematsu S., Hamaguchi I., Yasutomi Y., Kunisawa J., Yamasaki S., Coban C., Yamada H., Mizuguchi K., Ishii K.J.. "An adjuvant database for preclinical evaluation of vaccines and immunotherapeutics". Cell Chemical Biology, 2025-08. DOI
Hu Y., Mizuguchi K., Hashimoto K.. "Unveiling unique expression patterns of D20S16 satellite DNA in human embryonic development". Scientific Reports, 2025-07-23. DOI
Yoshimura E., Hamada Y., Hatamoto Y., Nakagata T., Nanri H., Nakayama Y., Iwasaka C., Hayashi T., Suzuki I., Ando T., Takata K.I., Tanaka S., Ono R., Araki M., Kawashima H., Chen Y.A., Park J., Hosomi K., Mizuguchi K., Kunisawa J., Miyachi M.. "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, 2025-06-09. DOI
Chen Y.A., Kawashima H., Park J., Mohsen A., Hosomi K., Nakagata T., Murakami H., Nanri H., Miyachi M., Kunisawa J., Mizuguchi K.. "NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health". Scientific Reports, 2025-06-04. DOI
Nojima Y., Mizuguchi K.. "Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning". Computational Biology and Chemistry, 2025-06. DOI
Song J., Ui A., Mizuguchi K., Watanabe R.. "A Novel Method for Endometrial Cancer Patient Stratification Considering ARID1A Protein Expression and Activity with Effective Use of Multi-omics Data". Computational and Structural Biotechnology Journal, 2025-06. DOI
Ardiansah B., Farhan A., Nurhasanah N.S., Nasution M.A.F., Salleh N.M., Mizuguchi K., Cahyana A.H., Mardiana L.. "Dual antioxidant and cytotoxic activities of novel 1,2,3-triazole-decorated unsymmetrical monocarbonyl curcumin analogs". Case Studies in Chemical and Environmental Engineering, 2025-06. DOI
Permadi E.E., Watanabe R., Mizuguchi K.. "Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning". Journal of Cheminformatics, 2025-04-30. DOI
Wang Q., Wang Z., Mizuguchi K., Takao T.. "Biological age prediction using a DNN model based on pathways of steroidogenesis". Science Advances, 2025-03-14. DOI
Doi M., Inoue R., Hosomi K., Park J., Yumioka H., Syauki A.Y., Kageyama S., Sakaue H., Tanabe K., Mizuguchi K., Kunisawa J., Irie Y.. "Effects of Malted Rice Amazake Consumption on Nutritional Status and Gut Microbiome in Older Patients and Residents of an Integrated Facility for Medical and Long-Term Care". Journal of Nutrition in Gerontology and Geriatrics, 2025-01-16. DOI
Qian J., Watanabe T., Watanabe R., Kanno S.I., Takahashi A., Kohsaka S., Yoshino Y., Chiba N., Tanaka K., Kohno T., Yasui A., Ui A.. "BET family BRD3 initiates DSB-induced chromatin remodeling with TIP60 to promote R-loop-mediated HR.". Cell reports, 2025-11-25. DOI
Kanno S.I., Kobayashi T., Watanabe R., Kurimasa A., Tanaka K., Yasui A., Ui A.. "Armadillo domain of ARID1A directly interacts with DNA-PKcs to couple chromatin remodeling with nonhomologous end joining (NHEJ) pathway.". Nucleic acids research, 2025-03-13. DOI
Inoue R., Hosomi K., Park J., Sakaue H., Yumioka H., Kamitani H., Kinugasa Y., Harano K., Syauki A.Y., Doi M., Kageyama S., Yamamoto K., Mizuguchi K., Kunisawa J., Irie Y.. "Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home". Nutrients, 2024-11-08. DOI
Maruyama S., Matsuoka T., Hosomi K., Park J., Murakami H., Miyachi M., Kawashima H., Mizuguchi K., Kobayashi T., Ooka T., Yamagata Z., Kunisawa J.. "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". Frontiers in Nutrition, 2024-10-31. DOI
Kageyama S., Inoue R., Hosomi K., Park J., Yumioka H., Doi M., Miyake M., Nagashio Y., Shibuya Y., Oka N., Akazawa H., Kanzaki S., Mizuguchi K., Kunisawa J., Irie Y.. "Association Between Gut Microbiome Composition and Physical Characteristics in Patients with Severe Motor and Intellectual Disabilities: Perspectives from Microbial Diversity". Nutrients, 2024-10-19. DOI
Osorio R.S.A., Kosugi Y., Persson J.T.N., Mizuguchi K., Kitatani Y.N.. "A modern multi-omics data exploration experience with Panomicon". Bioinformatics Advances, 2024-10-03. DOI
Shoji H., Hirano H., Nojima Y., Gunji D., Shinkura A., Muraoka S., Abe Y., Narumi R., Nagao C., Aoki M., Obama K., Honda K., Mizuguchi K., Tomonaga T., Saito Y., Yoshikawa T., Kato K., Boku N., Adachi J.. "Phosphoproteomic subtyping of gastric cancer reveals dynamic transformation with chemotherapy and guides targeted cancer treatment". Cell Reports, 2024-10. DOI
Sato H., Taketomi Y., Murase R., Park J., Hosomi K., Sanada T.J., Mizuguchi K., Arita M., Kunisawa J., Murakami M.. "Group X phospholipase A2 links colonic lipid homeostasis to systemic metabolism via host-microbiota interaction". Cell Reports, 2024-10. DOI
Kuroda M., Kasahara Y., Hirose M., Yamaguma H., Oda M., Nagao C., Mizuguchi K.. "Construction of a Tm-Value Prediction Model and Molecular Dynamics Study of AmNA-Containing Gapmer Antisense Oligonucleotide". Molecular Therapy - Nucleic Acids, 2024-07-16. DOI
Uchida M., Park J., Fujie S., Hosomi K., Horii N., Watanabe K., Sanada K., Shinohara Y., Mizuguchi K., Kunisawa J., Iemitsu M., Miyachi M.. "Effect of resistance training and chicken meat on muscle strength and mass and the gut microbiome of older women: A randomized controlled trial". Physiological Reports, 2024-06-18. DOI
Enomoto T., Shirai Y., Takeda Y., Edahiro R., Shichino S., Nakayama M., Itoh M.T., Noda Y., Adachi Y., Kawasaki T., Koba T., Futami Y., Yaga M., Hosono Y., Yoshimura H., Amiya S., Hara R., Yamamoto M., Nakatsubo D., Suga Y., Naito M., Masuhiro K., Hirata H., Iwahori K., Nagatomo I., Miyake K., Koyama S., Fukushima K., Shiroyama T., Naito Y., Futami S., Kitatani Y.N., Nojima S., Yanagawa M., Shintani Y., Itoh M.N., Mizuguchi K., Adachi J., Tomonaga T., Inoue Y., Kumanogoh A.. "SFTPB in serum extracellular vesicles as a biomarker of progressive pulmonary fibrosis". JCI Insight, 2024-06-10. DOI
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., Takahashi M.I., 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., Itoh M.N., Ueki S., Kumanogoh A.. "Galectin-10 in serum extracellular vesicles reflects asthma pathophysiology". Journal of Allergy and Clinical Immunology, 2024-03. DOI
Saqib U., Demaree I.S., Obukhov A.G., Baig M.S., Khan M.S., Altwaijry N., Nasution M.A.F., Mizuguchi K., Hajela K.. "Structural and accessibility studies highlight the differential binding of clemizole to TRPC5 and TRPC6". Journal of Biomolecular Structure and Dynamics, 2024-01-27. DOI
Tomoto M., Mineharu Y., Sato N., Tamada Y., Itoh M.N., Kuroda M., Adachi J., Takeda Y., Mizuguchi K., Kumanogoh A., Kitatani Y.N., Okuno Y.. "Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information". Scientific Reports, 2024-01-15. DOI
Nagao C., Okuda H., Bekker G.J., Noguchi A., Takahashi T., Koizumi A., Youssefian S., Tezuka T., Akioka S.. "Familial Episodic Pain Syndrome: A Japanese Family Harboring the Novel Variant c.2431C>T (p.Leu811Phe) in SCN11A.". Biochemical genetics 2024, 2024-07-25. DOI
Gou Y., Re S., Mizuguchi K., Nagao C.. "Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model". ACS Medicinal Chemistry Letters, 2023-12-21. DOI
Koyama K., Hashimoto K., Nagao C., Mizuguchi K.. "Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties". Frontiers in Bioinformatics, 2023-12-18. DOI
Iwasaka C., Nanri H., Nakagata T., Ohno H., Tanisawa K., Konishi K., Murakami H., Hosomi K., Park J., Yamada Y., Ono R., Mizuguchi K., Kunisawa J., Miyachi M.. "Association of skeletal muscle function, quantity, and quality with gut microbiota in Japanese adults: A cross-sectional study.". Geriatrics & gerontology international, 2023-12-14. DOI
Yoshimura E., Hamada Y., Hatamoto Y., Nakagata T., Nanri H., Nakayama Y., Hayashi T., Suzuki I., Ando T., Ishikawa‐takata K., Tanaka S., Ono R., Park J., Hosomi K., Mizuguchi K., Kunisawa J., Miyachi M.. "Effects of energy loads on energy and nutrient absorption rates and gut microbiome in humans: A randomized crossover trial". Obesity, 2023-11-05. DOI
Kageyama S., Inoue R., Park J., Hosomi K., Yumioka H., Suka T., Teramoto K., Syauki A.Y., Doi M., Sakaue H., Miyake M., Mizuguchi K., Kunisawa J., Irie Y.. "Changes in Fecal Gut Microbiome of Home Healthcare Patients with Disabilities through Consumption of Malted Rice Amazake". Physiological Genomics, 2023-09-11. DOI
Park J., Bushita H., Nakano A., Hara A., Ueno H.M., Ozato N., Hosomi K., Kawashima H., Chen Y.A., 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, 2023-07-26. DOI
Akazawa N., Nakamura M., Eda N., Murakami H., Nakagata T., Nanri H., Park J., Hosomi K., Mizuguchi K., Kunisawa J., Miyachi M., Hoshikawa M.. "Gut microbiota alternation with training periodization and physical fitness in Japanese elite athletes". Frontiers in Sports and Active Living, 2023-07-14. DOI
Kawashima H., Watanabe R., Esaki T., Kuroda M., Nagao C., Kitatani Y.N., Ohashi R., Komura H., Mizuguchi K.. "DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform". Journal of Medicinal Chemistry, 2023-07-14. DOI
Alarabi A.B., Mohsen A., Taleb Z.B., Mizuguchi K., Alshbool F.Z., Khasawneh F.T.. "Predicting thrombotic cardiovascular outcomes induced by waterpipe-associated chemicals using comparative toxicogenomic database: Genes, phenotypes, and pathways". Life Sciences, 2023-06. DOI
Martin , Watanabe R., Hashimoto K., Higashisaka K., Haga Y., Tsutsumi Y., Mizuguchi K.. "Evidence-Based Prediction of Cellular Toxicity for Amorphous Silica Nanoparticles". ACS Nano, 2023-05-30. DOI
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.. "Characteristic Gut Bacteria in High Barley Consuming Japanese Individuals without Hypertension". Microorganisms, 2023-05-09. DOI
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, 2023-03. DOI
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". Frontiers in Chemistry, 2023-01-09. DOI
Komura H., Watanabe R., Mizuguchi K.. "The Trends and Future Prospective of In Silico Models from the Viewpoint of ADME Evaluation in Drug Discovery". Pharmaceutics, 2023-11-12. DOI
Koyama K., Hashimoto K., Nagao C., Mizuguchi K.. "Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties". Frontiers in Bioinformatics 2023, 3, 2023-12-18. DOI
Watanabe R., Kawata T., Ueda S., Shinbo T., Higashimori M., Kitatani Y.N., Mizuguchi K.. "Prediction of the Contribution Ratio of a Target Metabolic Enzyme to Clearance from Chemical Structure Information". Molecular Pharmaceutics, 2022-12-20. DOI
Sawane K., Hosomi K., Park J., Ookoshi K., Nanri H., Nakagata T., Chen Y.A., Mohsen A., Kawashima H., Mizuguchi K., Miyachi M., Kunisawa J.. "Identification of Human Gut Microbiome Associated with Enterolignan Production". Microorganisms, 2022-10-31. DOI
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, 2022-10-25. DOI
Hosomi K., Saito M., Park J., Murakami H., Shibata N., Ando M., Nagatake T., Konishi K., Ohno H., Tanisawa K., Mohsen A., Chen Y.A., Kawashima H., Kitatani Y.N., 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, 2022-08-18. DOI
Chen Y.A., Osorio R.S.A., Mizuguchi K.. "TargetMine 2022: A new vision into drug target analysis.". Bioinformatics (Oxford, England), 2022-07-27. DOI
Gupta S., Vundavilli H., Osorio R.S.A., Itoh M.N., Mohsen A., Datta A., Mizuguchi K., Tripathi L.P.. "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, 2022-07-12. DOI
Mohsen A., Chen Y.A., Osorio R.S.A., Higuchi C., Mizuguchi K.. "Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2". Frontiers in Bioinformatics, 2022-07-01. DOI
Park J., Hosomi K., Kawashima H., Chen Y.A., Mohsen A., Ohno H., Konishi K., Tanisawa K., Kifushi M., Kogawa M., Takeyama H., Murakami H., Kubota T., Miyachi M., Kunisawa J., Mizuguchi K.. "Dietary Vitamin B1 Intake Influences Gut Microbial Community and the Consequent Production of Short-Chain Fatty Acids.". Nutrients, 2022-05-16. DOI
Alarabi A.B., Mohsen A., Mizuguchi K., Alshbool F.Z., Khasawneh F.T.. "Co-expression analysis to identify key modules and hub genes associated with COVID-19 in platelets". BMC Medical Genomics, 2022-04. DOI
Ikubo Y., Sanada T.J., 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, 2022-04. DOI
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, 2022-03-24. DOI
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, 2022-03-14. DOI
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, 2022-03. DOI
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, 2022-03. DOI
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, 2022-03. DOI
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.G.B., Ikeda K., Arita M., Murakami M.. "Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota". JCI Insight, 2022-01-25. DOI
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, 2022. DOI
Arakawa M., Tabata K., Ishida K., Kobayashi M., Arai A., Ishikawa T., Suzuki R., Takeuchi H., Tripathi L.P., Mizuguchi K., Morita E.. "Flavivirus recruits the valosin-containing protein (VCP)/NPL4 complex to induce stress granule disassembly for efficient viral genome replication". Journal of Biological Chemistry, 2022-01. DOI
Takano J., Ito S., Dong Y., Sharif J., Takagi Y.N., Umeyama T., Han Y.W., Isono K., Kondo T., Iizuka Y., Miyai T., Koseki Y., Ikegaya M., Sakihara M., Nakayama M., Ohara O., Hasegawa Y., Hashimoto K., Arner E., Klose R.J., Iwama A., Koseki H., Ikawa T.. "PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment". Nature Communications, 2022-11-28. DOI
Pascarella G., Hon C.C., Hashimoto K., Busch A., Luginbühl J., Parr C., Yip W.H., Abe K., Kratz A., Bonetti A., Agostini F., Severin J., Murayama S., Suzuki Y., Gustincich S., Frith M., Carninci P.. "Recombination of repeat elements generates somatic complexity in human genomes.". Cell, 2022-08-04. DOI
Vuoristo S., Bhagat S., Granskog C.H., Yoshihara M., Gawriyski L., Jouhilahti E.M., Ranga V., Tamirat M., Huhtala M., Kirjanov I., Nykänen S., Krjutškov K., Damdimopoulos A., Weltner J., Hashimoto K., Recher G., Ezer S., Paluoja P., Paloviita P., Takegami Y., Kanemaru A., Lundin K., Airenne T.T., Otonkoski T., Tapanainen J.S., Kawaji H., Murakawa Y., Bürglin T.R., Varjosalo M., Johnson M.S., Tuuri T., Katayama S., Kere J.. "DUX4 is a multifunctional factor priming human embryonic genome activation.". iScience, 2022-04-15. DOI
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, 2022-11. DOI
Kageyama S., Inoue R., Hosomi K., Park J., Yumioka H., Suka T., Kurohashi Y., Teramoto K., Syauki A.Y., 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, 2021-12-14. DOI
Park J., Kato K., Murakami H., Hosomi K., Tanisawa K., Nakagata T., Ohno H., Konishi K., Kawashima H., Chen Y.A., Mohsen A., Xiao J.Z., 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, 2021-12. DOI
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, 2021-11-19. DOI
Mohsen A., Tripathi L.P., Mizuguchi K.. "Deep Learning Prediction of Adverse Drug Reactions in Drug Discovery Using Open TG–GATEs and FAERS Databases". Frontiers in Drug Discovery, 2021-10-27. DOI
Tomizawa R., Park J., Matsumoto N., Hosomi K., Kawashima H., Mizuguchi K., Kunisawa J., Honda C.. "Relationship between Human Gut Microbiota and Nutrition Intake in Hypertensive Discordant Monozygotic Twins". Journal of Hypertension: Open Access, 2021-08.
Lee J., Mohsen A., Banerjee A., Mccullough L.D., Mizuguchi K., Shimaoka M., Kiyono H., Park E.J.. "Distinct Age-Specific miRegulome Profiling of Isolated Small and Large Intestinal Epithelial Cells in Mice". International Journal of Molecular Sciences, 2021-03-29. DOI
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, 2021-03-16. DOI
Vundavilli H., P.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, 2021-02-25. DOI
Watanabe R., Esaki T., Ohashi R., Kuroda M., Kawashima H., Komura H., Kitatani Y.N., 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, 2021-02-23. DOI
Re S., Mizuguchi K.. "Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein". The Journal of Physical Chemistry B, 2021-02-19. DOI
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, 2021-01. DOI
Hashimoto K., Jouhilahti E.M., Töhönen V., Carninci P., Kere J., Katayama S.. "Embryonic LTR retrotransposons supply promoter modules to somatic tissues". Genome Research, 2021-11. DOI
Abugessaisa I., Ramilowski J.A., Lizio M., Severin J., Hasegawa A., Harshbarger J., Kondo A., Noguchi S., Yip C.W., Ooi J.L.C., Tagami M., Hori F., Agrawal S., Hon C.C., Cardon M., Ikeda S., Ono H., Bono H., Kato M., Hashimoto K., Bonetti A., Kato M., Kobayashi N., Shin J., Hoon M.D., Hayashizaki Y., Carninci P., Kawaji H., Kasukawa T.. "FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.". Nucleic acids research, 2021-01-08. DOI
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, 2021-05. DOI
Tripathi L.P., Itoh M.N., 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, 2020-12-10. DOI
Chen Y.A., Park J., Kitatani Y.N., 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, 2020-12-04. DOI
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, 2020-12. DOI
Nojima Y., Takeda Y., Maeda Y., Bamba T., Fukusaki E., Itoh M.N., 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, 2020-09-22. DOI
Osorio R.S.A., Persson J.T.N., Nojima Y., Kosugi Y., Mizuguchi K., Kitatani Y.N.. "Panomicon: A web-based environment for interactive, visual analysis of multi-omics data.". Heliyon, 2020-08. DOI
Saito A., Tsuchiya D., Sato S., Okamoto A., Murakami Y., Mizuguchi K., Toh H., Nemoto W.. "Update of the GRIP web service.". Journal of receptor and signal transduction research, 2020-08. DOI
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.I.. "Gut microbial composition in patients with atrial fibrillation: effects of diet and drugs.". Heart and vessels, 2020-07-18. DOI
Sanada T.J., 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.. "Gut microbiota modification suppresses the development of pulmonary arterial hypertension in an SU5416/hypoxia rat model". Pulmonary Circulation, 2020-07. DOI
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, 2020-02. DOI
Kajihara D., Hon C.C., Abdullah A.N., Jr J.W., Moretti A.I.S., Poloni J.F., Bonatto D., Hashimoto K., Carninci P., Laurindo F.R.M.. "Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene.". BMC genomics, 2020-11-04. DOI
Taguchi A., Nagasaka K., Plessy C., Nakamura H., Kawata Y., Kato S., Hashimoto K., Nagamatsu T., Oda K., Kukimoto I., Kawana K., Carninci P., Osuga Y., Fujii T.. "Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages.". Scientific reports, 2020-10-22. DOI
Ramilowski J.A., Yip C.W., Agrawal S., Chang J.C., Ciani Y., Kulakovskiy I.V., Mendez M., Ooi J.L.C., Ouyang J.F., Parkinson N., Petri A., Roos L., Severin J., Yasuzawa K., Abugessaisa I., Akalin A., Antonov I.V., Arner E., Bonetti A., Bono H., Borsari B., Brombacher F., Cameron C.J., Cannistraci C.V., Cardenas R., Cardon M., Chang H., Dostie J., Ducoli L., Favorov A., Fort A., Garrido D., Gil N., Gimenez J., Guler R., Handoko L., Harshbarger J., Hasegawa A., Hasegawa Y., Hashimoto K., Hayatsu N., Heutink P., Hirose T., Imada E.L., Itoh M., Kaczkowski B., Kanhere A., Kawabata E., Kawaji H., Kawashima T., Kelly S.T., Kojima M., Kondo N., Koseki H., Kouno T., Kratz A., Stolarska M.K., Kwon A.T.J., Leek J., Lennartsson A., Lizio M., Redondo F.L., Luginbühl J., Maeda S., Makeev V.J., Marchionni L., Medvedeva Y.A., Minoda A., Müller F., Aguirre M.M., Murata M., Nishiyori H., Nitta K.R., Noguchi S., Noro Y., Nurtdinov R., Okazaki Y., Orlando V., Paquette D., Parr C.J.C., Rackham O.J.L., Rizzu P., Martinez D.F.S., Sandelin A., Sanjana P., Semple C.A.M., Shibayama Y., Sivaraman D.M., Suzuki T., Szumowski S.C., Tagami M., Taylor M.S., Terao C., Thodberg M., Thongjuea S., Tripathi V., Ulitsky I., Verardo R., Vorontsov I.E., Yamamoto C., Young R.S., Baillie J.K., Forrest A.R.R., Guigó R., Hoffman M.M., Hon C.C., Kasukawa T., Kauppinen S., Kere J., Lenhard B., Schneider C., Suzuki H., Yagi K., Hoon M.J.L.D., Shin J.W., Carninci P.. "Functional annotation of human long noncoding RNAs via molecular phenotyping.". Genome research, 2020-07. DOI
Bonetti A., Agostini F., Suzuki A.M., Hashimoto K., Pascarella G., Gimenez J., Roos L., Nash A.J., Ghilotti M., Cameron C.J.F., Valentine M., Medvedeva Y.A., Noguchi S., Agirre E., Kashi K., Samudyata , Luginbühl J., Cazzoli R., Agrawal S., Luscombe N.M., Blanchette M., Kasukawa T., Hoon M.D., Arner E., Lenhard B., Plessy C., Branco G.C., Orlando V., Carninci P.. "RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.". Nature communications, 2020-02-24. DOI
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, 2020-04-27. DOI
Mohsen A., Park J., Chen Y.A., Kawashima H., Mizuguchi K.. "Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks". BMC Bioinformatics, 2019-12. DOI
Allendes R.S., Tripathi L.P., Mizuguchi K.. "CLINE: a web-tool for the comparison of biological dendrogram structures". BMC Bioinformatics, 2019-12. DOI
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 Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains". Scientific Reports, 2019-12. DOI
Chiba S., Ohue M., Gryniukova A., Borysko P., Zozulya S., Yasuo N., Yoshino R., Ikeda K., Shin W.H., Kihara D., Iwadate M., Umeyama H., Ichikawa T., Teramoto R., Hsin K.Y., Gupta V., Kitano H., Sakamoto M., Higuchi A., Miura N., Yura K., Mochizuki M., Ramakrishnan C., Thangakani A.M., Velmurugan D., Gromiha M.M., Nakane I., Uchida N., Hakariya H., Tan M., Nakamura H.K., Suzuki S.D., Ito T., Kawatani M., Kudoh K., Takashina S., Yamamoto K.Z., Moriwaki Y., Oda K., Kobayashi D., Okuno T., Minami S., Chikenji G., Prathipati P., Nagao C., Mohsen A., Ito M., Mizuguchi K., Honma T., Ishida T., Hirokawa T., Akiyama Y., Sekijima M.. "A prospective compound screening contest identified broader inhibitors for Sirtuin 1". Scientific Reports, 2019-12. DOI
Watanabe R., Ohashi R., Esaki T., Kawashima H., Natsume Y., Nagao C., Mizuguchi K.. "Development of an in silico prediction system of human renal excretion and clearance from chemical structure information incorporating fraction unbound in plasma as a descriptor". Scientific Reports, 2019-12. DOI
Chen Y.A., Tripathi L.P., Fujiwara T., Kameyama T., Itoh M.N., Mizuguchi K.. "The TargetMine Data Warehouse: Enhancement and Updates". Frontiers in Genetics, 2019-10. DOI
Esaki T., Ohashi R., Watanabe R., Natsume Y., Kawashima H., Nagao C., Komura H., Mizuguchi K.. "Constructing an in silico three-class predictor of human intestinal absorption with Caco-2 permeability and dried-DMSO solubility". Journal of Pharmaceutical Sciences, 2019-07. DOI
Esaki T., Ohashi R., Watanabe R., Kitatani Y.N., Kawashima H., Nagao C., Mizuguchi K.. "Computational Model To Predict the Fraction of Unbound Drug in the Brain". Journal of Chemical Information and Modeling, 2019-07. DOI
Ohashi R., Watanabe R., Esaki T., Taniguchi T., Katori N.T., 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". Molecular Pharmaceutics, 2019-04. DOI
Kataoka Y., Fujita H., Afanaseva A., Nagao C., Mizuguchi K., Kasahara Y., Obika S., Kuwahara M.. "High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives". Biochemistry, 2019-02. DOI
Chen Y.A., Yogo E., Kurihara N., Ohno T., Higuchi C., Rokushima M., Mizuguchi K.. "Assessing drug target suitability using TargetMine". F1000Research, 2019-02. DOI
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, 2019-01-01. DOI
Afanasyeva A., Nagao C., Mizuguchi K.. "Prediction of the secondary structure of short DNA aptamers". Biophysics and Physicobiology, 2019. DOI
Hashimoto K., Kouno T., Ikawa T., Hayatsu N., Miyajima Y., Yabukami H., Terooatea T., Sasaki T., Suzuki T., Valentine M., Pascarella G., Okazaki Y., Suzuki H., Shin J.W., Minoda A., Taniuchi I., Okano H., Arai Y., Hirose N., Carninci P.. "Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians". Proceedings of the National Academy of Sciences, 2019-11-26. DOI
Yamanaka S., Nishihara H., Toh H., Nagai L.A.E., Hashimoto K., Park S.J., Shibuya A., Suzuki A.M., Tanaka Y., Nakai K., Carninci P., Sasaki H., Siomi H.. "Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation.". Developmental cell, 2019-10-07. DOI
Valentine M.N.Z., Hashimoto K., Fukuhara T., Saiki S., Ishikawa K.I., Hattori N., Carninci P.. "Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson's Disease.". Scientific data, 2019-04-05. DOI
Watanabe K., Liu Y., Noguchi S., Murray M., Chang J.C., Kishima M., Nishimura H., Hashimoto K., Minoda A., Suzuki H.. "OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages.". Scientific reports, 2019-04. DOI
Pawlak M., Kedzierska K.Z., Migdal M., Nahia K.A., Ramilowski J.A., Bugajski L., Hashimoto K., Marconi A., Piwocka K., Carninci P., Winata C.L.. "Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.". Genome research, 2019-03. DOI
Murakami K., Nguyen T.H.V., Nagao C., Mizuguchi K., Bitan G.. "Lysine-Targeting Inhibitors of Amyloidogenic Protein Aggregation: A Promise for Neurodegenerative Proteinopathies". JACS Au, 2025-08-11. DOI
Tripathi L.P., Osorio R.S.A., Murakami Y., Chen Y.A., Mizuguchi K.. "Network-Based Analysis for Biological Knowledge Discovery". Reference Module in Life Sciences, 2024-12. DOI
Komura H., Watanabe R., Mizuguchi K.. "The Trends and Future Prospective of In Silico Models from the Viewpoint of ADME Evaluation in Drug Discovery". Pharmaceutics, 2023-11-12. DOI
Murakami Y., Mizuguchi K.. "Recent developments of sequence-based prediction of protein-protein interactions.". Biophysical reviews, 2022-12-24. DOI
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, 2022-08-13. DOI
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, 2021-01. DOI
Chen Y.A., Tripathi L.P., Mizuguchi K.. "Data Warehousing with TargetMine for Omics Data Analysis". Methods in Molecular Biology, 2019. DOI
Tripathi L.P., Chen Y.A., Mizuguchi K., Morita E.. "Network-Based Analysis of Host-Pathogen Interactions". Encyclopedia of Bioinformatics and Computational Biology, 2019. DOI
Tripathi L.P., Chen Y.A., Mizuguchi K., Murakami Y.. "Network-Based Analysis for Biological Discovery". Encyclopedia of Bioinformatics and Computational Biology, 2019. DOI
Tripathi L.P., Esaki T., Itoh M.N., Chen Y.A., Mizuguchi K.. "Integrative Analysis of Multi-Omics Data". Encyclopedia of Bioinformatics and Computational Biology, 2019. DOI
Afanasyeva A., Nagao C., Mizuguchi K.. "Protein Interactions: Computational Methods, Analysis and Applications". , 2020-03.