Publications
Original articles
2024
- 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, 14(1)
https://doi.org/10.1038/s41598-023-50905-8
2023
- 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
https://doi.org/10.1021/acsmedchemlett.3c00376
- 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
https://doi.org/10.3389/fbinf.2023.1274599
- 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
https://doi.org/10.1111/ggi.14751
- 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
https://doi.org/10.1002/oby.23935
- 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
https://doi.org/10.1152/physiolgenomics.00062.2023
- 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, 11(8), 1892-1892
https://doi.org/10.3390/microorganisms11081892
- 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, 5
https://doi.org/10.3389/fspor.2023.1219345
- 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
https://doi.org/10.1021/acs.jmedchem.3c00481
- 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, 323121694-121694
https://doi.org/10.1016/j.lfs.2023.121694
- 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
https://doi.org/10.1021/acsnano.2c11968
- 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
https://doi.org/10.3390/microorganisms11051246
- 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
https://doi.org/10.1016/j.csbj.2023.03.006
- 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, 10
https://doi.org/10.3389/fchem.2022.1090643
- 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, 15(11), 2619-2619
https://doi.org/10.3390/pharmaceutics15112619
2022
- 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
https://doi.org/10.1021/acs.molpharmaceut.2c00698
- 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(11), 2169-2169
https://doi.org/10.3390/microorganisms10112169
- 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, 290(9), 2366-2378
https://doi.org/10.1111/febs.16666
- 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, 13(1), 4477-4477
https://doi.org/10.1038/s41467-022-32015-7
- Chen, Y.A.; Osorio, R.S.A.; Mizuguchi, K.
TargetMine 2022: A new vision into drug target analysis.
Bioinformatics (Oxford, England) 2022
https://doi.org/10.1093/bioinformatics/btac507
- 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, PP
https://doi.org/10.1109/JBHI.2022.3190038
- 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, 2893933-893933
https://doi.org/10.3389/fbinf.2022.893933
- 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, 14(10)
https://doi.org/10.3390/nu14102078
- 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, 15(1)
https://doi.org/10.1186/s12920-022-01222-y
- 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, 22(1)
https://doi.org/10.1186/s12890-022-01932-0
- Kitatani, Y.N.; Itoh, M.N.; Takeda, Y.; Kuroda, M.; Hirata, H.; Miyake, K.; Shiroyama,
T.; Shirai, Y.; Noda, Y.; Adachi, Y.; Enomoto, T.; Amiya, S.; Adachi, J.; Narumi, R.;
Muraoka, S.; Tomonaga, T.; Kurohashi, S.; Cheng, F.; Tanaka, R.; Yada, S.; Aramaki, E.;
Wakamiya, S.; Chen, Y.A.; Higuchi, C.; Nojima, Y.; Fujiwara, T.; Nagao, C.; Matsumura,
Y.; Mizuguchi, K.; Kumanogoh, A.; Ueda, N.
Data-driven patient stratification and drug target discovery by using medical
information and serum proteome data of idiopathic pulmonary fibrosis
patients
2022
https://doi.org/10.21203/rs.3.rs-405195/v2
- 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, 9
https://doi.org/10.3389/fnut.2022.812469
- 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, 1(4), 304-312
https://doi.org/10.1038/s44160-022-00037-0
- 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, 12(1)
https://doi.org/10.1038/s41598-022-08430-7
- 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, 8(1), 23-23
https://doi.org/10.1186/s40795-022-00500-3
- 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, 42(3), 1589-1598
https://doi.org/10.21873/anticanres.15633
- 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, 7(2)
https://doi.org/10.1172/jci.insight.152611
- 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, 13(10), 3027-3034
https://doi.org/10.1039/d1sc06596c
- 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, 101597-101597
https://doi.org/10.1016/j.jbc.2022.101597
- 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, 13(1), 7159-7159
https://doi.org/10.1038/s41467-022-34856-8
- 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, 185(16), 3025-3040
https://doi.org/10.1016/j.cell.2022.06.032
- 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, 25(4), 104137-104137
https://doi.org/10.1016/j.isci.2022.104137
- 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, 103339-103339
https://doi.org/10.1016/j.drudis.2022.103339
2021
- 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, 13(12), 4466-4466
https://doi.org/10.3390/nu13124466
- 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, 21(1), 151-151
https://doi.org/10.1186/s12866-021-02215-0
- 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,
11741654-741654
https://doi.org/10.3389/fcimb.2021.741654
- 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, 1
https://doi.org/10.3389/fddsv.2021.768792
- 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, 10(8)
https://www.hilarispublisher.com/open-access/relationship-between-human-gut-microbiota-and-nutrition-intake-in-hypertensive-discordant-monozygotic-twins-73881.html
- Kitatani, Y.N.; Mizuguchi, K.; Ueda, N.
Subset-binding: A novel algorithm to detect paired itemsets from heterogeneous data
including biological datasets
2021
https://doi.org/10.21203/rs.3.rs-405195/v1
- 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, 22(7),
3544-3544
https://doi.org/10.3390/ijms22073544
- 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, 57(3), 275-275
https://doi.org/10.3390/medicina57030275
- 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, 110647-110647
https://doi.org/10.1016/j.jtbi.2021.110647
- 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
https://doi.org/10.1021/acs.jmedchem.0c02011
- Re, S.; Mizuguchi, K.
Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop
Protein
The Journal of Physical Chemistry B 2021, 125(8), 2089-2097
https://doi.org/10.1021/acs.jpcb.0c11516
- 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, 7(1), 00658-2020
https://doi.org/10.1183/23120541.00658-2020
- 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, 31(11), 1983-1993
https://doi.org/10.1101/gr.275354.121
- 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, 49(D1), D892-D898
https://doi.org/10.1093/nar/gkaa1054
2020
- 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, 11585998-585998
https://doi.org/10.3389/fgene.2020.585998
- 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, 15(12), e0243609-e0243609
https://doi.org/10.1371/journal.pone.0243609
- 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, Volume
1327-40
https://doi.org/10.2147/aabc.s278900
- 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, 10(11), 2427-2436
https://doi.org/10.1002/2211-5463.12982
- 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, 6(8), e04618-e04618
https://doi.org/10.1016/j.heliyon.2020.e04618
- 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, 40(4),
348-356
https://doi.org/10.1080/10799893.2020.1734821
- 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, 36(1), 105-114
https://doi.org/10.1007/s00380-020-01669-y
- 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, 10(3),
204589402092914-204589402092914
https://doi.org/10.1177/2045894020929147
- 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, 54141-51
https://doi.org/10.1016/j.virol.2019.11.015
- 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, 21(1), 766-766
https://doi.org/10.1186/s12864-020-07164-y
- 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(1), 17991-17991
https://doi.org/10.1038/s41598-020-75133-2
- 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, 30(7), 1060-1072
https://doi.org/10.1101/gr.254219.119
- 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, 11(1), 1018-1018
https://doi.org/10.1038/s41467-020-14337-6
- 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 2020, 26(5), 1275-1283
https://doi.org/10.1016/j.drudis.2021.01.024
- 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, 20(0), 5-18
https://doi.org/10.1273/cbij.20.5
- 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, Volume
1327-40
https://doi.org/10.2147/AABC.S278900
2019
- 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, 20(1), 581
https://doi.org/10.1186/s12859-019-3187-5
- Allendes, R.S.; Tripathi, L.P.; Mizuguchi, K.
CLINE: a web-tool for the comparison of biological dendrogram structures
BMC Bioinformatics 2019, 20(1), 528
https://doi.org/10.1186/s12859-019-3149-y
- 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, 9(1), 12794-12794
https://doi.org/10.1038/s41598-019-49232-8
- 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, 9(1), 19585
https://doi.org/10.1038/s41598-019-55069-y
- 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, 9(1), 18782-18782
https://doi.org/10.1038/s41598-019-55325-1
- Afanasyeva, A.; Nagao, C.; Mizuguchi, K.
Prediction of the secondary structure of short DNA aptamers
Biophysics and Physicobiology 2019, 16(0), 287-294
https://doi.org/10.2142/biophysico.16.0_287
- R§, W.; R§, O.; Esaki, T.; Taniguchi, T.; Torimoto, 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. Pharmaceutics 2019, 16(5), 1851-1863
Reviews
2023
- 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, 15(11), 2619-2619
https://doi.org/10.3390/pharmaceutics15112619
2022
- Murakami, Y.; Mizuguchi, K.
Recent developments of sequence-based prediction of protein-protein
interactions.
Biophysical reviews 2022, 1-19
https://doi.org/10.1007/s12551-022-01038-1
- 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, 103339-103339
https://doi.org/10.1016/j.drudis.2022.103339
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
https://doi.org/10.1016/j.drudis.2021.01.024
2019
- Chen, Y.A.; Tripathi, L.P.; Mizuguchi, K.
Data Warehousing with TargetMine for Omics Data Analysis
Methods in Molecular Biology 2019, 35-64
https://doi.org/10.1007/978-1-4939-9442-7_3
- Tripathi, L.P.; Chen, Y.A.; Mizuguchi, K.; Morita, E.
Network-Based Analysis of Host-Pathogen Interactions
Encyclopedia of Bioinformatics and Computational Biology 2019, 932
https://doi.org/10.1016/b978-0-12-809633-8.20170-2
- Tripathi, L.P.; Chen, Y.A.; Mizuguchi, K.; Murakami, Y.
Network-Based Analysis for Biological Discovery
Encyclopedia of Bioinformatics and Computational Biology 2019, 283
https://doi.org/10.1016/b978-0-12-809633-8.20674-2
- 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, 194
https://doi.org/10.1016/b978-0-12-809633-8.20096-4
Books
2020
- Afanasyeva, A.; Nagao, C.; Mizuguchi, K.
Protein Interactions: Computational Methods, Analysis and Applications
World Scientific 2020 (DOI: 10.1142/11596)
https://doi.org/10.1142/11596
論文
原著論文
2023
- 長尾 知生子, 鎌田 真由美, 中津井 雅彦, 深川 明子, 片山 俊明, 川島 秀一, 水口 賢司, 安倍 理加
医薬品関連文書の利活用に向けたインタビューフォームの構造化の提案
医薬品情報学 2023, 24(4), 187-195
https://doi.org/10.11256/jjdi.24.187
総説
2023
- MARTIN, 渡邉怜子, 水口賢司
ナノ粒子をより安全に 設計するための新手法 ──ナノ粒子の安全性に革命を: AI が拓く未来
化学 2023, 78(11), 27-30
- 伊藤 眞里, 武田 吉人, 黒田 正孝, 荒牧 英治, 黒橋 禎夫, 武田 理宏, 梁川 雅弘, 富山 憲幸, 松村 泰志, 足立 淳, 水口 賢司, 上田 修功, 熊ノ郷 淳, 夏目 やよい
「新薬創出を加速する人工知能の開発」 IPF患者臨床データから創薬標的への知識処理
日本呼吸器学会誌 2023, 12(増刊), 293-293
https://search.jamas.or.jp/default/link?pub_year=2023&ichushi_jid=J05953&link_issn=&doc_id=20230602311042&doc_link_id=%2Fci6respo%2F2023%2Fv012s1%2F118%2F0293-0293%26dl%3D0&url=https%3A%2F%2Fwww.medicalonline.jp%2Fjamas.php%3FGoodsID%3D%2Fci6respo%2F2023%2Fv012s1%2F118%2F0293-0293%26dl%3D0&type=MedicalOnline&icon=https%3A%2F%2Fjk04.jamas.or.jp%2Ficon%2F00004_2.gif
- 橋本 浩介, 新井 康通
百寿者にみる老化後期におけるリンパ球の変化
実験医学 2023, 41(8), 1276-1279
https://doi.org/10.18958/7239-00001-0000457-00
- Martin, 渡邉怜子, 水口賢司
ナノ粒子をより安全に設計するための新手法~ナノ粒子の安全性に革命を: AIが拓く未来
化学 2023, 78(11), 27-30
2022
- 中村 恵宣, 北村 英也, 小倉 髙志, 夏目 やよい, 水口 賢司
官民研究開発投資拡大プログラム(PRISM)で構築する特発性肺線維症に対する創薬標的探索プラットフォームについて
MEDCHEM NEWS 2022, 32(3), 119-123
https://doi.org/10.14894/medchem.32.3_119
- 橋本浩介, 新井康通
加速する1細胞レベルのT細胞レセプター解析-百寿者研究への応用-
月刊臨床免疫・アレルギー科 2022, 78(2), 194-198
https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202202285768942279
- 橋本浩介
トランスクリプトームデータの一般的な解析手順
医学のあゆみ 2022, 280(12), 1267-1272
2021
- 陳 怡安, 李 秀栄, 水口 賢司
TargetMineによる生物学的知識の発見 (第1土曜特集 構造生命科学による創薬への挑戦) -- (計算機から創薬へ)
医学のあゆみ 2021, 278(6), 641-645
http://ci.nii.ac.jp/naid/40022640974
- 橋本浩介, 新井康通
百寿者免疫細胞の1細胞トランスクリプトーム解析
医学のあゆみ 2021, 276(10), 998-1002
https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202102229430192665
2020
- 渡邉 怜子, 水口 賢司
人工知能(AI)を用いた創薬プロセスの加速におけるデータの重要性 (第5土曜特集 AIが切り拓く未来の医療) -- (AI技術の創薬への応用)
医学のあゆみ 2020, 274(9), 838-842
http://ci.nii.ac.jp/naid/40022324961
- 夏目 やよい, 水口 賢司
【人工知能(AI)技術のヘルスケア利活用】新薬創出を加速するAIの開発
Precision Medicine 2020, 3(5), 410-413
- 長尾 知生子, 水口 賢司
【イメージング時代の構造生命科学 細胞の動態、膜のないオルガネラ、分子の構造変化をトランススケールに観る】(第4章)活用可能なデータベースとプラットフォーム
対象タンパク質を理解するための有用なデータベース
実験医学 2020, 38(5), 897-901
https://search.jamas.or.jp/index.php?module=Default&action=Link&pub_year=2020&ichushi_jid=J01704&link_issn=&doc_id=20200325180034&doc_link_id=%2Fai4jigkb%2F2020%2F003805%2F038%2F
0897b0901%26dl%3D3&url=http%3A%2F%2Fwww.medicalonline.jp%2Fjamas.php%3FGoodsID%3D%2Fai4jigkb%2F2020%2F003805%2F038%2F0897b0901%26dl%
3D3&type=MedicalOnline&icon=https%3A%2F%2Fjk04.jamas.or.jp%2Ficon%2F00004_4.gif
- 橋本浩介
一細胞トランスクリプトーム解析の現況
月刊臨床免疫・アレルギー科 2020, 74(1), 93-96
https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202002260551204881
- 渡邉 怜子, 水口 賢司
人工知能(AI)を用いた創薬プロセスの加速におけるデータの重要性 (第5土曜特集 AIが切り拓く未来の医療) -- (AI技術の創薬への応用)
医学のあゆみ 2020, 274(9), 838-842
http://ci.nii.ac.jp/naid/40022324961
書籍
2023
- 陳 怡安, 朴 鐘旭, 水口賢司
健康と疾患を制御する精密栄養学 : 「何を、いつ、どう食べるか?」に、食品機能の解析と個人差を生む分子メカニズムの解明から迫る
羊土社 2023 (ISBN: 9784758104111)
http://ci.nii.ac.jp/ncid/BD02380087
- 村上洋一, 長尾知生子, 水口賢司
ケモインフォマティクスにおけるデータ収集の最適化と解析手法
技術情報協会 2023 (ISBN: 9784861049446)
http://ci.nii.ac.jp/ncid/BD02068623
2022
- 夏目やよい, 水口賢司
革新的AI創薬 : 医療ビッグデータ、人工知能がもたらす創薬研究の未来像
エヌ・ティー・エス 2022 (ISBN: 9784860437886)
http://ci.nii.ac.jp/ncid/BC15983667
- 池田和由, 米澤朋起, 渡邉怜子, 渡邉博文, 高橋一敏, 半田佑磨, 増田友秀, 朴鐘旭, 櫻井研吾, 熊澤啓子, 江崎剛史
特別企画「気になるツールを使ってみよう(第1回)」
CBI学会誌編集委員会 2022
2021
- 長尾知生子, 李 秀栄, 水口賢司
創薬研究のための相互作用解析パーフェクト : 低中分子・抗体創薬におけるスクリーニング戦略と実例、in silico解析、一歩進んだ分析技術まで
羊土社 2021 (ISBN: 9784758122566)
http://ci.nii.ac.jp/ncid/BC11391757
- 渡邉怜子
ホットトピックス「自動化された薬物動態予測ワークフロー:創薬・開発プロセスへの適用」
CBI学会誌編集委員会 2021
- 長尾知生子, 李秀栄, 水口賢司
創薬研究のための相互作用解析パーフェクト〜低中分子・抗体創薬におけるスクリーニング戦略と実例、in silico解析、一歩進んだ分析技術まで
(実験医学別冊)
羊土社 2021 (ISBN: 4758122563)
http://ci.nii.ac.jp/ncid/BC11391757
2020
- 渡邉怜子, 水口賢司
人工知能(AI)を用いた創薬プロセスの加速におけるデータの重要性
医歯薬出版株式会社 2020
- 長尾 知生子, 水口 賢司
実験医学増刊 Vol.38 No.5 イメージング時代の構造生命科学〜細胞の動態、膜のないオルガネラ、分子の構造変化をトランススケールに観る
羊土社 2020 (ISBN: 4758103852)
http://ci.nii.ac.jp/ncid/BB29906634
2019
- 水口賢司
IT・ビッグデータと薬学 : 創薬・医薬品適正使用への活用
日本学術協力財団 2019
http://ci.nii.ac.jp/ncid/BB27803696