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Publications

Preprint

  1. Tanjo T., Yamamoto K., Noisagul P., ManabuIshii, Steinberg D., Goto N., Crusoe M R., Bendiken A., Higuchi C. 2024 DBCLS BioHackathon 2024 report: Everything about workflow and container BioHackrXiv doi
  2. Mohsen A., Yamamoto M., Martin-Morales A., Watanabe D., Nishi N., Nakagata T., Yoshida T., Miyachi M., Mizuguchi K., Araki M. 2023 Using Explainable AI to understand frailty indicators medRxiv https://www.medrxiv.org/content/10.1101/2023.05.30.23290760v1
  3. Natsume-Kitatani Y, Itoh M., 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., Wakiyama S., Chen Y-A., Higuchi C., Nojima Y., Fujiwara T., Nagao C., Matsumura Y., Mizuguchi K., Kumanogoh A., Ueda N. 2022 Data-driven patient stratification and drug target discovery by using medical information and serum proteome data of idiopathic pulmonary fibrosis patients Research Square - https://www.researchsquare.com/article/rs-405195/v3

2024

  1. Kuroda M., Kasahara Y., Hirose M., Yamaguma H., Oda M., Nagao C., Mizuguchi K. 2024 Construction of a Tm-value prediction model and molecular dynamics study of AmNA-containing gapmer antisense oligonucleotide Molecular Therapy - Nucleic Acids 35(3) doi
  2. Haga A., Iwasawa T., Misumi T., Okudela K., Oda T., Kitamura H., Saka T., Matsushita S., Baba T., Natsume‑Kitatani Y., Utsunomiya D., Ogura T. 2024 Correlation of CT-based radiomics analysis with pathological cellular infiltration in fibrosing interstitial lung diseases Japanese Journal of Radiology doi
  3. Uchida M., Park J., Fujie S., Hosomi K., Horii N., Watanabe K., Sanada K., Shinohara Y., Mizuguchi K., Kunisawa J., Iemitsu M., Miyachi M. 2024 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 12(12):e16100 doi
  4. Chyży P., Marta Kulik Ai Shinobu, Re S., Sugita Y., Trylska J. 2024 Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch Proceedings of the National Academy of Sciences of the United States of America 121:e2317197121 doi
  5. Ishikawa T., Masuda T., Hachiya T., Dina C., Simonet F., Nagata Y., Michael W T Tanck, Sonehara K., Glinge C., Tadros R., Khongphatthanayothin A., Lu T., Higuchi C., Nakajima T., Hayashi K., Aizawa Y., Nakano Y., Nogami A., Morita H., Ohno S., Aiba T., Christian Krijger Juárez, Mauleekoonphairoj J., Poovorawan Y., Gourraud J., Shimizu W., Probst V., Horie M., Arthur A M Wilde, Redon R., Jyh-Ming Jimmy Juang, Nademanee K., Connie R Bezzina, Barc J., Tanaka T., Okada Y., Schott J., Makita N. 2024 Brugada syndrome in Japan and Europe: a genome-wide association study reveals shared genetic architecture and new risk loci European Heart Journal ehae251 doi
  6. Enomoto T., Shirai1 Y., Takeda Y., Edahiro R., Shichino S., Nakayama M., Takahashi-Itoh M., Noda Y., Adachi Y., Kawasaki T., Koba T., Futami Y., Yaga M., Hosono Y., Yoshimura H., 1 Saori Amiya, 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., Natsume-Kitatani Y., Nojima S., Yanagawa M., Shintani Y., Nogami-Itoh M., Mizuguchi K., Adachi J., Tomonaga T., Inoue Y., Kumanogoh A. 2024 SFTPB in serum extracellular vesicles as a biomarker of progressive pulmonary fibrosis JCI Insight 9(11) doi
  7. Wariishi T., Kataoka Y., Nakamura T., Kasahara Y., Kuroda M., Obika S., Kuwahara M. 2024 Lantern-type G-quadruplex fluorescent sensors for detecting divalent metal ions Analytical Biochemistry 690:115525 doi
  8. 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. 2024 Association of skeletal muscle function, quantity, and quality with gut microbiota in Japanese adults: A cross-sectional study Geriatrics & Gerontology International 24(1):53-60 doi
  9. Gou Y., Re S., Mizuguchi K., Nagao C. 2024 Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model ACS Medicinal Chemistry Letters 15(1):54-89 doi

2023

  1. 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. 2023 Changes in Fecal Gut Microbiome of Home Healthcare Patients with Disabilities through Consumption of Malted Rice Amazake Physiological Genomics doi
  2. Bakonyi P., Kolonics A., Aczel D., Zhou L., Mozaffaritabar S., Molnár K., László L., Kutasi B., Tanisawa K., Park J., Gu Y., Pinho R. A., Radak Z. 2023 Voluntary exercise does not increase gastrointestinal motility but increases spatial memory, intestinal eNOS, Akt levels, and Bifidobacteria abundance in the microbiome Frontiers in Physiology 14 doi
  3. Park J., Bushita H., Nakano A., Hara A., Ueno H., Ozato N., Hosomi K., Kawashima H., Chen Y., Mohsen A., Ohno H., Konishi K., Tanisawa K., Nanri H., Murakami H., Miyachi M., Kunisawa J., Mizuguchi K., Araki M. 2023 Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study Microorganisms 11(8) doi
  4. Sanada T., Hosomi K., Park J., Naito A., Sakao S., Tanabe N., Kunisawa J., Tatsumi K., Suzuki T. 2023 Partially hydrolyzed guar gum suppresses the progression of pulmonary arterial hypertension in a SU5416/hypoxia rat model Pulmonary Circulation 13(3)e12266 doi
  5. Akazawa N., Nakamura M., Eda N., Murakami H., Nakagata T., Nanri H., Park J., Hosomi K., Mizuguchi K., Kunisawa J., Miyachi M., Hoshikawa M. 2023 Gut microbiota alternation with training periodization and physical fitness in Japanese elite athletes Frontiers in Sports and Active Living 5 doi
  6. Kawashima H., Watanabe R., Esaki T., Kuroda M., Nagao C., Natsume-Kitatani Y., Ohashi R., Komura H., Mizuguchi K. 2023 DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform Journal of Medicinal Chemistry doi
  7. 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. 2023 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 doi
  8. 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. 2023 Characteristic Gut Bacteria in High Barley Consuming Japanese Individuals without Hypertension microorganisms 11(5):1246 doi
  9. Martin, Watanabe R., Hashimoto K., Higashisaka K., Haga Y., Tsutsumi Y., Mizuguchi K. 2023 Evidence-Based Prediction of Cellular Toxicity for Amorphous Silica Nanoparticles ACS Nano doi
  10. Alarabi A., Mohsen A., Taleb Z., Mizuguchi K., Alshbool F., Khasawneh F. 2023 Predicting thrombotic cardiovascular outcomes induced by waterpipe-associated chemicals using comparative toxicogenomic database: Genes, phenotypes, and pathways Life Sciences 323 doi
  11. Nagano N., Tokunaga N., Ikeda M., Inoura H., Khoa D., Miwa M., Sohrab M., Topić G., Nogami-Itoh M., Takamura H. 2023 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 https://www.nature.com/articles/s41598-023-32915-8

2022

  1. Hosoe Y., Miyanoiri Y., Re S., Ochi S., Asahina Y., Kawakami T., Kuroda M., Mizuguchi K., Oda M. 2022 Structural dynamics of the N-terminal SH2 domain of PI3K in its free and CD28-bound states The FEBS Journal 290 (9): 2366-2378 doi
  2. 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. 2022 Identification of CD14 and lipopolysaccharide-binding protein as novel biomarkers for sarcoidosis using proteomics of serum extracellular vesicles International Immunology 34(6):327-340 doi
  3. Sohrab M., Duong K., Masami I., Topić G., Natsume-Kitatani Y., Kuroda M., Itoh M., Takamura H. 2022 BiomedCurator: Data Curation for Biomedical Literature Association for Computational Linguistics 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:63-71 https://aclanthology.org/2022.aacl-demo.8
  4. 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 2022 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 24(4)
  5. Murakami Y., Mizuguchi K. 2022 Recent developments of sequence-based prediction of protein–protein interactions. Biophysical Reviews. 14(6):1393-1411 doi
  6. Watanabe R., Kawata T., Ueda S., Shinbo T., Higashimori M., Natsume-Kitatani Y., Mizuguchi K. 2022 Prediction of the Contribution Ratio of a Target Metabolic Enzyme to Clearance from Chemical Structure Information. Molecular Pharmaceutics. - doi
  7. 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. 2022 Targeted deep sequencing analyses of long QT syndrome in a Japanese population. PLOS ONE. 17-12:e0277242 doi
  8. Iiyama M., Hantani Y., Wink R., Kuroda M., Oda M. 2022 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 doi
  9. 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. 2022 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 doi
  10. Kuroda M., Watanabe R., Esaki T., Kawashima H., Ohashi R., Sato T., Honma T., Komura H., Mizuguchi K. 2022 Utilizing public and private sector data to build better machine learning models for the prediction of pharmacokinetic parameters. Drug Discovery Today. 27-11:103339 doi
  11. Sawane K., Hosomi K., Park J., Ookoshi K., Nanri H., Nakagata T., Chen Y., Mohsen A., Kawashima H., Mizuguchi K., Miyachi M., Kunisawa J. 2022 Identification of Human Gut Microbiome Associated with Enterolignan Production Microorganisms. 10-11:2169 - doi
  12. Otaki M., Hirane N., Natsume-Kitatani Y., Nogami Itoh M., Shindo M., Kurebayashi Y., Nishimura S. 2022 Mouse tissue glycome atlas 2022 highlights inter-organ variation in major N-glycan profiles. Scientific Reports. 12-1:17804 doi
  13. 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. 2022 Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota. Nature Communications. 13:4477 doi
  14. Chen,Y.-A, Allendes Osorio,R.S., Mizuguchi K. 2022 TargetMine 2022: A new vision into drug target analysis. Bioinformatics. - doi
  15. Gupta S., Vundavilli H., Allendes Osorio,R.S., Itoh M., Mohsen A., Datta A., Mizuguchi K., Tripathi L. 2022 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. 1-8 doi
  16. Hioki K., Hayashi T., Natsume-Kitatani Y., Kouji K., Burcu T., Hideo N., Hitomi K., Hiroyuki F., Etsushi K., Cevayir C., Nobuo K., Ken J. I. 2022 Machine Learning-Assisted Screening of Herbal Medicine Extracts as Vaccine Adjuvants. Frontiers in Immunology - doi
  17. Mohsen A., Chen,Y.-A., Allendes Osorio,R.S., Higuchi C., Mizuguchi K. 2022 Snaq: A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2. Frontiers in Bioinformatics. - doi
  18. Park J., Hosomi K., Kawashima H., Chen Y., Mohsen A., Ohno H., Konishi K., Tanisawa K., Kifushi M., Kogawa M., Takeyama H., Murakami H., Kubota T., Miyachi M., Kunisawa J., Mizuguchi K. 2022 Dietary Vitamin B1 Intake Influences Gut Microbial Community and the Consequent Production of Short-Chain Fatty Acids. Nutrients. 14(10):2078 doi
  19. 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. 2022 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 doi
  20. Alarabi A., Mohsen A., Mizuguchi K., Alshbool F., Khasawneh F. 2022 Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets. BMC Medical Genomics. 15(83) doi
  21. Shinobu A., Re S., Sugita Y. 2022 Practical Protocols for efficient sampling of kinase-inhibitor binding pathways using two-dimensional replica-exchange molecular dynamics. Frontiers in Molecular Biosciences. - doi
  22. Yamane D., Onitsuka S., Re S., Isogai H., Hamada R., Hiramoto T., Kawanishi E., Mizuguchi K., Shindo N., Ojida A. 2022 Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide. Chemical Science. 13(10):3027-3034 doi
  23. Dokainish H., Re S., Mori T., Kobayashi C., Jung J., Sugita Y. 2022 The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife. 11:e75720 doi
  24. 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. 2022 Classification of the Occurrence of Dyslipidemia Based on Gut Bacteria Related to Barley Intake. Frontiers in Nutrition. 9 doi
  25. Hirano H., Abe Y., Nojima Y., Aoki M., Shoji H., Isoyama J., Honda K., Boku N., Mizuguchi K., Tomonaga T., Adachi J. 2022 Temporal dynamics from phosphoproteomics using endoscopic biopsy specimens provides new therapeutic targets in stage IV gastric cancer. Scientific Reports. 12(1):4419 doi
  26. 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. 2022 The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma. Anticancer Research. 42(3):1589-1598 doi
  27. Tsuji T., Hashiguchi K., Yoshida M., Ikeda T., Koga Y., Honda Y., Tanaka T., Re S., Mizuguchi K., Takahashi D., Yazaki R., Ohshima T. 2022 α-Amino acid and peptide synthesis using catalytic cross-dehydrogenative coupling. Nature Synthesis. - doi
  28. 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. 2022 Relationships between barley consumption and gut microbiome characteristics in a healthy Japanese population: a cross-sectional study. BMC Nutrition. 8(1):23 doi
  29. Arakawa M., Tabata K., Ishida K., Kobayashi M., Arai A., Ishikawa T., Suzuki R., Takeuchi H., Tripathi L., Mizuguchi K., Morita E. 2022 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 doi
  30. Yagi K., Re S., Mori T., Sugita Y. 2022 Weight average approaches for predicting dynamical properties of biomolecules. Current Opinion in Structural Biology. 72:88-94 doi
  31. 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. 2022 Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota. JCI Insight. 2(7) doi
  32. Takegawa-Araki T., Kumagai S., Yasukawa K., Kuroda M., Sasaki T., Obika S. 2022 Structure–Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids. Journal of Medicinal Chemistry. - doi

2021

  1. 尾嶋拓.,李秀栄.,新津藍., 杉田有治 2021 分子動力学ソフトウェアGENESISを用いたタンパク質―リガンド結合の自由エネルギー計算, 日本シミュレーション学会学会誌「シミュレーション」. 40(1),22-28
  2. 夏目やよい 2021 機械学習によって加速される次世代アジュバント開発, 医学のあゆみ. 279
  3. 陳怡安.,李秀栄.,水口賢司 2021 TargetMineによる生物学的知識の発見, 医学のあゆみ. 278,641-645
  4. 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. 2021 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 https://www.mdpi.com/2072-6643/13/12/4466/htm
  5. Sakib S., Fouda M. M., Al-Mahdawi M., Mohsen A., Oogane M., Ando Y., Fadlullah Md. Z., 2021 Deep Learning Models for Magnetic Cardiography Edge Sensors Implementing Noise Processing and Diagnostics IEEE Access. 10,2656-2668 https://ieeexplore.ieee.org/document/9663379
  6. Ueta M., Hosomi K., Park J., Mizuguchi K., Sotozono C., Kinoshita S., Kunisawa J. 2021 Categorization of the Ocular Microbiome in Japanese Stevens-Johnson Syndrome Patients With Severe Ocular Complications. Frontiers in Cellular and Infection Microbiology. 11,1130 https://www.frontiersin.org/article/10.3389/fcimb.2021.741654
  7. Mohsen A., Lokesh P. Tripathi., Mizuguchi K. 2021 Deep Learning Prediction of Adverse Drug Reactions In Drug Discovery Using Open TG–GATEs and FAERS Databases. Frontiers in Drug Discovery. - https://www.frontiersin.org/articles/10.3389/fddsv.2021.768792/abstract?fbclid=…
  8. Tomizawa R., Park J., Hosomi K., Matsumoto N., Kawashima H., Mizuguchi K., Kunisawa J., Honda C. 2021 Relationship between Human Gut Microbiota and Nutrition Intake in Hypertensive Discordant Monozygotic Twins. Journal of Hypertension. 10(8) https://www.hilarispublisher.com/open-access/relationship-between-human-gut-mic…
  9. Fujiyama K., Kato N., Re S., Kinugasa K., Watanabe K., Takita R., Nogawa T., Hino T., Osada H., Sugita Y., Takahashi S., Nagano S. 2021 Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons. Angewandte Chemie International Edition. 60,2-12 doi
  10. 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. 2021 Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nature Communications. 12(1),4099 doi
  11. 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. 2021 Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts. BMC Microbiology. 21(1),151 doi
  12. Lee J., Mohsen A., Banerjee A., McCullough L., Mizuguchi K., Shimaoka M., Kiyono H., Park E. 2021 Distinct Age-Specific miRegulome Profiling of Isolated Small and Large Intestinal Epithelial Cells in Mice. International Journal of Molecular Sciences. 22(7),3544 doi
  13. 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. 2021 Proteomics of serum extracellular vesicles identifies a novel COPD biomarker, fibulin-3 from elastic fibres. ERJ open research. - doi
  14. Matsumoto N., Park J., Tomizawa R., Kawashima H., Hosomi K., Mizuguchi K., Honda C., Ozaki R., Iwatani Y., Watanabe M., Kunisawa J. 2021 Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins. Medicina - doi
  15. Vundavilli H., Tripathi L., Datta A., Mizuguchi K. 2021 Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity. Journal of Theoretical Biology . - doi
  16. Watanabe R., Esaki T., Ohashi R., Kuroda M., Kawashima H., Komura H., Natsume-Kitatani Y., Mizuguchi K. 2021 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. - doi
  17. Re S., Mizuguchi K. 2021 Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein The Journal of Physical Chemistry B. 125(8) doi
  18. Chyży P., Kulik M., Re S., Sugita Y., Trylska J. 2021 Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection. Frontiers in Molecular Biosciences. - doi
  19. Komura H., Watanabe R., Kawashima H., Ohashi R., Kuroda M., Sato T., Honma T., Mizuguchi K. 2021 A public–private partnership to enrich the development of in silico predictive models for pharmacokinetic and cardiotoxic properties. Drug Discovery Today. - doi
  20. Mori T., Jung J., Kobayashi C., Dokainish H., Re S., Sugita Y. 2021 Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein. Biophysical Journal. - doi

2020

  1. Iiyama M., Numoto N., Ogawa S., Kuroda M., Morii H., Abe R., Ito N., Oda M. 2020 Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains. Molecular Immunology 131 doi
  2. Vos, R. A., Katayama, T., Mishima, H., Kawano, S., Kawashima, S., Kim, J.-D., Moriya, Y., Tokimatsu, T., Yamaguchi, A., Yamamoto, Y., Wu, H., Amstutz, P., Antezana, E., Aoki, N. P., Arakawa, K., Bolleman, J. T., Bolton, E., Bonnal, R. J. P., Bono, H., … Takagi, T. 2020 BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9, 136 doi
  3. Tripathi, L. P., Itoh, M. N., Takeda, Y., Tsujino, K., Kondo, Y., Kumanogoh, A., & Mizuguchi, K. 2020 Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema. Frontiers in Genetics 11 doi
  4. 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. 2020 Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein. Virology 541, 41–51 doi
  5. 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. 2020 Gut microbial composition in patients with atrial fibrillation: Effects of diet and drugs. Heart and Vessels. - doi
  6. Takayuki Jujo Sanada, Koji Hosomi, Hiroki Shoji, Jonguk Park, Akira Naito, Yumiko Ikubo, Asako Yanagisawa, Takayuki Kobayashi, Hideki Miwa, Rika Suda, Seiichiro Sakao, Kenji Mizuguchi, Jun Kunisawa, Nobuhiro Tanabe, & Koichiro Tatsumi. 2020 Gut microbiota modification suppresses the development of pulmonary arterial hypertension in a Su/Hx rat model. Pulmonary Circulation 10(4) doi
  7. Saito A., Tsuchiya D., Satoh S., Okamoto A., Murakami Y., Mizuguchi K., Toh H., & Nemoto W. (n.d.). 2020 Update of the GRIP web service. JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION 40(4), 348-356 doi
  8. Nojima, Y., Takeda, Y., Maeda, Y., Bamba, T., Fukusaki, E., Itoh, M. N., Mizuguchi, K., & Kumanogoh, A. 2020 Metabolomic analysis of fibrotic mice combined with public RNA-Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis. FEBS Open Bio 10(11), 2427–2436 doi
  9. Mohsen, A., Tripathi, L. P., & Mizuguchi, K. 2020 Deep Learning Prediction of Adverse Drug Reactions Using Open TG-GATEs and FAERS Databases. ArXiv: 2010.05411 [q-Bio] arxiv
  10. Mohsen, A., & Alarabi, A. 2020 The impact of community containment implementation timing on the spread of COVID-19: A simulation study. F1000Research 9, 452 doi
  11. Esaki, T., Kumazawa, K., Takahashi, K., Watanabe, R., Masuda, T., Watanabe, H., Shimizu, Y., Okada, A., Takimoto, S., Shimada, T., & Ikeda, K. 2020 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 doi
  12. Esaki, T., Horinouchi, T., Natsume-Kitatani, Y., Nojima, Y., Sakane, I., & Matsui, H. 2020 Estimation of relationships between chemical substructures and antibiotic resistance-related gene expression in bacteria: Adapting a canonical correlation analysis for small sample data of gathered features using consensus clustering. Chem-Bio Informatics Journal 20, 58–61 doi
  13. Chen, Y.-A., 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. 2020 MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data. PLOS ONE 15(12), e0243609 doi
  14. Allendes Osorio, R. S., Nyström-Persson, J. T., Nojima, Y., Kosugi, Y., Mizuguchi, K., & Natsume-Kitatani, Y. 2020 Panomicon: A web-based environment for interactive, visual analysis of multi-omics data. Heliyon 6(8), e04618 doi
  15. Afanaseva A., Nagao C., Mizuguchi K. 2020 Developing a kinase-specific target selection method using a structure-based deep learning approach. JCUP IX, OpenEye Scientific Software Meeting. -
  16. 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. 2020 Sphingomyelin Deacylase, the Enzyme Involved in the Pathogenesis of Atopic Dermatitis, Is Identical to the β-Subunit of Acid Ceramidase. Int J Mol Sci. 21(22)8789 doi
  17. Takayuki Jujo Sanada, Koji Hosomi, Hiroki Shoji, Jonguk Park, Akira Naito, Yumiko Ikubo, Asako Yanagisawa, Takayuki Kobayashi, Hideki Miwa, Rika Suda, Seiichiro Sakao, Kenji Mizuguchi, Jun Kunisawa, Nobuhiro Tanabe, Koichiro Tatsumi 2020 Gut microbiota modification suppresses the development of pulmonary arterial hypertension in a Su/Hx rat model. Pulmonary Circulation. - doi

2019

  1. 水口賢司. 2019 創薬の初期研究におけるデータベース構築とモデリング. 学術会議叢書25 IT・ビッグデータと薬学 25–31
  2. 野島陽水, & 水口賢司. 2019 人工知能による創薬ターゲットの同定－“新薬創出を加速する人工知能の開発”プロジェクトの現状と課題. 医学のあゆみ 268, 988–991
  3. 藤原大, & 水口賢司. 2019 コンピュータサイエンスの応用 異なるデータベースの有機的統合と医療への応用. Lung Perspectives 27, 205-208
  4. 夏目やよい, 相崎健一, 北嶋聡, GOSH Samik, 北野宏明, 水口賢司, & 菅野純. 2019 Garudaプラットフォームによる多角的毒性予測. Journal of Toxicological Sciences 44 (Supplement), S132
  5. Chen, Y.-A., Tripathi, L. P., Fujiwara, T., Kameyama, T., Itoh, M. N., & Mizuguchi, K. 2019 The TargetMine Data Warehouse: Enhancement and Updates. Frontiers in Genetics 10, 934 doi
  6. 江崎剛史, 渡邉怜子, 夏目やよい, 伊藤眞里, 長尾知生子, 川島和, & 水口賢司. 2019 AI活用による薬物動態予測システムの開発. 人と共生するAI革命～活用事例からみる生活･産業･社会の未来展望～, エヌ・ティー・エス, 237–242.
  7. Yamada, T., Habara, O., Yoshii, Y., Matsushita, R., Kubo, H., Nojima, Y., & Nishimura, T. 2019 The role of glycogen in development and adult fitness in Drosophila. Development 146(8), dev176149 doi
  8. 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. 2020 Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein. Virology 541, 41–51 doi
  9. Afanasyeva, A., Nagao, C., & Mizuguchi, K. 2019 Prediction of the secondary structure of short DNA aptamers. Biophysics and Physicobiology 16, 287–294 doi
  10. Kataoka, Y., Fujita, H., Afanaseva, A., Nagao, C., Mizuguchi, K., Kasahara, Y., Obika, S., & Kuwahara, M. 2019 High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives. Biochemistry 58(6), 493–498 doi
  11. Mohsen, A., Park, J., Chen, Y.-A., Kawashima, H., & Mizuguchi, K. 2019 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 20(1), 581. doi doi
  12. Watanabe, R., Ohashi, R., Esaki, T., Kawashima, H., Natsume-Kitatani, Y., Nagao, C., & Mizuguchi, K. 2019 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 9(1), 18782 doi
  13. Ohashi, R., Watanabe, R., Esaki, T., Taniguchi, T., Torimoto-Katori, N., Watanabe, T., Ogasawara, Y., Takahashi, T., Tsukimoto, M., & Mizuguchi, K. 2019 Development of Simplified in Vitro P-Glycoprotein Substrate Assay and in Silico Prediction Models To Evaluate Transport Potential of P-Glycoprotein. Molecular Pharmaceutics 16(5), 1851–1863 doi
  14. Esaki, T., Ohashi, R., Watanabe, R., Natsume-Kitatani, Y., Kawashima, H., Nagao, C., Komura, H., & Mizuguchi, K. 2019 Constructing an In Silico Three-Class Predictor of Human Intestinal Absorption With Caco-2 Permeability and Dried-DMSO Solubility. Journal of Pharmaceutical Sciences 108(11), 3630–3639 doi
  15. Chen, Y.-A., Tripathi, L. P., & Mizuguchi, K. 2019 Data Warehousing with TargetMine for Omics Data Analysis. Methods in Molecular Biology (Clifton, N.J.) 1986, 35–64 doi
  16. Esaki, T., Ohashi, R., Watanabe, R., Natsume-Kitatani, Y., Kawashima, H., Nagao, C., & Mizuguchi, K. 2019 Computational Model To Predict the Fraction of Unbound Drug in the Brain. Journal of Chemical Information and Modeling 59(7), 3251–3261 doi
  17. 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. 2019 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 doi
  18. Allendes Osorio, R. S., Tripathi, L. P., & Mizuguchi, K. 2019 CLINE: a web-tool for the comparison of biological dendrogram structures. BMC Bioinformatics 20(1), 528 doi
  19. Chen, Y.-A., Yogo, E., Kurihara, N., Ohno, T., Higuchi, C., Rokushima, M., & Mizuguchi, K. 2019 Assessing drug target suitability using TargetMine. F1000Research 8, 233 doi
  20. Takahashi, Y., Park, J., Hosomi, K., Yamada, T., Kobayashi, A., Yamaguchi, Y., Iketani, S., Kunisawa, J., Mizuguchi, K., Nobuko, M., & Ohshima, T. 2019 Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing. Journal of Oral Biosciences 61(2), 120-128 doi
  21. Miyake, K., Sakane, A., Tsuchiya, Y., Sagawa, I., Tomida, Y., Kasahara, J., Imoto, I., Watanabe, S., Higo, D., Mizuguchi, K., & Sasaki, T. 2019 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 9(1), 12794 doi
  22. Chiba S., Ohue M., Gryniukova A., Borysko P., Zozulya S., Yasuo N., Yoshino R., Ikeda K., Shin WH., Kihara D., Iwadate M., Umeyama H., Ichikawa T., Teramoto R., Hsin KY., Gupta V., Kitano H., Sakamoto M., Higuchi A., Miura N., Yura K., Mochizuki M., Ramakrishnan C., Thangakani AM., Velmurugan D., Gromiha MM., Nakane I., Uchida N., Hakariya H., Tan M., Nakamura HK., Suzuki SD., Ito T., Kawatani M., Kudoh K., Takashina S., Yamamoto KZ., 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. 2019 A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific Reports 9(1), 19585 doi

2018

  1. Tsuyoshi Esaki, Reiko Watanabe, Hitoshi Kawashima, Rikiya Ohashi, Yayoi Natsume-Kitatani, Chioko Nagao, Kenji Mizuguchi 2018 Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance Molecular Informatics Volume38, Issue1-2 doi
  2. Kikuchi, A., Nasir, F. B. M., Inami, A., Mohsen, A., Watanuki, S., Miyake, M., Takeda, K., Koike, D., Ito, T., Sasakawa, J., Matsuda, R., Hiraoka, K., Maurer, M., Yanai, K., Watabe, H., & Tashiro, M. 2018 Effects of levocetirizine and diphenhydramine on regional glucose metabolic changes and hemodynamic responses in the human prefrontal cortex during cognitive tasks. Human Psychopharmacology 33(2), e2655 doi
  3. 水口 賢司. 2017 『創薬の初期研究におけるデータベース構築とモデリング』. 学術会議叢書 25, 25–31 doi
  4. Park, J., Li, P.-F., Ichijo, T., Nasu, M., & Yamaguchi, N. 2018 Effects of Asian dust events on atmospheric bacterial communities at different distances downwind of the source region. Journal of Environmental Sciences 72,133-139 doi
  5. Fujiwara T., Kamada M., & Okuno Y. 2018 Artificial Intelligence in Drug Discovery. Gan to Kagaku Ryoho 4, 593–596
  6. 藤原大, & 水口賢司. 2018 『創薬とファーマコゲノミクス』. 小児内科 1号, 103–106
  7. 渡邉怜子, 江崎剛史, 夏目やよい, 佐藤朋広, 長尾知生子, 川島和, & 水口賢司. 2018 『薬物動態・毒性予測のためのデータベースと創薬』. マテリアルズ・インフォマティクスによる材料開発と活用集　～データベースの構築、記述子の設計法、モデル作成～ 技術情報協会 -
  8. 長尾知生子, & 種石慶. 2018 『データベース・計算環境～知識データベース・AI基礎』. 医薬ジャーナル 54巻9号, 2063–2067
  9. 夏目やよい. 2018 『４．バイオメディカル・基礎から臨床への開発プロセス（２）１）トランスレーショナルリサーチと機械学習』. 医薬ジャーナル 9号, 2049–2053
  10. 伊藤眞里. 2018 『４．バイオメディカル・基礎から臨床への開発プロセス（1）～人工知能を用いる創薬テーマ創出』. 医薬ジャーナル 9号, 2029–2032
  11. 奥野恭史, 水口賢司, & 本間光貴. 2018 『１．序文　～LINCの設立とAI創薬～』. 医薬ジャーナル 9号, 2015–2017
  12. 長尾 知生子, 夏目 やよい, & 水口 賢司. 2018 『創薬における計算機の果たす役割　～　プレシジョンメディシンに向けて』. Presicion Medicine 1, 28–31
  13. 夏目 やよい, 相㟢 健一, 北嶋 聡, 陳 怡安, 水口 賢司, & 菅野 純. 2018 『TargetMineによる標的予測』. 日本毒性学会学術年会 45.1, S11-4 doi
  14. Afanasyeva, A., Bockwoldt, M., Cooney, C. R., Heiland, I., & Gossmann, T. I. 2018 Human long intrinsically disordered protein regions are frequent targets of positive selection. Genome Research 28(7), 975–982 doi
  15. Tripathi, L. P., Chen, Y.-A., Mizuguchi, K., & Morita, E. 2019b Network-Based Analysis of Host-Pathogen Interactions. Encyclopedia of Bioinformatics and Computational Biology 932–937 doi
  16. Tripathi, L. P., Esaki, T., N. Itoh, M., Chen, Y.-A., & Mizuguchi, K. 2018 Integrative Analysis of Multi-Omics Data. Encyclopedia of Bioinformatics and Computational Biology 3,194-199 doi
  17. Watanabe, R., Esaki, T., Kawashima, H., Natsume-Kitatani, Y., Nagao, C., Ohashi, R., & Mizuguchi, K. 2018 Predicting Fraction Unbound in Human Plasma from Chemical Structure: Improved Accuracy in the Low Value Ranges. Molecular Pharmaceutics 15(11), 5302–5311 doi
  18. Tripathi, L. P., Murakami, Y., Chen, Y.-A., & Mizuguchi, K. 2018 Network-Based Analysis for Biological Discovery. Encyclopedia of Bioinformatics and Computational Biology 3,283-291 doi
  19. Tripathi, L. P., Chen, Y.-A., Mizuguchi, K., & Morita, E. 2019a Network-Based Analysis of Host-Pathogen Interactions. Encyclopedia of Bioinformatics and Computational Biology 3, 932-937 doi
  20. Masuta, Y., Yamamoto, T., Natsume-Kitatani, Y., Kanuma, T., Moriishi, E., Kobiyama, K., Mizuguchi, K., Yasutomi, Y., & Ishii, K. J. 2018 An Antigen-Free, Plasmacytoid Dendritic Cell–Targeting Immunotherapy To Bolster Memory CD8+ T Cells in Nonhuman Primates. The Journal of Immunology 200(6), 2067–2075 doi
  21. Jin, Y., Takeda, Y., Kondo, Y., Tripathi, L. P., Kang, S., Takeshita, H., Kuhara, H., Maeda, Y., Higashiguchi, M., Miyake, K., Morimura, O., Koba, T., Hayama, Y., Koyama, S., Nakanishi, K., Iwasaki, T., Tetsumoto, S., Tsujino, K., Kuroyama, M., Iwahori, K., Hirata, H., Takimoto, T., Suzuki, M., Nagatomo, I., Sugimoto, K., Fujii, Y., Kida, H., Mizuguchi, K., Ito, M., Kijima, T., Rakugi, H., Mekada, E., Tachibana, I., & Kumanogoh, A. 2018 Double deletion of tetraspanins CD9 and CD81 in mice leads to a syndrome resembling accelerated aging. Scientific Reports 8(1), 5145 doi
  22. Ahmad, S., Prathipati, P., Tripathi, L. P., Chen, Y.-A., Arya, A., Murakami, Y., & Mizuguchi, K. 2018 Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism. Nucleic Acids Research 46(1), 54–70 doi

2017

  1. Murakami Y., & Mizuguchi K. 2017 PSOPIA: Toward more reliable protein-protein interaction prediction from sequence information. 2017 International Conference on Intelligent Informatics and Biomedical Sciences, Okinawa. - Web
  2. Murakami Y., & Mizuguchi K. 2017 Making protein-protein interaction prediction more reliable with a large-scale dataset at the proteome level – ASCSPub. Journal of Bioinformatics and Neuroscience. - Web
  3. Tanaka, M., Kobiyama, K., Honda, T., Uchio-Yamada, K., Natsume-Kitatani, Y., Mizuguchi, K., Kabashima, K., & Ishii, K. J. 2018 Essential Role of CARD14 in Murine Experimental Psoriasis. The Journal of Immunology 200(1), 71–81 doi
  4. Wijaya, E., Igarashi, Y., Nakatsu, N., Haseda, Y., Billaud, J., Chen, Y.-A., Mizuguchi, K., Yamada, H., Ishii, K., & Aoshi, T. 2017 Quantifying the relative immune cell activation from whole tissue/organ-derived differentially expressed gene data. Scientific Reports 7(1), 12847 doi
  5. Mizuguchi, K. 2017 Database Development and Computational Modelling in Early-Stage Drug Discovery. Trends in the Sciences 22(7), 7_62-7_65 doi
  6. Esaki, T., Watanabe, R., Kawashima, H., Natsume-Kitatani, Y., & Mizuguchi, K. 2017 Development of a Drug Discovery Informatics System: An Integrated Platform for Pharmacokinetic and Toxicological Modelling. Journal of Pharmaceutical Science and Technology, Japan 77(4), 211–215 doi
  7. Hosomi, K., Ohno, H., Murakami, H., Natsume-Kitatani, Y., Tanisawa, K., Hirata, S., Suzuki, H., Nagatake, T., Nishino, T., Mizuguchi, K., Miyachi, M., & Kunisawa, J. 2017 Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity. Scientific Reports 7(1), 4339 doi
  8. Sowdhamini, R., & Mizuguchi, K. 2017 Editorial—Sequences and topology. Current Opinion in Structural Biology 44, vii–viii doi
  9. Andrabi, M., Hutchins, A. P., Miranda-Saavedra, D., Kono, H., Nussinov, R., Mizuguchi, K., & Ahmad, S. 2017 Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Scientific Reports 7(1), 4071 doi
  10. Yoshimaru, T., Ono, M., Bando, Y., Chen, Y.-A., Mizuguchi, K., Shima, H., Komatsu, M., Imoto, I., Izumi, K., Honda, J., Miyoshi, Y., Sasa, M., & Katagiri, T. 2017 A-kinase anchoring protein BIG3 coordinates oestrogen signalling in breast cancer cells. Nature Communications 8, 15427 doi
  11. Nyström-Persson, J., Natsume-Kitatani, Y., Igarashi, Y., Satoh, D., & Mizuguchi, K. 2017 Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. Scientific Reports 7(1), 1390 doi
  12. Murakami, Y., Tripathi, L. P., Prathipati, P., & Mizuguchi, K. 2017 Network analysis and in silico prediction of protein–protein interactions with applications in drug discovery. Current Opinion in Structural Biology 44, 134–142 doi
  13. Hamano, Y., Kida, H., Ihara, S., Murakami, A., Yanagawa, M., Ueda, K., Honda, O., Tripathi, L. P., Arai, T., Hirose, M., Hamasaki, T., Yano, Y., Kimura, T., Kato, Y., Takamatsu, H., Otsuka, T., Minami, T., Hirata, H., Inoue, K., Nagatomo, I., Takeda, Y., Mori, M., Nishikawa, H., Mizuguchi, K., Kijima, T., Kitaichi, M., Tomiyama, N., Inoue, Y., & Kumanogoh, A. 2017 Classification of idiopathic interstitial pneumonias using anti–myxovirus resistance-protein 1 autoantibody. Scientific Reports 7 doi
  14. Natsume-Kitatani Y., & Mizuguchi K. 2017 Computational systems biology for drug discovery: from molecules, structures to networks. Folia Pharmacologica Japonica 149(2), 91–95 doi
  15. Natsume-Kitatani, Y., Nyström-Persson, J., Igarashi, Y., Satoh, D., & Mizuguchi, K. 2017 Integrated toxicogenomics analysis with Toxygates for inferring molecular mechanisms. Genomics and Computational Biology 3(1), e37–e37 doi

2016

  1. Takashima, S., Oka, Y., Fujiki, F., Morimoto, S., Nakajima, H., Nakae, Y., Nakata, J., Nishida, S., Hosen, N., Tatsumi, N., Mizuguchi, K., Hashimoto, N., Oji, Y., Tsuboi, A., Kumanogoh, A., & Sugiyama, H. 2016 Syndecan-4 as a biomarker to predict clinical outcome for glioblastoma multiforme treated with WT1 peptide vaccine. Future Science OA 2(4) doi
  2. Tsuchiya, Y., & Mizuguchi, K. 2016 The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops. Protein Science : A Publication of the Protein Society 25(4), 815–825 doi
  3. Sequence and Structural Determinants of Antigen Binding in Antibody CDR Loops. 2016 Asia Pacific Biotech News – Featuring News, Interviews Information in APAC. NULL Web
  4. Prathipati, P., Nagao, C., Ahmad, S., & Mizuguchi, K. 2016 Improved pose and affinity predictions using different protocols tailored on the basis of data availability. Journal of Computer-Aided Molecular Design 30(9), 817–828 doi
  5. Murakami, Y., Omori, S., & Kinoshita, K. 2016 NLDB: a database for 3D protein–ligand interactions in enzymatic reactions. Journal of Structural and Functional Genomics 17(4), 101–110 doi
  6. Tsuchiya, Y., Jounai, N., Takeshita, F., Ishii, K. J., & Mizuguchi, K. 2016 Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1. EBioMedicine 9, 87–96 doi
  7. Sakane, A., Yoshizawa, S., Nishimura, M., Tsuchiya, Y., Matsushita, N., Miyake, K., Horikawa, K., Imoto, I., Mizuguchi, C., Saito, H., Ueno, T., Matsushita, S., Haga, H., Deguchi, S., Mizuguchi, K., Yokota, H., & Sasaki, T. 2016 Conformational plasticity of JRAB/MICAL-L2 provides “law and order” in collective cell migration. Molecular Biology of the Cell 27(20), 3095–3108 doi
  8. Yotsukura, S., duVerle, D., Hancock, T., Natsume-Kitatani, Y., & Mamitsuka, H. 2017 Computational recognition for long non-coding RNA (lncRNA): Software and databases. Briefings in Bioinformatics 18(1), 9–27 doi
  9. Natsume-Kitatani, Y., & Mamitsuka, H. 2016 Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns. PLoS ONE 11(3) doi
  10. Chen, Y.-A., Tripathi, L. P., & Mizuguchi, K. 2016 An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. Database: The Journal of Biological Databases and Curation 2016 doi

2015

  1. 水口賢司 2015 タンパク質間相互作用「生命ネットワークの基本部品の構造を解明する」 日本生物物理学会
  2. Nakae, Y., Oka, Y., Fujiki, F., Morimoto, S., Kamiya, T., Takashima, S., Nakata, J., Nishida, S., Nakajima, H., Hosen, N., Tsuboi, A., Kyo, T., Oji, Y., Mizuguchi, K., Kumanogoh, A., & Sugiyama, H. 2015 Two distinct effector memory cell populations of WT1 (Wilms’ tumor gene 1)-specific cytotoxic T lymphocytes in acute myeloid leukemia patients. Cancer Immunology, Immunotherapy; Heidelberg 64(7), 791–804 Web
  3. Philip Prathipati, Kenji Mizuguchi 2016 Systems Biology Approaches to a Rational Drug Discovery Paradigm. Current Topics in Medicinal Chemistry. doi
  4. Koo, C. X., Kobiyama, K., Shen, Y. J., LeBert, N., Ahmad, S., Khatoo, M., Aoshi, T., Gasser, S., & Ishii, K. J. 2015 RNA Polymerase III Regulates Cytosolic RNA:DNA Hybrids and Intracellular MicroRNA Expression. Journal of Biological Chemistry 290(12), 7463–7473 doi
  5. Tsujii, A., Miyamoto, Y., Moriyama, T., Tsuchiya, Y., Obuse, C., Mizuguchi, K., Oka, M., & Yoneda, Y. 2015 Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence. The Journal of Biological Chemistry 290(49), 29375–29388 doi
  6. Lee, J., Park, E. J., Yuki, Y., Ahmad, S., Mizuguchi, K., Ishii, K. J., Shimaoka, M., & Kiyono, H. 2015 Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis. Scientific Reports 5, 18174 doi
  7. Camargo, L. M., Zhang, X. D., Loerch, P., Caceres, R. M., Marine, S. D., Uva, P., Ferrer, M., Rinaldis, E. de, Stone, D. J., Majercak, J., Ray, W. J., Yi-An, C., Shearman, M. S., & Mizuguchi, K. 2015 Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing. PLOS ONE 10(2), e0115369 doi
  8. Ito, M., Nakagawa, S., Mizuguchi, K., & Okumura, T. 2015 Integration of Disease Entries Across OMIM, Orphanet, and a Proprietary Knowledge Base. Current Approaches in Applied Artificial Intelligence 120–130 doi
  9. Chiba, S., Ikeda, K., Ishida, T., Gromiha, M. M., Taguchi, Y. -h, Iwadate, M., Umeyama, H., Hsin, K.-Y., Kitano, H., Yamamoto, K., Sugaya, N., Kato, K., Okuno, T., Chikenji, G., Mochizuki, M., Yasuo, N., Yoshino, R., Yanagisawa, K., Ban, T., Teramoto, R., Ramakrishnan, C., Thangakani, A. M., Velmurugan, D., Prathipati, P., Ito, J., Tsuchiya, Y., Mizuguchi, K., Honma, T., Hirokawa, T., Akiyama, Y., & Sekijima, M. 2015 Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. Scientific Reports 5, 17209 doi
  10. Kim, N.-H., Yoshimaru, T., Chen, Y.-A., Matsuo, T., Komatsu, M., Miyoshi, Y., Tanaka, E., Sasa, M., Mizuguchi, K., & Katagiri, T. 2015 BIG3 Inhibits the Estrogen-Dependent Nuclear Translocation of PHB2 via Multiple Karyopherin-Alpha Proteins in Breast Cancer Cells. PLoS ONE 10(6) doi

2014

  1. 2014年9月22日 乳癌細胞増殖の分子機構解明から創薬へ 読売新聞 朝刊
  2. Nagao, C., Nagano, N., & Mizuguchi, K. 2014 Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests. PLOS ONE 9(1), e84623 doi
  3. Ito, J., Ikeda, K., Yamada, K., Mizuguchi, K., & Tomii, K. 2015 PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Research 43(Database issue), D392–D398 doi
  4. Yamashita, K., Ikeda, K., Amada, K., Liang, S., Tsuchiya, Y., Nakamura, H., Shirai, H., & Standley, D. M. 2014 Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. Bioinformatics 30(22), 3279–3280 doi
  5. Chen, Y.-A., Tripathi, L. P., Dessailly, B. H., Nyström-Persson, J., Ahmad, S., & Mizuguchi, K. 2014 Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation. PLOS ONE 9(6), e99030 doi
  6. Murakami, Y., & Mizuguchi, K. 2014 Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. BMC Bioinformatics 15, 213 doi
  7. Shirai, H., Ikeda, K., Yamashita, K., Tsuchiya, Y., Sarmiento, J., Liang, S., Morokata, T., Mizuguchi, K., Higo, J., Standley, D. M., & Nakamura, H. 2014 High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations. Proteins: Structure, Function, and Bioinformatics 82(8), 1624–1635 doi
  8. Yamada, H., Nagao, C., Haredy, A. M., Mori, Y., Mizuguchi, K., Yamanishi, K., & Okamoto, S. 2014 Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein. Antiviral Research 111, 69–77 doi
  9. Fujita, J., Maeda, Y., Nagao, C., Tsuchiya, Y., Miyazaki, Y., Hirose, M., Mizohata, E., Matsumoto, Y., Inoue, T., Mizuguchi, K., & Matsumura, H. 2014 Crystal structure of FtsA from Staphylococcus aureus. FEBS Letters 588(10), 1879–1885 doi
  10. Chen, Y.-A., Murakami, Y., Ahmad, S., Yoshimaru, T., Katagiri, T., & Mizuguchi, K. 2014 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. BMC Research Notes 7, 435 doi
  11. Takemura, N., Kawasaki, T., Kunisawa, J., Sato, S., Lamichhane, A., Kobiyama, K., Aoshi, T., Ito, J., Mizuguchi, K., Karuppuchamy, T., Matsunaga, K., Miyatake, S., Mori, N., Tsujimura, T., Satoh, T., Kumagai, Y., Kawai, T., Standley, D. M., Ishii, K. J., Kiyono, H., Akira, S., & Uematsu, S. 2014 Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome. Nature Communications 5, 3492 doi
  12. Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S. J., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A. M. J. J., Eisenstein, M., Jiménez-García, B., Grosdidier, S., Solernou, A., Pérez-Cano, L., Pallara, C., Fernández-Recio, J., Xu, J., Muthu, P., Kilambi, K. P., Gray, J. J., Grudinin, S., Derevyanko, G., Mitchell, J. C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D. M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D. W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P. J., Vakser, I. A., Pierce, B. G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H. J., Zacharias, M., Qin, S., Zhou, H.-X., Huang, S.-Y., Zou, X., Wojdyla, J. A., Kleanthous, C., & Wodak, S. J. 2014 Blind Prediction of Interfacial Water Positions in CAPRI. Proteins 82(4), 620–632 doi
  13. Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J.-D., Wang, Y., Wu, H., Kano, Y., Ono, H., Bono, H., Kocbek, S., Aerts, J., Akune, Y., Antezana, E., Arakawa, K., Aranda, B., Baran, J., Bolleman, J., Bonnal, R. J., Buttigieg, P. L., Campbell, M. P., Chen, Y., Chiba, H., Cock, P. J., Cohen, K. B., Constantin, A., Duck, G., Dumontier, M., Fujisawa, T., Fujiwara, T., Goto, N., Hoehndorf, R., Igarashi, Y., Itaya, H., Ito, M., Iwasaki, W., Kalaš, M., Katoda, T., Kim, T., Kokubu, A., Komiyama, Y., Kotera, M., Laibe, C., Lapp, H., Lütteke, T., Marshall, M. S., Mori, T., Mori, H., Morita, M., Murakami, K., Nakao, M., Narimatsu, H., Nishide, H., Nishimura, Y., Nystrom-Persson, J., Ogishima, S., Okamura, Y., Okuda, S., Oshita, K., Packer, N. H., Prins, P., Ranzinger, R., Rocca-Serra, P., Sansone, S., Sawaki, H., Shin, S.-H., Splendiani, A., Strozzi, F., Tadaka, S., Toukach, P., Uchiyama, I., Umezaki, M., Vos, R., Whetzel, P. L., Yamada, I., Yamasaki, C., Yamashita, R., York, W. S., Zmasek, C. M., Kawamoto, S., & Takagi, T. 2014 BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics 5, 5 doi
  14. Kumagai, A., Fujita, A., Yokoyama, T., Nonobe, Y., Hasaba, Y., Sasaki, T., Itoh, Y., Koura, M., Suzuki, O., Adachi, S., Ryo, H., Kohara, A., Tripathi, L. P., Sanosaka, M., Fukushima, T., Takahashi, H., Kitagawa, K., Nagaoka, Y., Kawahara, H., Mizuguchi, K., Nomura, T., Matsuda, J., Tabata, T., & Takemori, H. 2014 Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line. Genes 5(4), 1095–1114 doi

2013

  1. Tripathi, L. P., Kambara, H., Chen, Y.-A., Nishimura, Y., Moriishi, K., Okamoto, T., Morita, E., Abe, T., Mori, Y., Matsuura, Y., & Mizuguchi, K. 2013 Understanding the Biological Context of NS5A–Host Interactions in HCV Infection: A Network-Based Approach. Journal of Proteome Research 12(6), 2537–2551 doi
  2. Tang, C. K., Aoshi, T., Jounai, N., Ito, J., Ohata, K., Kobiyama, K., Dessailly, B. H., Kuroda, E., Akira, S., Mizuguchi, K., Coban, C., & Ishii, K. J. 2013 The Chemotherapeutic Agent DMXAA as a Unique IRF3-Dependent Type-2 Vaccine Adjuvant. PLoS ONE 8(3) doi
  3. Nyström-Persson, J., Igarashi, Y., Ito, M., Morita, M., Nakatsu, N., Yamada, H., & Mizuguchi, K. 2013 Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform. Bioinformatics 29(23), 3080–3086 doi
  4. Yoshimaru, T., Komatsu, M., Matsuo, T., Chen, Y.-A., Murakami, Y., Mizuguchi, K., Mizohata, E., Inoue, T., Akiyama, M., Yamaguchi, R., Imoto, S., Miyano, S., Miyoshi, Y., Sasa, M., Nakamura, Y., & Katagiri, T. 2013 Targeting BIG3–PHB2 interaction to overcome tamoxifen resistance in breast cancer cells. Nature Communications 4 doi
  5. Tiwari, P., Tripathi, L. P., Nishikawa-Matsumura, T., Ahmad, S., Song, S.-N. J., Isobe, T., Mizuguchi, K., & Yoshizaki, K. 2013 Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter. Biochimica et Biophysica Acta (BBA) – General Subjects 1830(6), 3650–3655 doi
  6. Fujita, J., Miyazaki, Y., Hirose, M., Nagao, C., Mizohata, E., Matsumoto, Y., Mizuguchi, K., Inoue, T., & Matsumura, H. 2013 Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 69(Pt 8), 895–898 doi
  7. Dessailly, B. H., Dawson, N. L., Mizuguchi, K., & Orengo, C. A. 2013 Functional site plasticity in domain superfamilies. Biochimica et Biophysica Acta 1834(5), 874–889 doi
  8. Hutchins, A. P., Diez, D., Takahashi, Y., Ahmad, S., Jauch, R., Tremblay, M. L., & Miranda-Saavedra, D. 2013 Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions. Nucleic Acids Research 41(4), 2155–2170 doi
  9. Hobro, A. J., Standley, D. M., Ahmad, S., & Smith, N. I. 2013 Deconstructing RNA: optical measurement of composition and structure. Physical Chemistry Chemical Physics 15(31), 13199–13208 doi
  10. Andrabi, M., Mizuguchi, K., & Ahmad, S. 2014 Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability. Proteins: Structure, Function, and Bioinformatics 82(5), 841–857 doi
  11. Moretti R., Fleishman SJ., Agius R., Torchala M., Bates PA., Kastritis PL., Rodrigues JP., Trellet M., Bonvin AM., Cui M., Rooman M., Gillis D., Dehouck Y., Moal I., Romero-Durana M., Perez-Cano L., Pallara C., Jimenez B., Fernandez-Recio J., Flores S.,Pacella M., Praneeth Kilambi K., Gray JJ., Popov P., Grudinin S., Esquivel-Rodríguez J., Kihara D., Zhao N., Korkin D., Zhu X., Demerdash ON., Mitchell JC., Kanamori E., Tsuchiya Y., Nakamura H., Lee H., Park H., Seok C., Sarmiento J., Liang S., Teraguchi S., Standley DM., Shimoyama H., Terashi G., Takeda-Shitaka M., Iwadate M., Umeyama H., Beglov D., Hall DR., Kozakov D., Vajda S., Pierce BG., Hwang H., Vreven T., Weng Z., Huang Y., Li H., Yang X., Ji X., Liu S., Xiao Y., Zacharias M., Qin S., Zhou HX., Huang SY., Zou X., Velankar S., Janin J., Wodak SJ., Baker D. 2013 Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions. Proteins 81(11), 1980–1987 doi

2012

  1. Tripathi, L. P., Kambara, H., Moriishi, K., Morita, E., Abe, T., Mori, Y., Chen, Y.-A., Matsuura, Y., & Mizuguchi, K. 2012 Proteomic Analysis of Hepatitis C Virus (HCV) Core Protein Transfection and Host Regulator PA28γ Knockout in HCV Pathogenesis: A Network-Based Study. Journal of Proteome Research 11(7), 3664–3679 doi
  2. Morita, M., Igarashi, Y., Ito, M., Chen, Y.-A., Nagao, C., Sakaguchi, Y., Sakate, R., Masui, T., & Mizuguchi, K. 2012 Sagace: A web-based search engine for biomedical databases in Japan. BMC Research Notes 5(1), 604 doi
  3. Ihara, S., Kida, H., Arase, H., Tripathi, L. P., Chen, Y.-A., Kimura, T., Yoshida, M., Kashiwa, Y., Hirata, H., Fukamizu, R., Inoue, R., Hasegawa, K., Goya, S., Takahashi, R., Minami, T., Tsujino, K., Suzuki, M., Kohmo, S., Inoue, K., Nagatomo, I., Takeda, Y., Kijima, T., Mizuguchi, K., Tachibana, I., & Kumanogoh, A. 2012 Inhibitory Roles of Signal Transducer and Activator of Transcription 3 in Antitumor Immunity during Carcinogen-Induced Lung Tumorigenesis. Cancer Research 72(12), 2990–2999 doi
  4. Blower, T. R., Short, F. L., Rao, F., Mizuguchi, K., Pei, X. Y., Fineran, P. C., Luisi, B. F., & Salmond, G. P. C. 2012 Identification and classification of bacterial Type III toxin–antitoxin systems encoded in chromosomal and plasmid genomes. Nucleic Acids Research 40(13), 6158–6173 doi
  5. Nagao, C., Izako, N., Soga, S., Khan, S. H., Kawabata, S., Shirai, H., & Mizuguchi, K. 2012 Computational design, construction, and characterization of a set of specificity determining residues in protein–protein interactions. Proteins: Structure, Function, and Bioinformatics 80(10), 2426–2436 doi
  6. Keeble-Gagnère, G., Nyström-Persson, J., Bellgard, M. I., & Mizuguchi, K. 2012 An Open Framework for Extensible Multi-stage Bioinformatics Software. Pattern Recognition in Bioinformatics 106–117 doi
  7. Tripathi, L. P., & Mizuguchi, K. 2012 A combined proteomics and computational approach provides a better understanding of HCV-induced liver disease. Expert Review of Proteomics 9(5), 493–496 doi

2011

  1. Williams, S. G., Madan, R., Norris, M. G. S., Archer, J., Mizuguchi, K., Robertson, D. L., & Lovell, S. C. 2011 Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1. Journal of Molecular Biology 410(5), 1023–1034 doi
  2. Chen, Y.-A., Tripathi, L. P., & Mizuguchi, K. 2011 TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery. PLOS ONE 6(3), e17844 doi
  3. Kahali, B., Ahmad, S., & Ghosh, T. C. 2011 Selective constraints in yeast genes with differential expressivity: Codon pair usage and mRNA stability perspectives. Gene 481(2), 76–82 doi
  4. 平田 みつひ, シャンダー・ アハマド, 菅 三佳, 藤木 彩加, 松村 紘子, 若林 真理, 上田 直子, 劉 克紅, 林田 みどり, 平山 知子, 小原 有弘, 柳原 佳奈, 水口 賢司, & 古江－楠田 美保. 2011 日本におけるヒトES、iPS細胞研究標準化：. 組織培養研究 30(2+3+4), 145–157 doi
  5. Firoz, A., Malik, A., Joplin, K. H., Ahmad, Z., Jha, V., & Ahmad, S. 2011 Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC Biochemistry 12, 20 doi
  6. Fernandez, M., Kumagai, Y., Standley, D. M., Sarai, A., Mizuguchi, K., & Ahmad, S. 2011 Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics 12(13), S5 doi
  7. Morita, M., Katta, A. M., Ahmad, S., Mori, T., Sugita, Y., & Mizuguchi, K. 2011 Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data. BMC Biophysics 4(1), 21 doi
  8. Ahmad, S., & Mizuguchi, K. 2011 Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data. PLOS ONE 6(12), e29104 doi
  9. Schwarz, U. I., Meyer zu Schwabedissen, H. E., Tirona, R. G., Suzuki, A., Leake, B. F., Mokrab, Y., Mizuguchi, K., Ho, R. H., & Kim, R. B. 2011 Identification of novel functional Organic Anion-transporting Polypeptide 1B3 (OATP1B3) polymorphisms and assessment of substrate specificity. Pharmacogenetics and Genomics 21(3), 103–114 doi
  10. Ahmad, S., & Sarai, A. 2011 Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. BMC Structural Biology 11(1), 8 doi

2010

  1. Nagao, C., Nagano, N., & Mizuguchi, K. 2010 Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies. Proteins: Structure, Function, and Bioinformatics 78(10), 2369–2384 doi
  2. Fernandez, M., Ahmad, S., & Sarai, A. 2010 Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines. Journal of Chemical Information and Modeling 50(6), 1179–1188 doi
  3. Murakami, Y., Spriggs, R. V., Nakamura, H., & Jones, S. 2010 PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. Nucleic Acids Research 38(Web Server issue), W412–W416 doi
  4. Someya, S., Kakuta, M., Morita, M., Sumikoshi, K., Cao, W., Ge, Z., Hirose, O., Nakamura, S., Terada, T., & Shimizu, K. 2010 Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines. Advances in Bioinformatics 2010 doi
  5. Singh, Y. H., Andrabi, M., Kahali, B., Ghosh, T. C., Mizuguchi, K., Kochetov, A. V., & Ahmad, S. 2010 On nucleotide solvent accessibility in RNA structure. Gene 463(1), 41–48 doi
  6. Tripathi, L. P., Kataoka, C., Taguwa, S., Moriishi, K., Mori, Y., Matsuura, Y., & Mizuguchi, K. 2010 Network based analysis of hepatitis C virus Core and NS4B protein interactions. Molecular BioSystems 6(12), 2539–2553 doi
  7. Mondal, S., Nagao, C., & Mizuguchi, K. 2010 Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores. Protein Engineering, Design and Selection 23(11), 859–869 doi
  8. Yoshioka, Y., Watanabe, H., Morishige, T., Yao, X., Ikemizu, S., Nagao, C., Ahmad, S., Mizuguchi, K., Tsunoda, S., Tsutsumi, Y., Mukai, Y., Okada, N., & Nakagawa, S. 2010 Creation of lysine-deficient mutant lymphotoxin-α with receptor selectivity by using a phage display system. Biomaterials 31(7), 1935–1943 doi
  9. Ahmad, S., Singh, Y. H., Paudel, Y., Mori, T., Sugita, Y., & Mizuguchi, K. 2010 Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. BMC Bioinformatics 11, 533 doi
  10. Ahmad, S., Keskin, O., Mizuguchi, K., Sarai, A., & Nussinov, R. 2010 CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Research, 38(Web Server issue), W398–W401. doi
  11. Murakami, Y., & Mizuguchi, K. 2010 Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites. Bioinformatics 26(15), 1841–1848 doi
  12. Mokrab, Y., Stevens, T. J., & Mizuguchi, K. 2010 A structural dissection of amino acid substitutions in helical transmembrane proteins. Proteins: Structure, Function, and Bioinformatics 78(14), 2895–2907 doi

2009

  1. Morita, M., Saito, S., Ikeda, K., Ohno, K., Sugawara, K., Suzuki, T., Togawa, T., & Sakuraba, H. 2009 Structural bases of GM1 gangliosidosis and Morquio B disease. Journal of Human Genetics 54(9), 510–515 doi
  2. Ahmad, S. 2009 Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA. Gene 428(1), 25–30 doi
  3. Andrabi, M., Mizuguchi, K., Sarai, A., & Ahmad, S. 2009 Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. BMC Structural Biology 9, 30 doi
  4. Spriggs, R. V., Murakami, Y., Nakamura, H., & Jones, S. 2009 Protein function annotation from sequence: prediction of residues interacting with RNA. Bioinformatics 25(12), 1492–1497 doi
  5. Tateishi, Y., Ariyoshi, M., Igarashi, R., Hara, H., Mizuguchi, K., Seto, A., Nakai, A., Kokubo, T., Tochio, H., & Shirakawa, M. 2009 Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2. Journal of Biological Chemistry 284(4), 2435–2447 doi
  6. Kahali, B., Ahmad, S., & Ghosh, T. C. 2009 Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein–protein interaction network. Gene 429(1), 18–22 doi
  7. Singh, H., & Ahmad, S. 2009 Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis. BMC Structural Biology 9, 25 doi
  8. Furusawa, H., Ozeki, T., Morita, M., & Okahata, Y. 2009 Added Mass Effect on Immobilizations of Proteins on a 27 MHz Quartz Crystal Microbalance in Aqueous Solution. Analytical Chemistry 81(6), 2268–2273 doi
  9. Mondal, S., & Mizuguchi, K. 2009 Structural insights into the enzyme mechanism of a new family of d-2-hydroxyacid dehydrogenases, a close homolog of 2-ketopantoate reductase. Genome Informatics. International Conference on Genome Informatics 23(1), 98–105 doi

2008

  1. Singh, R., Ali Dar, T., Ahmad, S., Moosavi-Movahedi, A. A., & Ahmad, F. 2008 A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea). Biophysical Chemistry 133(1), 81–89 doi
  2. Malik, A., Arija M Arif, S., Ahmad, S., & Elumalai, S. 2008 A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen. International Journal of Biological Macromolecules 42, 185–190 doi
  3. Hart, S. E., Howe, C. J., Mizuguchi, K., & Fernandez-Recio, J. 2008 Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum. Protein Engineering, Design and Selection 21(12), 689–698 doi
  4. Bailly, X., Vanin, S., Chabasse, C., Mizuguchi, K., & Vinogradov, S. N. 2008 A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins. BMC Evolutionary Biology 8(1), 244 doi
  5. Mokrab, Y., Stevens, T. J., & Mizuguchi, K. 2009 Lipophobicity and the residue environments of the transmembrane α-helical bundle. Proteins: Structure, Function, and Bioinformatics 74(1), 32–49 doi
  6. Zhu, B., Pennack, J. A., McQuilton, P., Forero, M. G., Mizuguchi, K., Sutcliffe, B., Gu, C.-J., Fenton, J. C., & Hidalgo, A. 2008 Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation. PLOS Biology 6(11), e284 doi
  7. Ali, R., Hussain, A., Raish, M., Noor, A., Mohammad, S., Sarin, R., Kukreti, H., Khan, N., Ahmad, S., V.S. Deo, S., Husain, S., Tazeen Pasha, S., Basir, S., & Shukla, nootan kumar. 2008 Specific 5′CpG Island Methylation Signatures of FHIT and p16 Genes and Their Potential Diagnostic Relevance in Indian Breast Cancer Patients. DNA and Cell Biology 27, 517–525 doi
  8. Ahmad, S., Keskin, O., Sarai, A., & Nussinov, R. 2008 Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Research 36(18), 5922–5932 doi
  9. Kochetov, A. V., Ahmad, S., Ivanisenko, V., Volkova, O. A., Kolchanov, N. A., & Sarai, A. 2008 uORFs, reinitiation and alternative translation start sites in human mRNAs. FEBS Letters 582(9), 1293–1297 doi

2007

  1. Ahmad, S., Singh, Y. H., Araúzo‐Bravo, M. J., & Sarai, A. 2008 Sequence-Based Prediction of Residue-Level Properties in Proteins. Machine Learning in Bioinformatics 157–187 doi
  2. Camargo, L. M., Collura, V., Rain, J.-C., Mizuguchi, K., Hermjakob, H., Kerrien, S., Bonnert, T. P., Whiting, P. J., & Brandon, N. J. 2007 Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. Molecular Psychiatry 12(1), 74–86 doi
  3. Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W., Mclaren, P., North, P., Rana, D., Riley, T., Sullivan, J., Watkins, X., Woodbridge, M., Lilley, K., Russell, S., Ashburner, M., Mizuguchi, K., & Micklem, G. 2007 FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biology 8(7), R129 doi
  4. Mizuguchi, K., Sele, M., & Cubellis, M. 2007 Environment specific substitution tables for thermophilic proteins. BMC Bioinformatics 8(Suppl 1), S15 doi
  5. Mokrab, Y., Bavro, V. N., Mizuguchi, K., Todorov, N. P., Martin, I. L., Dunn, S. M. J., Chan, S. L., & Chau, P.-L. 2007 Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor. Journal of Molecular Graphics and Modelling 26(4), 760–774 doi
  6. Vinogradov, S. N., Hoogewijs, D., Bailly, X., Mizuguchi, K., Dewilde, S., Moens, L., & Vanfleteren, J. R. 2007 A model of globin evolution. Gene 398(1), 132–142 doi
  7. Wang, J.-Y., Lee, H.-M., & Ahmad, S. 2007 SVM-Cabins: Prediction of solvent accessibility using accumulation cutoff set and support vector machine. Proteins: Structure, Function, and Bioinformatics 68(1), 82–91 doi

2006

  1. Shiozawa, K., Goda, N., Shimizu, T., Mizuguchi, K., Kondo, N., Shimozawa, N., Shirakawa, M., & Hiroaki, H. 2006 The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97. The FEBS Journal 273(21), 4959–4971 doi
  2. Shirai, H., Mokrab, Y., & Mizuguchi, K. 2006 The guanidino-group modifying enzymes: Structural basis for their diversity and commonality. Proteins: Structure, Function, and Bioinformatics 64(4), 1010–1023 doi
  3. Shiozawa, K., Goda, N., Shimizu, T., Mizuguchi, K., Kondo, N., Shimozawa, N., Shirakawa, M., & Hiroaki, H. 2006 The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97. The FEBS Journal 273(21), 4959–4971 doi

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