National Institutes of Biomedical Innovation, Health and Nutrition
Institute for Protein Research

Publications

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2021

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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

2020

  1. 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
  2. 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
  3. 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.
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  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]. doi
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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

2019

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Afanasyeva, A., Nagao, C., & Mizuguchi, K. (2019). Prediction of the secondary structure of short DNA aptamers. Biophysics and Physicobiology, 16, 287–294. doi
  16. 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
  17. 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
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.

2018

  1. 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
  2.  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
  3.  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
  4.  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
  5.  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
  6.  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
  7.  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
  8.  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
  9.  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
  10.  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
  11.  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.
  12.  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.
  13.  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.
  14.  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.
  15.  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.
  16.  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
  17.  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.
  18.  Fujiwara T., Kamada M., & Okuno Y. (2018). Artificial Intelligence in Drug Discovery. Gan to Kagaku Ryoho, 4, 593–596.
  19.  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
  20.  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
  21. 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

2017

  1. 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 Biology3(1), e37–e37. doi
  2.  Natsume-Kitatani Y., & Mizuguchi K. (2017). Computational systems biology for drug discovery: from molecules, structures to networks. Folia Pharmacologica Japonica149(2), 91–95. doi
  3.  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 Reports7doi
  4.  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 Biology44, 134–142. doi
  5.  Nyström-Persson, J., Natsume-Kitatani, Y., Igarashi, Y., Satoh, D., & Mizuguchi, K. (2017). Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. Scientific Reports7(1), 1390. doi
  6.  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 Communications8, 15427. doi
  7.  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 Reports7(1), 4071. doi
  8.  Sowdhamini, R., & Mizuguchi, K. (2017). Editorial—Sequences and topology. Current Opinion in Structural Biology44, vii–viii. doi
  9.  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 Reports7(1), 4339. doi
  10.  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, Japan77(4), 211–215. doi
  11.  Mizuguchi, K. (2017). Database Development and Computational Modelling in Early-Stage Drug Discovery. Trends in the Sciences22(7), 7_62-7_65. doi
  12.  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 Reports7(1), 12847. doi
  13.  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 Immunology200(1), 71–81. doi
  14.  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. Retrieved from Web
  15.  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. Retrieved from Web

2016

  1. 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 Curation2016doi
  2.  Natsume-Kitatani, Y., & Mamitsuka, H. (2016). Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns. PLoS ONE11(3). doi
  3.  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 Bioinformatics18(1), 9–27. doi
  4.  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 Cell27(20), 3095–3108. doi
  5.  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 Design30(9), 817–828. 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. EBioMedicine9, 87–96. doi
  7.  Murakami, Y., Omori, S., & Kinoshita, K. (2016). NLDB: a database for 3D protein–ligand interactions in enzymatic reactions. Journal of Structural and Functional Genomics17(4), 101–110. doi
  8.  Sequence and Structural Determinants of Antigen Binding in Antibody CDR Loops. (2016). Asia Pacific Biotech News – Featuring News, Interviews Information in APAC. Retrieved from Web
  9.  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 OA2(4). doi
  10.  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 Society25(4), 815–825. doi

2015

  1. 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 ONE10(6). doi
  2.  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 Reports5, 17209. doi
  3.  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
  4.  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 ONE10(2), e0115369. doi
  5.  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 Reports5, 18174. doi
  6.  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 Chemistry290(49), 29375–29388. doi
  7.  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 Chemistry290(12), 7463–7473. doi
  8. Philip Prathipati, Kenji Mizuguchi (2016). Systems Biology Approaches to a Rational Drug Discovery Paradigm. Current Topics in Medicinal Chemistrydoi
  9.  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; Heidelberg64(7), 791–804. Web

2014

  1. 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. Genes5(4), 1095–1114. doi
  2.  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 Semantics5, 5. doi
  3.  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. Proteins82(4), 620–632. doi
  4.  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 Communications5, 3492. doi
  5.  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 Notes7, 435. doi
  6.  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 Letters588(10), 1879–1885. doi
  7.  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 Research111, 69–77. doi
  8.  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 Bioinformatics82(8), 1624–1635. doi
  9.  Murakami, Y., & Mizuguchi, K. (2014). Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. BMC Bioinformatics15, 213. doi
  10.  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 ONE9(6), e99030. doi
  11.  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. Bioinformatics30(22), 3279–3280. doi
  12.  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 Research43(Database issue), D392–D398. doi
  13.  Nagao, C., Nagano, N., & Mizuguchi, K. (2014). Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests. PLOS ONE9(1), e84623. doi

2013

  1. 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. Proteins81(11), 1980–1987. doi
  2. 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 Bioinformatics82(5), 841–857. doi
  3.  Hobro, A. J., Standley, D. M., Ahmad, S., & Smith, N. I. (2013). Deconstructing RNA: optical measurement of composition and structure. Physical Chemistry Chemical Physics15(31), 13199–13208. doi
  4.  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 Research41(4), 2155–2170. doi
  5.  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 Communications69(Pt 8), 895–898. doi
  6.  Dessailly, B. H., Dawson, N. L., Mizuguchi, K., & Orengo, C. A. (2013). Functional site plasticity in domain superfamilies. Biochimica et Biophysica Acta1834(5), 874–889. doi
  7.  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 Subjects1830(6), 3650–3655. doi
  8.  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 Communications4doi
  9.  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 ONE8(3). doi
  10.  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. Bioinformatics29(23), 3080–3086. doi
  11.  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 Research12(6), 2537–2551. doi

2012

  1. Tripathi, L. P., & Mizuguchi, K. (2012). A combined proteomics and computational approach provides a better understanding of HCV-induced liver disease. Expert Review of Proteomics9(5), 493–496. doi
  2.  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
  3.  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 Bioinformatics80(10), 2426–2436. 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 Research40(13), 6158–6173. doi
  5.  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 Research72(12), 2990–2999. doi
  6.  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 Research11(7), 3664–3679. doi
  7.  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 Notes5(1), 604. doi

2011

  1. Ahmad, S., & Sarai, A. (2011). Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. BMC Structural Biology11(1), 8. doi
  2.  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 Genomics21(3), 103–114. doi
  3.  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 Biophysics4(1), 21. doi
  4.  Ahmad, S., & Mizuguchi, K. (2011). Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data. PLOS ONE6(12), e29104. doi
  5.  Fernandez, M., Kumagai, Y., Standley, D. M., Sarai, A., Mizuguchi, K., & Ahmad, S. (2011). Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics12(13), S5. doi
  6.  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 Biochemistry12, 20. doi
  7.  Kahali, B., Ahmad, S., & Ghosh, T. C. (2011). Selective constraints in yeast genes with differential expressivity: Codon pair usage and mRNA stability perspectives. Gene481(2), 76–82. doi
  8.  Chen, Y.-A., Tripathi, L. P., & Mizuguchi, K. (2011). TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery. PLOS ONE6(3), e17844. doi
  9.  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 Biology410(5), 1023–1034. doi
  10.  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

2010

  1. Mokrab, Y., Stevens, T. J., & Mizuguchi, K. (2010). A structural dissection of amino acid substitutions in helical transmembrane proteins. Proteins: Structure, Function, and Bioinformatics78(14), 2895–2907. doi
  2.  Murakami, Y., & Mizuguchi, K. (2010). Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites. Bioinformatics26(15), 1841–1848. doi
  3.  Ahmad, S., Keskin, O., Mizuguchi, K., Sarai, A., & Nussinov, R. (2010). CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Research38(Web Server issue), W398–W401. doi
  4.  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. Biomaterials31(7), 1935–1943. doi
  5.  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 Selection23(11), 859–869. doi
  6.  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 Bioinformatics11, 533. doi
  7.  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 BioSystems6(12), 2539–2553. doi
  8.  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. Gene463(1), 41–48. doi
  9.  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 Research38(Web Server issue), W412–W416. doi
  10.  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 Bioinformatics2010doi
  11.  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 Modeling50(6), 1179–1188. doi
  12.  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 Bioinformatics78(10), 2369–2384. doi

2009

  1.  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 Chemistry81(6), 2268–2273. doi
  2.  Singh, H., & Ahmad, S. (2009). Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis. BMC Structural Biology9, 25. doi
  3.  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. Gene429(1), 18–22. doi
  4.  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 Chemistry284(4), 2435–2447. doi
  5.  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 Biology9, 30. doi
  6.  Spriggs, R. V., Murakami, Y., Nakamura, H., & Jones, S. (2009). Protein function annotation from sequence: prediction of residues interacting with RNA. Bioinformatics25(12), 1492–1497. doi
  7.  Ahmad, S. (2009). Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA. Gene428(1), 25–30. doi
  8.  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 Genetics54(9), 510–515. 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 Informatics23(1), 98–105. doi

2008

  1. 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 Macromolecules42, 185–190. doi
  2.  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 Chemistry133(1), 81–89. doi
  3.  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 Biology8(1), 244. doi
  4.  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 Selection21(12), 689–698. doi
  5.  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 Biology6(11), e284. doi
  6.  Mokrab, Y., Stevens, T. J., & Mizuguchi, K. (2009). Lipophobicity and the residue environments of the transmembrane α-helical bundle. Proteins: Structure, Function, and Bioinformatics74(1), 32–49. doi
  7.  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 Research36(18), 5922–5932. doi
  8.  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 Biology27, 517–525. 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 Letters582(9), 1293–1297. doi

2007

  1. 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 Bioinformatics68(1), 82–91. doi
  2.  Vinogradov, S. N., Hoogewijs, D., Bailly, X., Mizuguchi, K., Dewilde, S., Moens, L., & Vanfleteren, J. R. (2007). A model of globin evolution. Gene398(1), 132–142. doi
  3.  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 Modelling26(4), 760–774. doi
  4.  Mizuguchi, K., Sele, M., & Cubellis, M. (2007). Environment specific substitution tables for thermophilic proteins. BMC Bioinformatics8(Suppl 1), S15. doi
  5.  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 Biology8(7), R129. doi
  6.  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 Psychiatry12(1), 74–86. doi
  7.  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

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 Journal273(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 Bioinformatics64(4), 1010–1023. doi