Publications

2019
  1. 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, 0(0). doi
  2.  Esaki, T., Watanabe, R., Kawashima, H., Ohashi, R., Natsume‐Kitatani, Y., Nagao, C., & Mizuguchi, K. (2019). Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance. Molecular Informatics, 38(1–2), e1800086. doi
  3.  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
  4.  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
  5. 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
  6.  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. doi
  7. 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), 1–13. doi
  8. 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. doi
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.. doi
  5.  Tripathi, L., Murakami, Y., Chen, Y.-A., & Mizuguchi, K. (2018). Network-Based Analysis for Biological Discovery. Encyclopedia of Bioinformatics and Computational Biology.. doi
  6.  Tripathi, L., Esaki, T., N. Itoh, M., Chen, Y.-A., & Mizuguchi, K. (2018). Integrative Analysis of Multi-Omics Data. Encyclopedia of Bioinformatics and Computational Biology.. 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, 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, 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, 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を用いた新材料開発へのアプローチ.
  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, 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. 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 Biology, 3(1), e37–e37. doi
  2.  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
  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 Reports, 7. doi
  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 Biology, 44, 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 Reports, 7(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 Communications, 8, 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 Reports, 7(1), 4071. doi
  8.  Sowdhamini, R., & Mizuguchi, K. (2017). Editorial—Sequences and topology. Current Opinion in Structural Biology, 44, 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 Reports, 7(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, Japan, 77(4), 211–215. doi
  11.  Mizuguchi, K. (2017). Database Development and Computational Modelling in Early-Stage Drug Discovery. Trends in the Sciences, 22(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 Reports, 7(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 Immunology, 200(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 Curation, 2016. doi
  2.  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
  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 Bioinformatics, 18(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 Cell, 27(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 Design, 30(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. EBioMedicine, 9, 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 Genomics, 17(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 OA, 2(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 Society, 25(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 ONE, 10(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 Reports, 5, 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 ONE, 10(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 Reports, 5, 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 Chemistry, 290(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 Chemistry, 290(12), 7463–7473. doi
  8.  Mizuguchi, P. P. and K. (2016). Systems Biology Approaches to a Rational Drug Discovery Paradigm. Current Topics in Medicinal Chemistry. doi
  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; Heidelberg, 64(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. Genes, 5(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 Semantics, 5, 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. Proteins, 82(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 Communications, 5, 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 Notes, 7, 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 Letters, 588(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 Research, 111, 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 Bioinformatics, 82(8), 1624–1635. doi
  9.  Murakami, Y., & Mizuguchi, K. (2014). Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. BMC Bioinformatics, 15, 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 ONE, 9(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. Bioinformatics, 30(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 Research, 43(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 ONE, 9(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. Proteins, 81(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 Bioinformatics, 82(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 Physics, 15(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 Research, 41(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 Communications, 69(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 Acta, 1834(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 Subjects, 1830(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 Communications, 4. doi
  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 ONE, 8(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. Bioinformatics, 29(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 Research, 12(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 Proteomics, 9(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 Bioinformatics, 80(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 Research, 40(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 Research, 72(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 Research, 11(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 Notes, 5(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 Biology, 11(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 Genomics, 21(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 Biophysics, 4(1), 21. doi
  4.  Ahmad, S., & Mizuguchi, K. (2011). Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data. PLOS ONE, 6(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 Bioinformatics, 12(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 Biochemistry, 12, 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. Gene, 481(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 ONE, 6(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 Biology, 410(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 Bioinformatics, 78(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. Bioinformatics, 26(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 Research, 38(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. Biomaterials, 31(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 Selection, 23(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 Bioinformatics, 11, 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 BioSystems, 6(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. Gene, 463(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 Research, 38(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 Bioinformatics, 2010. doi
  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 Modeling, 50(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 Bioinformatics, 78(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 Chemistry, 81(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 Biology, 9, 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. Gene, 429(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 Chemistry, 284(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 Biology, 9, 30. doi
  6.  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
  7.  Ahmad, S. (2009). Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA. Gene, 428(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 Genetics, 54(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 Informatics, 23(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 Macromolecules, 42, 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 Chemistry, 133(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 Biology, 8(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 Selection, 21(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 Biology, 6(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 Bioinformatics, 74(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 Research, 36(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 Biology, 27, 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 Letters, 582(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 Bioinformatics, 68(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. Gene, 398(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 Modelling, 26(4), 760–774. doi
  4.  Mizuguchi, K., Sele, M., & Cubellis, M. (2007). Environment specific substitution tables for thermophilic proteins. BMC Bioinformatics, 8(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 Biology, 8(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 Psychiatry, 12(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 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