原著論文Original Article

  • 2018)
    • Tamada, Y. Memory Efficient Parallel Algorithm for Optimal DAG Structure Search using Direct Communication. Journal of Parallel and Distributed Computing, 119, 27-35, 2018. doi.org/10.1016/j.jpdc.2018.03.011
    • Kawai, R.*, Araki, M.*, Yoshimura, M., Kamiya, N., Ono, M., Saji, H., Okuno, Y. “Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods” ACSChemical Neuroscience. 2018. doi: 10.1021/acschemneuro.7b00389.
    • Nakaoku, T., Kohno T.*, Araki M., Niho, S., Chauhan, R., Knowles, P.P.,  Tsuchihara, K., Matsumoto, S., Shimada, Y., Mimaki, S., Ishii, G., Ichikawa, H., Nagatoishi, S., Tsumoto, K., Okuno, Y., Yoh, K., McDonald, N.Q., Goto, K. “A secondary RET mutation in the activation loop conferring resistance to vandetanib” Nature Communications, 2018 Feb 12; 9(1): 625. doi: 10.1038/s41467-018-02994-7.
  • 2017)
    • Fujita, K., Taneishi, K., Inamoto, T., Ishizuya, Y., Takada, S., Tsujihata, M., Tanigawa, G., Minato, N., Nakazawa, S., Takada, T., Iwanishi, T., Uemura, M., Okuno, Y., Azuma, H., Norio, N. “Adjuvant chemotherapy improves survival of patients with high-risk upper urinary tract urothelial carcinoma: a propensity score-matched analysis” BMC Urol. 17(1), 110, 2017. doi: 10.1186/s12894-017-0305-4.
    • Terayama, K., Iwata, H., Araki, M., Okuno, Y., Tsuda, K. “Machine Learning Accelerates MD-based Binding-Pose Prediction between Ligands and Proteins” Bioinformatics. Oct 11, 2017. doi: 10.1093/bioinformatics/btx638. [Epub ahead of print] PMID: 29040432
    • Uneno, Y., Taneishi, K., Kanai, M., Okamoto, K., Yamamoto, Y., Yoshioka, A., Hiramoto, S., Nozaki, A., Nishikawa, Y., Yamaguchi, D., Tomono, T., Nakatsui, M., Baba, M., Morita, T., Mataumoto, S., Kuroda, T., Okuno, Y., Muto, M. “Development and validation of a set of six adaptable prognosis prediction (SAP) models based on time-series real-world big data analysis for patients with cancer receiving chemotherapy: A multicenter case crossover study” PloS One. 12(8) 2017. e0183291. doi: 10.1371/journal.pone.0183291. eCollection 2017
    • Kiyan, W., Ito, A., Nakagawa, Y., Mukai, S., Mori, K., Arai, T., Uchino, E,, Okuno, Y., Kuroki, H. “Relationships Between Quantitative Pulse-Echo Ultrasound Parameters from the Superficial Zone of the Human Articular Cartilage and Changes in Surface Roughness, Collagen Content or Collagen Orientation Caused by Early Degeneration” Ultrasound.Med.Biol. 43(8), 1703-1715, 2017.
    • Bekker, G., Kamiya, N., Araki, M., Fukuda, I., Okuno, Y., Nakamura, H. “Accurate prediction of complex structure and affinity for a flexible protein receptor and its inhibitor” J. Chem. Theory Comput. 13(6), 2389–2399, 2017.
    • Kou, T., Kanai, M., Yamamoto, Y., Kamada, M., Nakatsui, M., Sakuma, T., Mochizuki, H., Hiroshima, A., Sugiyama, A., Nakamura, E., Miyake, H., Minamiguchi, S., Takaori, K., Matsumoto, S., Haga, H., Seno, H., Kosugi, S., Okuno, Y., Muto, M. “Clinical sequencing using a next-generation sequencing-based multiplex gene assay in patients with advanced solid tumors” Cancer Science 108(7), 1440-1446, 2017.
    • Uchibori, K., Inase, N., Araki, M., Kamada, M., Sato, S., Okuno, Y., Fujita, N., Katayama, R.,              Brigatinib combined with anti-EGFR antibody overcomes osimertinib resistance in EGFR-mutated        non-small-cell lung cancer” Nature  Communications. 8, 2017.
  • 2016)
    • Hamanaka, M., Taneishi, Kei., Iwata, H., Ye, J., Pei, J., Hou, J., Okuno, Y. “CGBVS-DNN: prediction of  compound-protein Interactions based on deep learning” Molecular Informatics. 36(1-2), 2016.
    •  Araki, M., Kamiya, N., Sato, M., Nakatsui, M., Hirokawa, T., Okuno, Y., The effect of conformational flexibility on binding free energy estimation between kinases and their Inhibitors Journal of Chemical Information and Modeling. 56(12), 2445-2456, 2016.
    •  Nishikawa, Y., Kanai, M., Narahara, M., Tamon, A., Brown, J.B., Taneishi, K., Nakatsui, M., Okamoto, K., Uneno, Y., Yamaguchi, D., Tomono, T., Mori, Y., Matsumoto, S., Okuno, Y., Muto, M. “Association between UGT1A1*28*28 genotype and lung cancer in the Japanese population” Int J Clin Oncol., 2016 Nov.
  • 2015)
    • Kikuchi, O., Ohashi, S., Nakai, Y., Nakagawa, S., Matsuoka, K., Kobunai, T., Takechi, T., Amanuma, Y., Yoshioka, M., Ida, T., Yamamoto, Y., Okuno, Y., Miyamoto, S., Nakagawa, H., Matsubara, K., Chiba, T., Muto, M. Novel 5-fluorouracil-resistant human esophageal squamous cell carcinoma cells with dihydropyrimidine dehydrogenase overexpression Am. J. Cancer Res. 5(8), 2431-2440, 2015.
    • Kimura, G., Kadoyama, K., Brown, J.B., Nakamura, T., Miki, I., Nisiguchi, K., Sakaeda, T., Okuno, Y. “Antipsychotics-associated serious adverse events in children: An analysis of the FAERS database” Int. J. Med. Sci. 12(2), 135-140, 2015.
    • Kawasaki, K., Kondoh, E., Chigusa, Y., Ujita, M., Murakami, R., Mogami, H., Brown, J.B., Okuno, Y., Konishi, I. “Reliable pre-eclampsia pathways based on multiple independent microarray data sets” Molecular Human Reproduction 21(2), 217-224, 2015.
  • 2014)
    • Katayama, R., Friboulet, L., Koike, S., Lockerman, E.L., Khan, T.M., Gainor, J.F., Iafrate, A.J., Takeuchi, K., Taiji, M., Okuno, Y., Fujita, N., Engelman, J.A., Shaw, A.T. Two novel ALK mutations mediate acquired resistance to the next-generation ALK inhibitor Alectinib” Clinical Cancer Research 20(22), 5686-5696, 2014.
    • Brown, J.B., Nakatsui, M.Okuno, Y. “Constructing a foundational platform driven by Japan’s K supercomputer for next-generation drug design” Molecular Informatics 33, 732-741, 2014.
    • Aoyama, A., Katayama, R., Oh-hara, T., Sato, S., Okuno, Y., Fujita, N. “Tivantinib (ARQ 197) exhibits antitumor activity by directly interacting with tubulin and overcomes ABC transporter-mediated drug resistance” Molecular Cancer Therapeutics 13(12), 2978-2990, 2014.
    • Sakaeda, T., Kadoyama, K., Minami, K., Okuno, Y. “Commonality of drug-associated adverse events detected by 4 commonly used data mining algorithms” Int. J. Med. Sci. 11(5), 461-465, 2014.
    • Brown, J.B., Okuno, Y., Marcou, G., Varnek, A., Horvath, D. “Computational chemogenomics: Is it more than inductive transfer?” J. Comput. Aided Mol. Des. 28(6), 597-618, 2014.
    • Zannas, A.S., Okuno, Y., Doraiswamy, P.M. “Cholinesterase inhibitors and Pisa syndrome: A pharmacovigilance study” Pharmacotherapy 34(3), 272-278, 2014.
    • Nakazawa, S., Sakanaka, M., Furuta, K., Natsuhara, M., Takano, H., Tsuchiya, S., Okuno, Y., Ohtsu, H., Nishibori, M., Thurmond, R.L., Hirasawa, N., Nakayama, K., Ichikawa, A., Sugimoto, Y., Tanaka, S. “Histamine synthesis is required for granule maturation in murine mast cells” Eur. J. Immunol. 44(1), 204-214, 2014.
  • 2013)
    • Yamaguchi, Y., Suzuki, T., Mizoro, Y., Kori, H., Okada, K., Chen, Y., Fustin, J.M., Yamazaki, F., Mizuguchi, N., Zhang, J., Dong, X., Tsujimoto, G., Okuno, Y., Doi, M., Okamura, H. “Mice genetically deficient in vasopressin V1a and V1b receptors are resistant to jet lag” Science, 342(6154), 85-90, 2013.
    • Sakaida, M., Sukeno, M., Imoto, Y., Tsuchiya, S., Sugimoto, Y., Okuno, Y., Segi-Nishida, E. “Electroconvulsive seizure-induced changes in gene expression in the mouse hypothalamic paraventricular nucleus” J Psychopharmacology, 27(11), 1058-1069, 2013.
    • Kobayashi, D., Hosaka, S., Inoue, E., Ohshima, K., Kutsuma, N., Oshima, S., Okuno, Y. “Quantitative Evaluation of Initial Symptoms as Predictors to Detect Adverse Drug Reactions Using Bayes’ Theory: Expansion and Evaluation of Drug-Adverse Drug Reaction-Initial Symptom Combinations Using Adverse Event Reporting System Database” Biol. Pharm. Bull., 36(12), 1891 -1901, 2013
    • Shiraishi, A., Niijima, S., Brown, J.B., Nakatsui, M., Okuno, Y. “Chemical genomics approach for GPCR-ligand interaction prediction and extraction of ligand binding determinants” J. Chem. Inf. Model., 53(6), 1253-1262, 2013.
    • Murakami, H., Sakaeda, T., Kadoyama, K., Okuno, Y. “Gender Effects on Statin-Associated Muscular Adverse Events: An Analysis of the FDA AERS Database” Pharmacology & Pharmacy, 4, 340-346, 2013.
    • Seki, S., Okuno, Y. “On the behavior of tile assembly model at high temperatures” Computability, 2(2), 107-124, 2013.
    • Fazekas, S.Z., Ito, H., Okuno, Y., Seki, S., Taneishi, K. “On computational complexity of graph inference from counting” Natural Computing, 12(4), 589-603, 2013.
    • Yoshimura, K., Kadoyama, K., Sakaeda, T., Sugino, Y., Ogawa, O., Okuno, Y. “A Survey of the FAERS Database Concerning the Adverse Event Profiles of α1-Adrenoreceptor Blockers for Lower Urinary Tract Symptoms” Int. J. Med. Sci., 10(7), 864-869, 2013.
    • Segi-Nishida, E., Sukeno, M., Imoto, Y., Kira, T., Sakaida, M., Tsuchiya, S., Sugimoto, Y., Okuno, Y. “Electroconvulsive seizures activate anorexigenic signals in the ventromedial nuclei of the hypothalamus” Neuropharmacology, 71C, 164-173, 2013.
  • 2012)
    • Brown J.B., Niijima S., Shiraishi A., Nakatsui M., Okuno Y. “Chemogenomic approach to comprehensive predictions of ligand-target interactions: A comparative study” IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Workshop on Pharmaco-informatics for Drug Discovery (PIDD), 136-142, 2012.
    • Niijima, S., Shiraishi, A., Okuno, Y. “Dissecting kinase profiling data to predict activity and understand cross-reactivity of kinase inhibitors” J. Chem. Inf. Model., 52, 901-912, 2012.
    • Fazekas, S.Z., Ito, H., Okuno Y., Seki S., Taneishi K. “On computational complexity of graph inference from counting” Natural Computing, DOI 10.1007/s11047-012-9349-2, 2012.
    • Tamura T., Sakaeda T, Kadoyama K, Okuno, Y. “Aspirin- and clopidogrel-associated bleeding complications: Data mining of the public version of the FDA adverse event reporting system, AERS” Int. J. Med. Sci., 9, 441-446, 2012.
    • Tamura T., Sakaeda T, Kadoyama K, Okuno, Y. “Omeprazole- and esomeprazole-associated hypomagnesaemia: Data mining of the public version of the FDA adverse event reporting system” Int. J. Med. Sci., 9, 322-326, 2012.
    • Kadoyama, K., Sakaeda, T., Tamon, A., Okuno, Y. “Adverse event profile of tigecycline: Data mining of the public version of the U.S. Food and Drug Administration adverse event reporting system” Biol. Pharm. Bull., 35, 967-970, 2012.
    • Minowa, Y., Kondo, C., Uehara, T., Morikawa, Y., Okuno, Y., Nakatsu, N., Ono, A., Maruyama, T., Kato, I., Yamate, J., Yamada, H., Ohno, Y., Urushidani, T. “Toxicogenomic multigene biomarker for predicting the future onset of proximal tubular injury in rats” Toxicology, 297, 47-56, 2012.
    • Sakaeda, T., Kadoyama, K., Okuno, Y. “Statin-associated Muscular and Renal Adverse Events: Data mining of the public version of the FDA adverse event reporting system” PLoS ONE, 6(12): e28124, 2012.
    • Katoh-Fukui, Y., Miyabayashi, K., Komatsu, T., Owaki, A., Baba, T., Shima, Y., Kidokoro, T., Kanai, Y., Schedl, A., Wilhelm, D., Koopman, P., Okuno, Y., Morohashi, K. “Cbx2, a polycomb group gene, is required for sry gene expression in mice” Endocrinology, 153(2), 913-24, 2012.
    • Kadoyama, K., Miki, I., Tamura, T., Brown, J.B., Sakaeda, T., Okuno, Y. “Adverse event profiles of 5-fluorouracil and capecitabine: Data mining of the public version of the FDA adverse event reporting system, AERS, and reproducibility of clinical observations” Int. J. Med. Sci., 9, 33-39, 2012.
  • 2011)
    • Yabuuchi, H., Niijima, S., Takematsu, H., Ida, T., Hirokawa, T., Hara, T., Ogawa, T., Minowa, Y., Tsujimoto, G., Okuno, Y. Analysis of multiple compound-protein interactions reveals novel bioactive molecules” Molecular Systems Biology, 7, 472, 2011.
    • Niijima, S., Yabuuchi, H., Okuno, Y. Cross-target view to feature selection: identification of molecular interaction features in ligand-target spaceJ. Chem. Inf. Model., 51, 15-24, 2011.
    • Sakaeda, T., Kadoyama, K., Tamon, A., Okuno, Y.Data mining of the public version of the FDA adverse event reporting system, AERS: Colistin-associated adverse events” Jpn. J. Chemother., 59, 610-613, 2011.
    • Sakaeda, T., Kadoyama, K., Okuno, Y. “Adverse event profiles of platinum agents: Data mining of the public version of the FDA adverse event reporting system, AERS, and reproducibility of clinical observations” Int. J. Med. Sci., 8, 487-491, 2011.
    • Kadoyama, K., Kuwahara, A., Yamamori, M., Brown, J.B., Sakaeda, T., Okuno, Y. “Hypersensitivity reactions to anticancer agents: Data mining of the public version of the FDA adverse event reporting system, AERS” J. Exp. Clin. Cancer Res., 30, 93, 2011.
    • Takematsu, H., Yamamoto, H., Naito-Matsui, Y., Fujinawa, R., Tanaka, K., Okuno, Y., Tanaka, Y., Kyogashima, M., Kannagi, R., Kozutsumi, Y., “Quantitative transcriptomic profiling of branching in a glycosphingolipid biosynthetic pathway” J. Biol. Chem., 286, 27214-27224, 2011.
    • Shibata, M.-A., Iinuma, M., Morimoto, J., Kurose, H., Akamatsu, K., Okuno, Y., Akao, Y., Otsuki, Y. alpha-Mangostin extracted from the pericarp of the mangosteen (Garcinia mangostana Linn) reduces tumor growth and lymph node metastasis in an immunocompetent xenograft model of metastatic mammary cancer carrying a p53 mutation BMC Med., 9, 69, 2011.
    • Sakaeda, T., Kadoyama, K., Yabuuchi, H., Niijima, S., Seki, K., Shiraishi, Y., Okuno, Y. “Platinum agent-induced hypersensitivity reactions: data mining of the public version of the FDA adverse event reporting system, AERS” Int. J. Med. Sci. 8, 332-338, 2011.
  • 2010)
    • Doi, M., Takahashi, Y., Komatsu, R., Yamazaki, F., Yamada, H., Haraguchi, S., Emoto, N., Okuno, Y., Tsujimoto, G., Kanematsu, A., Ogawa, O., Todo, T., Tsutsui, K., van der Horst, G.T., Okamura, H.Salt-sensitive hypertension in circadian clock-deficient Cry-null mice involves dysregulated adrenal Hsd3b6Nature Medicine, 16, 67-74, 2010.
    • Kusaka, M., Katoh-Fukui, Y., Ogawa, H., Miyabayashi, K., Baba, T., Shima, Y., Sugiyama, N., Sugimoto, Y., Okuno, Y., Kodama, R., Iizuka-Kogo, A., Senda, T., Sasaoka, T., Kitamura, K., Aizawa, S., Morohashi, KI. Abnormal Epithelial Cell Polarity and Ectopic Epidermal Growth Factor Receptor (EGFR) Expression Induced in Emx2 KO Embryonic GonadsEndocrinology, 151, 5893-5904, 2010.
    • van der Horst, E., Peironcely, JE., Ijzerman, AP., Beukers, MW., Lane, JR., van Vlijmen, HW., Emmerich, MT., Okuno, Y., Bender, A.A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization BMC Bioinformatics, 11, 316, 2010.
    • Tamba, S., Yodoi, R., Morimoto, K., Inazumi, T., Sukeno, M., Segi-Nishida, E., Okuno, Y., Tsujimoto, G., Narumiya, S., Sugimoto, Y. “Expression profiling of cumulus cells reveals functional changes during ovulation and central roles of prostaglandin EP2 receptor in cAMP signaling” Biochimie, 92, 665-675, 2010.
    • Hagihara, M., Yoneda, K., Yabuuchi, H., Okuno, Y., Nakatani, K. A reverse transcriptase stop assay revealed diverse quadruplex formations in UTRs in mRNABioorg. Med. Chem. Lett., 20, 2350-2353, 2010.
    • Terada, N., Shimizu, Y., Kamba, T., Inoue, T., Maeno, A., Kobayashi, T., Nakamura, E., Kamoto, T., Kanaji, T., Maruyama, T., Mikami, Y., Toda, Y., Matsuoka, T., Okuno, Y., Tsujimoto, G., Narumiya, S., Ogawa, O. “Identification of EP4 as a potential target for the treatment of castration-resistant prostate cancer using a novel xenograft model” Cancer Res., 70, 1606-1615, 2010.
    • Takahashi, J., Hijikuro, I., Kihara, T., Murugesh, M.G., Fuse, S., Kunimoto, R., Tsumura, Y., Akaike, A., Niidome, T., Okuno, Y., Takahashi, T., Sugimoto, H. “Design, synthesis, evaluation and QSAR analysis of N(1)-substituted norcymserine derivatives as selective butyrylcholinesterase inhibitors” Bioorg. Med. Chem. Lett., 20, 1718-1720, 2010.
  • 2009)
    • Kondo, C., Minowa, Y., Uehara, T., Okuno, Y., Nakatsu, N., Ono, A., Maruyama, T., Kato, I., Yamate, J., Yamada, H., Ohno, Y., Urushidani, T. “Identification of genomic biomarkers for concurrent diagnosis of drug-induced renal tubular injury using a large-scale toxicogenomics database” Toxicology, 265, 15-26, 2009.
    • Feng, C., Araki, H., Kunimoto, R., Tamon, A., Makiguchi, H., Niijima, S., Tsujimoto, G., Okuno, Y. “GEM-TREND: a web tool for Gene Expression data Mining Toward Relevant Network Discovery” BMC Genomics, 10:411, 2009.
    • Tsuchiya, S., Oku, M., Imanaka, Y., Kunimoto, R., Okuno, Y., Terasawa, K., Sato, F., Tsujimoto, G., Shimizu, K. “MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells” Nucleic Acids Res., 37, 3821-3827, 2009.
    • Ichimi, T., Enokida, H., Okuno, Y., Kunimoto, R., Chiyomaru, T., Kawamoto, K., Kawahara, K., Toki, K., Kawakami, K., Nishiyama, K., Tsujimoto, G., Nakagawa, M., Seki, N. “Identification of novel microRNA targets based on microRNA signatures in bladder cancer ” Int. J. Cancer, 125, 345-352, 2009.
    • van der Horst, E., Okuno, Y., Bender, A., Ijzerman, A.P. “Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner” J. Chem. Inf. Model., 49, 348-60, 2009.
    • Tsuchiya, S., Tachida, Y., Segi-Nishida, E., Okuno, Y., Tamba, S., Tsujimoto, G., Tanaka, S., Sugimoto, Y. “Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification methodBMC Genomics, 10: 35, 2009.
    • Niijima, S., Okuno, Y. “Laplacian linear discriminant analysis approach to unsupervised feature selection” IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 605-614, 2009.