原著論文Original Article

  • 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. 2014;20(22):5686-5696. Available from: https://doi.org/10.1158/1078-0432.ccr-14-1511
    • Brown J.B, Nakatsui M, Okuno Y. “Constructing a foundational platform driven by Japan’s K supercomputer for next-generation drug design” Molecular Informatics. 2014;33:732-741. Available from: https://doi.org/10.1002/minf.201400067
    • 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. 2014;13(12):2978-2990. Available from: https://doi.org/10.1158/1535-7163.mct-14-0462
    • 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. 2014;11(5):461-465. Available from: https://doi.org/10.7150/ijms.7967
    • Brown J.B, Okuno Y, Marcou G, Varnek A, Horvath D. “Computational chemogenomics: Is it more than inductive transfer?” J. Comput. Aided Mol. Des. 2014;28(6):597-618. Available from: https://doi.org/10.1007/s10822-014-9743-1
    • Zannas A.S, Okuno Y, Doraiswamy P.M. “Cholinesterase inhibitors and Pisa syndrome: A pharmacovigilance study” Pharmacotherapy 2014;34(3):272-278. Available from: https://doi.org/10.1002/phar.1359
    • 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. 2014;44(1):204-214. Available from: https://doi.org/10.1002/eji.201343838
  • 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. 2013;342(6154):85-90. Available from: https://doi.org/10.1126/science.1238599
    • 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. 2013;27(11):1058-1069. Available from: https://doi.org/10.1177/0269881113497612
    • 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. 2013;36(12):1891-1901. Available from: https://doi.org/10.1248/bpb.b12-01006
    • 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. 2013; 53(6):1253-1262. Available from: https://doi.org/10.1021/ci300515z
    • 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. 2013;4:340-346. Available from: https://10.4236/pp.2013.43049
    • Seki S, Okuno Y. “On the behavior of tile assembly model at high temperatures” Computability. 2013;2(2):107-124. Available from: https://link.springer.com/content/pdf/10.1007%2F978-3-642-30870-3_55.pdf
    • Fazekas S.Z, Ito H, Okuno Y, Seki S, Taneishi K. “On computational complexity of graph inference from counting” Natural Computing. 2013;12(4):589-603. Available from: https://doi.org/10.1007/s11047-012-9349-2
    • 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. 2013;10(7):864-869. Available from: https://doi.org/10.7150/ijms.5892
    • 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. 2013;71C:164-173. Available from: https://doi.org/10.1016/j.neuropharm.2013.03.033
  • 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). 2012:136-142. Available from: https://doi.org/10.1109/BIBMW.2012.6470295
    • Niijima S, Shiraishi A, Okuno Y. “Dissecting kinase profiling data to predict activity and understand cross-reactivity of kinase inhibitors” J. Chem. Inf. Model. 2012;52:901-912. Available from: https://doi.org/10.1021/ci200607f
    • Fazekas S.Z, Ito H, Okuno Y, Seki S, Taneishi K. “On computational complexity of graph inference from counting” Nat Comput. 2012;12:589-603. Available from: https://doi.org/10.1007/s11047-012-9349-2
    • 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. 2012;9:441-446. Available from: https://doi.org/10.7150/ijms.4549
    • 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. 2012;9:322-326. Available from: https://dx.doi.org/10.7150%2Fijms.4397
    • 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. 2012;35:967-970. Available from: https://doi.org/10.1248/bpb.35.967
    • 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 2012;297:47-56. Available from: https://doi.org/10.1016/j.tox.2012.03.014
    • 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. 2011;6(12):e28124. Available from: https://doi.org/10.1371/journal.pone.0028124
    • 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. 2012;153(2):913-24. Available from: https://doi.org/10.1210/en.2011-1055
    • 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. 2012;9:33-39. Available from: https://doi.org/10.7150/ijms.9.33
  • 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. 2011;7:472. Available from: https://dx.doi.org/10.1038%2Fmsb.2011.5
    • Niijima S, Yabuuchi H, Okuno Y. “Cross-target view to feature selection: identification of molecular interaction features in ligand-target space” J. Chem. Inf. Model. 2011;51:15-24. Available from: https://doi.org/10.1021/ci1001394
    • 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. 2011;59:610-613. Available from: https://doi.org/10.7150/ijms.6048
    • 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. 2011;8(6):487-491. Available from: https://doi.org/10.7150/ijms.8.487
    • 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.CancerRes. 2011;30:93. Available from: https://doi.org/10.1186/1756-9966-30-93
    • 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., 2011;286(11):27214-24. Available from: https://doi.org/10.1074/jbc.m111.234526
    • 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. 2011;9:69. Available from: https://doi.org/10.1186/1741-7015-9-69
    • 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. 2011;8:332-338. Available from: https://doi.org/10.7150/ijms.8.332
  • 2010)
    • 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. 2011;7:472. Available from: https://dx.doi.org/10.1038%2Fmsb.2011.5
    • 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 Hsd3b6” Nature Medicine, 16, 67-74, 2010. Available from: https://dx.doi.org/10.1038/nm.2061
    • 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 Gonads” Endocrinology. 2010;151:5893-5904. Available from: https://doi.org/10.1210/en.2010-0915
    • van der Horst E, Peironcely JE, 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. 2010;11:316. Available from: https://doi.org/10.1186/1471-2105-11-316
    • 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, 2010;92:665-675. Available from: https://doi.org/10.1016/j.biochi.2010.04.006
    • Hagihara M, Yoneda K, Yabuuchi H, Okuno Y, Nakatani K. “A reverse transcriptase stop assay revealed diverse quadruplex formations in UTRs in mRNA” Bioorg. Med. Chem. Lett., 2010;20:2350-2353. Available from: https://doi.org/10.1016/j.bmcl.2010.01.158
    • 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. 2010;70:1606-1615. Available from: https://doi.org/10.1158/0008-5472.can-09-2984
    • 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. 2010;20:1718-1720. Available from: https://doi.org/10.1016/j.bmcl.2010.01.057
  • 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. 2009;265:15-26. Available from: https://doi.org/10.1016/j.tox.2009.09.003
    • 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. 2009;10:411. Available from: https://doi.org/10.1186/1471-2164-10-411
    • 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. 2009;37:3821-3827. Available from: https://dx.doi.org/10.1093%2Fnar%2Fgkp255
    • 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. 2009;125:345-352. Available from: https://doi.org/10.1002/ijc.24390
    • 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., 2009;49:348-60. Available from: https://doi.org/10.1021/ci8003896
    • 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 method” BMC Genomics, 2009;10:35. Available from: https://doi.org/10.1186/1471-2164-10-35
    • Niijima S, Okuno Y. “Laplacian linear discriminant analysis approach to unsupervised feature selection” IEEE/ACM Trans. Comput. Biol. Bioinform. 2009;6:605-614. Available from: https://doi.org/10.1109/TCBB.2007.70257
  • 2008)
    • Ruike Y, Ichimura A, Tsuchiya S, Shimizu K, Kunimoto R, Okuno Y, Tsujimoto G. “Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines” J. Hum. Genet. 2008;53:515-23. Available from: https://doi.org/10.1007/s10038-008-0279-x
    • Kawanishi H, Matsui Y, Ito M, Watanabe J, Takahashi T, Nishizawa K, Nishiyama H, Kamoto T, Mikami Y, Tanaka Y, Jung G, Akiyama H, Nobumasa H, Guilford P, Reeve A, Okuno Y, Tsujimoto G, Nakamura E, Ogawa O. “Secreted CXCL1 is a potential mediator and marker of the tumor invasion of bladder cancer” Clin. Cancer Res., 2008;14:2579-87. Available from: https://doi.org/10.1158/1078-0432.ccr-07-1922
    • Takano H, Nakazawa S, Okuno Y, Shirata N, Tsuchiya S, Kainoh T, Takamatsu S, Furuta K, Taketomi Y, Naito Y, Takematsu H, Kozutsumi Y, Tsujimoto G, Murakami M, Kudo I, Ichikawa A, Nakayama K, Sugimoto Y, Tanaka S. “Establishment of the culture model system that reflects the process of terminal differentiation of connective tissue-type mast cells” FEBS Lett. 2008;582:1444-50. Available from: https://doi.org/10.1016/j.febslet.2008.03.033
    • Okuno Y, Tamon A, Yabuuchi H, Niijima S, Minowa Y, Tonomura K, Kunimto R, Feng C. “GLIDA: GPCR-ligand database for chemical genomics drug discovery – Database and tools update” Nucleic Acids Res. 2008;36:D907-12. Available from: https://dx.doi.org/10.1093%2Fnar%2Fgkm948
  • 2007)
    • Kitajima M, Minowa Y, Matsuda H, Okuno Y. “Compound-transporter interaction studies using canonical correlation analysis” Chem-Bio Inform. J., 7, 24-34, 2007. Available from: https://doi.org/10.1273/cbij.7.24
    • Yamamoto H, Takematsu H, Fujinawa R, Naito Y, Okuno Y, Tsujimoto G, Suzuki A, Kozutsumi Y. “Correlation index-based responsible-enzyme gene screening (CIRES), a novel DNA microarray-based method for glycan biosynthesis enzyme gene” PLoS ONE. 2007;2:e1232. Available from: https://doi.org/10.1371/journal.pone.0001232
    • Ikeda A, Miyazaki T, Kakizawa S, Okuno Y, Tsuchiya S, Myomoto A, Saito SY, Yamamoto T, Yamazaki T, Iino M, Tsujimoto G, Watanabe M, Takeshima H. “Abnormal features in mutant cerebellar Purkinje cells lacking junctophilins” Biochem. Biophys. Res. Commun. 2007;363:835-9. Available from: https://doi.org/10.1016/j.bbrc.2007.09.062
    • Yamazaki T, Sasaki N, Nishi M, Yamazaki D, Ikeda A, Okuno Y, Komazaki S, Takeshima H. “Augmentation of drug-induced cell death by ER protein BRI3BP” Biochem. Biophys. Res. Commun. 2007;362:971-5. Available from: https://doi.org/10.1016/j.bbrc.2007.08.082
    • Naito Y, Takematsu H, Koyama S, Miyake S, Yamamoto H, Fujinawa R, Sugai M, Okuno Y, Tsujimoto G, Yamaji T, Hashimoto Y, Itohara S, Kawasaki T, Suzuki A, Kozutsumi Y. “Germinal center marker GL7 probes activation-dependent repression of N-glycolylneuraminic acid, a sialic acid species involved in the negative modulation of B cell activation” Mol. Cell Biol. 2007;27:3008-22. Available from: https://doi.org/10.1128/mcb.02047-06
  • 2006)
    • Zhu S, Okuno Y, Tsujimoto G, Mamitsuka H. “Application of a new probabilistic model for mining implicit associated cancer genes from OMIM and Medline” Cancer Inform. 2006;2:361-71. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2675505/
    • Osada S, Naganawa A, Misonou M, Tsuchiya S, Tamba S, Okuno Y, Nishikawa J, Satoh K, Imagawa I, Tsujimoto G, Sugimoto Y, Nishihara T. “Altered gene expression of transcriptional regulatory factors in tumor marker-positive cells during chemically induced hepatocarcinogenesis” Toxicol. Lett. 2006;167:106-13. Available from: https://doi.org/10.1016/j.toxlet.2006.08.014
    • Tsuchiya S, Okuno Y, Tsujimoto G. “MicroRNA: biogenetic and functional mechanisms and involvements in cell differentiation and cancer” J. Pharmacol. Sci. 2006;101:267-70. Available from: https://doi.org/10.1254/jphs.cpj06013x
    • Okuno Y, Yang J, Taneishi K, Yabuuchi H, Tsujimoto G. “GLIDA: GPCR-Ligand database for chemical genomic drug discovery” Nucleic Acids Res. 2006;34:D673-7. Available from: https://doi.org/10.1093/nar/gkj028
  • 2005)
    • Okuno Y. “Chemical-genomic network for integrating bioinformatics and chemoinformatics” J. Pharmacol. Sci. 2005;97:29.
    • Zhu S, Okuno Y, Tsujimoto G, Mamitsuka H. “A probabilistic model for mining implicit ‘chemical compound-gene’ relations from literature” Bioinformatics. 2005;21:ii245-51. Available from: https://doi.org/10.1093/bioinformatics/bti1141
    • Sugimoto Y, Fukada Y, Mori D, Tanaka S, Yamane H, Okuno Y, Deai K, Tsuchiya S, Tsujimoto G, Ichikawa A. “Prostaglandin E2 stimulates granulocyte colony-stimulating factor production via the prostanoid EP2 receptor in mouse peritoneal neutrophils” J. Immunol. 2005;175:2606-12. Available from: https://doi.org/10.4049/jimmunol.175.4.2606
    • Adachi T, Okuno Y, Takenaka S, Matsuda K, Ohta N, Takashima K, Yamazaki K, Nishimura D, Miyatake K, Mori C, Tsujimoto G. “Comprehensive analysis of the effect of phytoestrogen, daidzein, on a testicular cell line, using mRNA and protein expression profile” Food Chem. Toxicol. 2005;43:529-35. Available from: https://doi.org/10.1016/j.fct.2004.12.006
    • Yamada M, Katsuma S, Adachi T, Hirasawa A, Shiojima S, Kadowaki T, Okuno Y, Koshimizu TA, Fujii S, Sekiya Y, Miyamoto Y, Tamura M, Yumura Y, Nihei H, Kobayashi M, Tsujimoto G. “Inhibition of protein kinase CK2 prevents the progression of glomerulonephritis” Proc. Natl. Acad. Sci. U. S. A. 2005;102:7736-41. Available from: https://doi.org/10.1073/pnas.0409818102