Research Topics
Genomes and Genes | Yasushi OkunoSummaryAffiliation: Kyoto University Country: Japan Publications
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Detail Information
Publications
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chainsKiyoko F Aoki
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 32:W267-72. 2004..Analogously to BLAST, users are thus able to compare glycan structures of interest with glycans from different glycan databases using a variety of tree-alignment options. KCaM is currently available at http://glycan.genome.ad.jp...
Efficient tree-matching methods for accurate carbohydrate database queriesKiyoko F Aoki
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 14:134-43. 2003..Because we use similarity scores as opposed to a distance metric, our methods are more readily used to display trees of higher similarity. We present the two methods developed for this purpose and illustrate its validity...- GEM-TREND: a web tool for gene expression data mining toward relevant network discoveryChunlai Feng
Department of Systems Bioscience for Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 29 Yoshidashimoadachi cho, Sakyo ku, Kyoto 606 8501, Japan
BMC Genomics 10:411. 2009..In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database... - GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools updateYasushi Okuno
Department of Pharmacoinformatics, Center for Integrative Education of Pharmacy Frontier, Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
Nucleic Acids Res 36:D907-12. 2008..GLIDA is publicly available at http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/. We hope that it will prove very useful for Chemical Genomics research and GPCR-related drug discovery... - Adverse event profiles of platinum agents: data mining of the public version of the FDA adverse event reporting system, AERS, and reproducibility of clinical observationsToshiyuki Sakaeda
Center for Integrative Education in Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606 8501, Japan
Int J Med Sci 8:487-91. 2011..Adverse event reports (AERs) submitted to the US Food and Drug Administration (FDA) were reviewed to confirm platinum agent-associated adverse events, and to clarify the rank-order of these drugs in terms of susceptibility... - Analysis of multiple compound-protein interactions reveals novel bioactive moleculesHiroaki Yabuuchi
Department of Systems Biosciences for Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
Mol Syst Biol 7:472. 2011..The results of this study indicate that data derived from chemical genomics can be highly useful for exploring chemical space, and this systems biology perspective could accelerate drug discovery processes... - Heuristics for chemical compound matchingMasahiro Hattori
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 14:144-53. 2003..Finally, we showed the effectiveness of our heuristics for compound pairs along metabolic pathways... 
Correlation index-based responsible-enzyme gene screening (CIRES), a novel DNA microarray-based method for enzyme gene involved in glycan biosynthesisHarumi Yamamoto
Laboratory of Membrane Biochemistry and Biophysics, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
PLoS ONE 2:e1232. 2007..However, a systematic approach for assessing the correlation between glycan expression and glycan-related gene expression has not been reported previously...
Laplacian linear discriminant analysis approach to unsupervised feature selectionSatoshi Niijima
Department of Pharmacoinformatics, Center for Integrative Education of Pharmacy Frontier, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 29 Yoshida Shimoadachi cho, Sakyo ku, Kyoto 606 8501, Japan
IEEE/ACM Trans Comput Biol Bioinform 6:605-14. 2009..It performs even better than Fisher score for some of the data sets, despite the fact that LLDA-RFE is fully unsupervised...- The KEGG resource for deciphering the genomeMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 32:D277-80. 2004..New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database... - Hypersensitivity reactions to anticancer agents: data mining of the public version of the FDA adverse event reporting system, AERSKaori Kadoyama
Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606 8501, Japan
J Exp Clin Cancer Res 30:93. 2011..The present study was performed to confirm whether the database could suggest the hypersensitivity reactions caused by anticancer agents, paclitaxel, docetaxel, procarbazine, asparaginase, teniposide, and etoposide... - GLIDA: GPCR-ligand database for chemical genomic drug discoveryYasushi Okuno
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 29 Yoshida shimo adachi cho, Sakyo ku, Kyoto 606 8501, Japan
Nucleic Acids Res 34:D673-7. 2006..GLIDA is publicly available at http://gdds.pharm.kyoto-u.ac.jp:8081/glida. We hope that it will prove very useful for chemical genomic research and GPCR-related drug discovery... - Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification methodSoken Tsuchiya
Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto, Japan
BMC Genomics 10:35. 2009..Mast cells (MCs) play pivotal roles in allergy and innate immunity and consist of heterogenous subclasses. However, the molecular basis determining the different characteristics of these multiple MC subclasses remains unclear... - MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cellsSoken Tsuchiya
Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 29 Yoshida Shimoadachi, Sakyo ku, Kyoto 606 8501, Japan
Nucleic Acids Res 37:3821-7. 2009..Therefore, we concluded that both miR-338-3p and miR-451 are necessary for the development of epithelial cell polarity... - Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactionsMasaaki Kotera
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
J Am Chem Soc 126:16487-98. 2004.... - Cross-target view to feature selection: identification of molecular interaction features in ligand-target spaceSatoshi Niijima
Department of Systems Bioscience for Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
J Chem Inf Model 51:15-24. 2011..These results suggest that our approach has the potential to uncover the molecular basis for ligand selectivity and off-target effects... - Quantitative transcriptomic profiling of branching in a glycosphingolipid biosynthetic pathwayHiromu Takematsu
Laboratory of Membrane Biochemistry and Biophysics, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606 8501, Japan
J Biol Chem 286:27214-24. 2011..Collectively, these data suggest that transcriptomic assessment of macromolecule biosynthetic pathways can disclose a global regulatory mechanism(s) even when unexpected... - Global correlation analysis for micro-RNA and mRNA expression profiles in human cell linesYoshinao Ruike
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 29 Yoshida Shimoadachi cho Sakyo ku, Kyoto 606 8501, Japan
J Hum Genet 53:515-23. 2008..The data collected here will be of value for further studies into the function of miRNA... - Adverse event profile of tigecycline: data mining of the public version of the U.S. Food and Drug Administration adverse event reporting systemKaori Kadoyama
Center for Integrative Education in Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
Biol Pharm Bull 35:967-70. 2012..The adverse events suggested were in agreement with information provided by the manufacturer, suggesting that off-label use hardly results in unexpected adverse events, presumably due to usage with extreme caution... - 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 observationsKaori Kadoyama
Center for Integrative Education in Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606 8501, Japan
Int J Med Sci 9:33-9. 2012..The safety profiles of oral fluoropyrimidines were compared with 5-fluorouracil (5-FU) using adverse event reports (AERs) submitted to the Adverse Event Reporting System, AERS, of the US Food and Drug Administration (FDA)... - Systems biology and systems chemistry: new directions for drug discoveryJ B Brown
Department of Systems Bioscience for Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606 8501, Japan
Chem Biol 19:23-8. 2012..We review some of the recent developments in systems-level research for drug design and discovery, and discuss the directions that some drug design efforts are heading toward... - Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathwaysMasahiro Hattori
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
J Am Chem Soc 125:11853-65. 2003..Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes... - Statin-associated muscular and renal adverse events: data mining of the public version of the FDA adverse event reporting systemToshiyuki Sakaeda
Center for Development of Integrative Education in Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
PLoS ONE 6:e28124. 2011.... - A probabilistic model for mining implicit 'chemical compound-gene' relations from literatureShanfeng Zhu
Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Japan
Bioinformatics 21:ii245-51. 2005..We validated them from biological, medical and pharmaceutical viewpoints... - Establishment of the culture model system that reflects the process of terminal differentiation of connective tissue-type mast cellsHirotsugu Takano
Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto 606 8501, Japan
FEBS Lett 582:1444-50. 2008..The gene expression profile obtained by the microarray analyses was found to reflect many aspects of the differentiation. Our system is thus helpful to gain deeper insights into terminal differentiation of CTMCs... - Germinal center marker GL7 probes activation-dependent repression of N-glycolylneuraminic acid, a sialic acid species involved in the negative modulation of B-cell activationYuko Naito
Laboratory of Membrane Biochemistry and Biophysics, Graduate School of Biostudies, Kyoto University, Yoshida Shimoadachi, Sakyo ku, Kyoto 606 8501, Japan
Mol Cell Biol 27:3008-22. 2007..Thus, Neu5Gc is required for optimal negative regulation, and the reaction is specifically suppressed in activated B cells, i.e., germinal center B cells... - Augmentation of drug-induced cell death by ER protein BRI3BPTetsuo Yamazaki
The 21st Century Center of Excellence Program, Tohoku University Graduate School of Medicine, Sendai 980 8575, Japan
Biochem Biophys Res Commun 362:971-5. 2007..Taken together, BRI3BP, widely expressed in animal cell types, seems to possess a pro-apoptotic property and can potentiate drug-induced apoptosis... - Comprehensive analysis of the effect of phytoestrogen, daidzein, on a testicular cell line, using mRNA and protein expression profileTetsuya Adachi
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida Shimoadachicho, Sakyo ku, Kyoto 606 8501, Japan
Food Chem Toxicol 43:529-35. 2005.... - LIGAND: database of chemical compounds and reactions in biological pathwaysSusumu Goto
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 30:402-4. 2002..genome.ad.jp/ligand/). LIGAND may be also downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/kegg/ligand/)... - Salt-sensitive hypertension in circadian clock-deficient Cry-null mice involves dysregulated adrenal Hsd3b6Masao Doi
Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto, Japan
Nat Med 16:67-74. 2010..Translation of these findings to humans will require clinical examination of human HSD3B1 gene, which we found to be functionally similar to mouse Hsd3b6... - Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and MedlineShanfeng Zhu
Bioinformatics Center, Institute for Chemical Research, Kyoto University
Cancer Inform 2:361-71. 2007..Further experiments showed that MAM found new cancer-gene relations which are unknown in the literature. Supplementary information can be found at http://www.bic.kyotou.ac.jp/pathway/zhusf/CancerInformatics/Supplemental2006.html... - MicroRNA: biogenetic and functional mechanisms and involvements in cell differentiation and cancerSoken Tsuchiya
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
J Pharmacol Sci 101:267-70. 2006..These evidences offer the possibility that miRNAs would be potentially useful for drug discovery... - Platinum agent-induced hypersensitivity reactions: data mining of the public version of the FDA adverse event reporting system, AERSToshiyuki Sakaeda
Center for Development of Integrative Education in Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
Int J Med Sci 8:332-8. 2011..Adverse event reports (AERs) submitted to the US Food and Drug Administration (FDA) were reviewed to confirm the platinum agent-associated mild, severe, and lethal hypersensitivity reactions... - [In silico drug discovery based on the integration of bioinformatics and chemoinformatics]Yasushi Okuno
Department of Pharmacoinformatics, Centre for Integrative Education of Pharmacy Frontier, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
Yakugaku Zasshi 128:1645-51. 2008..These are promising approaches to accelerating drug discovery processes... - Design, synthesis, evaluation and QSAR analysis of N(1)-substituted norcymserine derivatives as selective butyrylcholinesterase inhibitorsJun Takahashi
Department of Neuroscience for Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 29 Yoshida Shimoadachi cho, Sakyo ku, Kyoto 606 8501, Japan
Bioorg Med Chem Lett 20:1718-20. 2010..A quantitative structure-activity relationship (QSAR) study indicated that logS might be a key feature of the improved compounds... - Abnormal features in mutant cerebellar Purkinje cells lacking junctophilinsAtsushi Ikeda
Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606 8501, Japan
Biochem Biophys Res Commun 363:835-9. 2007..Moreover, gene expression was slightly altered in the JP-DKO cerebellum. Therefore, the mutant PCs bear marginal but widespread abnormalities, all of which likely cause cerebellar motor defects in JP-DKO mice... - Prostaglandin E2 stimulates granulocyte colony-stimulating factor production via the prostanoid EP2 receptor in mouse peritoneal neutrophilsYukihiko Sugimoto
Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
J Immunol 175:2606-12. 2005..These results suggest that the PGE2-EP2 system contributes to the local production of G-CSF during acute inflammation... - Secreted CXCL1 is a potential mediator and marker of the tumor invasion of bladder cancerHiroaki Kawanishi
Department of Urology, Graduate School of Medicine, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
Clin Cancer Res 14:2579-87. 2008..The purpose of this study was to identify proteins that are potentially involved in the tumor invasion of bladder cancer... - Microarray evaluation of EP4 receptor-mediated prostaglandin E2 suppression of 3T3-L1 adipocyte differentiationYukihiko Sugimoto
Department of Physiological Chemistry, Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo ku, Kyoto 606 8501, Japan
Biochem Biophys Res Commun 322:911-7. 2004..These results suggest that PGE(2) inhibits a crucial step of the adipocyte differentiation process by acting on the EP4 receptor in 3T3-L1 cells... - Inhibition of protein kinase CK2 prevents the progression of glomerulonephritisMasateru Yamada
Pharmaceutical Research Laboratories, Toray Industries, Inc, 1111 Tebiro Kamakura, Kanagawa 248 8555, Japan
Proc Natl Acad Sci U S A 102:7736-41. 2005..Our results show that CK2 plays a critical role in the progression of immunogenic renal injury, and therefore, CK2 is a potential target for GN therapy... - [New progress in crystallization technology of membrane protein and introduction of pharamaceutical innovation value chain]Tsuyoshi Inoue
Graduate School of Engineering Osaka University, Yamada oka, Suita City, Japan
Yakugaku Zasshi 128:497-505. 2008..In this paper, we report the recent research work on the crystallization of membrane proteins and the development of a method for in silico drug discovery... - Altered gene expression of transcriptional regulatory factors in tumor marker-positive cells during chemically induced hepatocarcinogenesisShigehiro Osada
Laboratory of Environmental Biochemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1 6 Yamada oka, Suita, Osaka 565 0871, Japan
Toxicol Lett 167:106-13. 2006..DNA microarray analysis using RNA prepared from tumor marker-positive foci and control tissues provided a candidate gene link to the early stage of carcinogenesis and hepatotoxicity...