Supercomputer

Results Achieved by Using the Supercomputer (Published Papers)

If there are any additional papers that have not been included in the above list, please contact us at the e-mail address below. Thank you.
    

Published Papers List in 2014
Published Papers List in 2013
Published Papers List in 2012
Published Papers List in 2011
Published Papers List in 2010
Published Papers List in 2009
Published Papers List in 2008
Published Papers List before 2008

Published Papers List in 2008

AuthorTitleJournal/Book
Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H Membrane attachment facilitates ligand access to the active site in monoamine oxidase A Biochemistry. 2009 Jun 30;48(25):5864-73. doi: 10.1021/bi900493n. pubmed
Maruyama S, Matsuzaki M, Misawa K, Nozaki H Cyanobacterial contribution to the genomes of the plastid-lacking protists BMC Evol Biol. 2009 Aug 11;9:197. doi: 10.1186/1471-2148-9-197. pubmed
Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay Nature. 2009 Apr 30;458(7242):1185-90. doi: 10.1038/nature07924. Epub 2009 Mar 25. pubmed
Misawa K, Kamatani N ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing Source Code Biol Med. 2009 Oct 21;4:7. doi: 10.1186/1751-0473-4-7. pubmed
Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes Mol Phylogenet Evol. 2009 Dec;53(3):872-80. doi: 10.1016/j.ympev.2009.08.015. Epub 2009 Aug 19. pubmed
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA Outcome of a workshop on applications of protein models in biomedical research Structure. 2009 Feb 13;17(2):151-9. doi: 10.1016/j.str.2008.12.014. pubmed
Shimozono S, Shinohara A, Shinohara T, Miyano S, Kuhara S, Arikawa S Knowledge acquisition from amino acid sequences by machine learning system BONSAI Transactions on Information Processing Society of Japan, 35(10), 2009-2018, 1993
Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, Soldati-Favre D, Takeda K A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 J Exp Med. 2009 Nov 23;206(12):2747-60. doi: 10.1084/jem.20091703. Epub 2009 Nov 9. pubmed
Kaneiwa K, Iwazume M, Fukuda K An Upper Ontology for Event Classifications and Relations Proc. of AI2007, Lecture Notes in Computer Science, 394-404, 2008
酒井 紀子, 山本 智子, 中村 浩実, 福田 賢一郎 パスウェイデータベースの基本操作 マイクロアレイデータ統計解析プロトコール, 194-204, ISBN:978-4-758101-73-8, 2008
Do JH, Miyano S The GC and window-averaged DNA curvature profile of secondary metabolite gene cluster in Aspergillus fumigatus genome Appl Microbiol Biotechnol. 2008 Oct;80(5):841-7. doi: 10.1007/s00253-008-1638-4. Epub 2008 Aug 22. pubmed
Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates BMC Syst Biol. 2008 Dec 5;2:106. doi: 10.1186/1752-0509-2-106. pubmed
Fujita A, Sato JR, Garay-Malpartida HM, Sogayar MC, Ferreira CE, Miyano S Modeling nonlinear gene regulatory networks from time series gene expression data J Bioinform Comput Biol. 2008 Oct;6(5):961-79. pubmed
Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K, Miyano S A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human Genome Inform. 2008;20:212-21. pubmed
Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T Bayesian learning of biological pathways on genomic data assimilation Bioinformatics. 2008 Nov 15;24(22):2592-601. doi: 10.1093/bioinformatics/btn483. Epub 2008 Sep 25. pubmed
Fukuda K INOH pathway database: Curation, Annotation, Integration Interdisciplinary Ontology, 47-50, ISBN:978-4-904239-00-1, 2008
Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, Charnock-Jones DS, Print C, Miyano S Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models Bioinformatics. 2008 Apr 1;24(7):932-42. doi: 10.1093/bioinformatics/btm639. Epub 2008 Feb 21. pubmed
Hirose O, Yoshida R, Yamaguchi R, Imoto S, Higuchi T, Miyano S Analyzing time course gene expression data with biological and technical replicates to estimate gene networks by state space models Proc. 2nd Asia International Conference on Modelling & Simulation, 940-946, 2008. (AMS2008: Refereed conference)
Jeong E, Nagasaki M, Miyano S Rule-based reasoning for system dynamics in cell systems Genome Inform. 2008;20:25-36. pubmed
Kitakaze H, Kanda M, Nakatsuka H, Ikeda N, Matsuno H, Miyano S Prediction of fragile points for robustness checking of cell systems IEICE TRANSACTIONS on Information and Systems D, J91-D(9), 2404-2417, 2008
Kojima K, Fujita A, Shimamura T, Imoto S, Miyano S Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data Genome Inform. 2008;20:37-51. pubmed
Kojima K, Nagasaki M, Miyano S Fast grid layout algorithm for biological networks with sweep calculation Bioinformatics. 2008 Jun 15;24(12):1433-41. doi: 10.1093/bioinformatics/btn196. Epub 2008 Apr 18. pubmed
Mitou N, Ikegami Y, Matsuno H, Miyano S, Inouye ST Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm Genome Inform. 2008;21:212-23. pubmed
Nagasaki M, Saito A, Li C, Jeong E, Miyano S Systematic reconstruction of TRANSPATH data into cell system markup language BMC Syst Biol. 2008 Jun 23;2:53. doi: 10.1186/1752-0509-2-53. pubmed
Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells BMC Bioinformatics. 2008 Sep 29;9:404. doi: 10.1186/1471-2105-9-404. pubmed
Numata K, Imoto S, Miyano S Partial order-based Bayesian network learning algorithm for estimating gene networks Proc. IEEE 8th International Symposium on Bioinformatics & Bioengineering, IEEE Computer Society, 357-360, 2008. (BIBE2008: Refereed conference; Digital Object Identifier 10.1109/BIBM.2008.85)
Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S ExonMiner: Web service for analysis of GeneChip Exon array data BMC Bioinformatics. 2008 Nov 26;9:494. doi: 10.1186/1471-2105-9-494. pubmed
Perrier E, Imoto S, Miyano S Finding optimal Bayesian network given a super-structure J. Machine Learning Research, 9, 2251-2286, 2008
Yamaguchi R, Imoto S, Yamauchi M, Nagasaki M, Yoshida R, Shimamura T, Hatanaka Y, Ueno K, Higuchi T, Gotoh N, Miyano S Predicting differences in gene regulatory systems by state space models Genome Inform. 2008;21:101-13. pubmed
Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T Bayesian learning of biological pathways on genomic data assimilation Bioinformatics. 2008 Nov 15;24(22):2592-601. doi: 10.1093/bioinformatics/btn483. Epub 2008 Sep 25. pubmed
Published Papers List in 2014
Published Papers List in 2013
Published Papers List in 2012
Published Papers List in 2011
Published Papers List in 2010
Published Papers List in 2009
Published Papers List in 2008
Published Papers List before 2008

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