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Supercomputer
Results Achieved by Using the Supercomputer (Published Papers)
Published Papers List in 2008

Supercomputer

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.
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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

Author	Title	Journal/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.
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.
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.
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.
Fukuda K	INOH pathway database: Curation, Annotation, Integration	Interdisciplinary Ontology, 47-50, ISBN:978-4-904239-00-1, 2008
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Perrier E, Imoto S, Miyano S	Finding optimal Bayesian network given a super-structure	J. Machine Learning Research, 9, 2251-2286, 2008
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.
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
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.
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.
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.
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.
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