Supercomputer

Results Achieved by Using the Supercomputer (Published Papers)

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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 2009

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;48(25):5864-5873. pubmed
Araki H, Tamada Y, Imoto S, Dunmore B, Sanders D, Humphrey S, Nagasaki M, Doi A, Nakanishi Y, Yasuda K, Tomiyasu Y, Tashiro K, Print C, Charnock-Jones DS, Kuhara S, Miyano S Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells Angiogenesis. 12(3): 221-229, 2009. pubmed
Asano K, Matsushita T, Umeno J, Hosono N, Takahashi A, Kawaguchi T, Matsumoto T, Matsui T, Kakuta Y, Kinouchi Y, Shimosegawa T, Hosokawa M, Arimura Y, Shinomura Y, Kiyohara Y, Tsunoda T, Kamatani N, Iida M, Nakamura Y, Kubo M A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population Nat Genet. 2009 Dec;41(12):1325-9. doi: 10.1038/ng.482. Epub 2009 Nov 15. pubmed
Do JH, Miyano S, Choi DK Statistical approaches to genome-wide biological networks Biochip J. 3(3): 190-202, 2009
Do JH, Yamaguchi R, Miyano S Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model BMC Genomics. 10:306, 2009. pubmed
Frith MC, Hamada M, Horton P Parameters for accurate genome alignment BMC Bioinformatics 11:80, 2010. pubmed
Fujita A, Patriota AG, Sato JR, Miyano S The impact of measurement error in the identification of regulatory networks BMC Bioinformatics. 10:412, 2009. pubmed
Fujita A, Sato JR, Demasi MA, Sogayar MC, Ferreira CE, Miyano S Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis. J Bioinform Comput Biol. 2009 Aug;7(4):663-84. pubmed
Fujita A, Sato JR, Angelo M, Demasi A, Yamaguchi R, Shimamura T, Ferreira CE, Sogayar MC, Miyano S Inferring contagion in regulatory networks IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):570-76. doi: 10.1109/TCBB.2010.40. pubmed
Fujita A, Sato JR, Kojima K, Gomes LR, Nagasaki M, Sogayar MC, Miyano S Identification of Granger causality between gene sets Journal of Bioinformatics and Computational Biology (accepted)
Fujita A, Sato JR, DA Silva FH, Galvao MC, Sogayar MC, Miyano S Quality control and reproducibility in DNA microarray experiments Genome Inform. 2009 Oct;23(1):21-31. pubmed
Fukui R, Saitoh S, Matsumoto F, Kozuka-Hata H, Oyama M, Tabeta K, Beutler B, Miyake K Unc93B1 biases Toll-like receptor responses to nucleic acid in dendritic cells towards DNA- but against RNA-sensing J. Exp. Med., 206: 1339-1350, 2009
Hashimoto TB, Nagasaki M, Kojima K, Miyano S BFL: a node and edge betweenness based fast layout algorithm for large scale networks BMC Bioinformatics. 10:19, 2009. pubmed
Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions PLoS Genet. 2009 May;5(5):e1000468. doi: 10.1371/journal.pgen.1000468. Epub 2009 May 8. pubmed
Higurashi M, Ishida T, Kinoshita K PiSite: a database of protein interaction sites using multiple binding states in the PDB Nucleic Acids Res. 37: D360-364, 2009. pubmed
Imada M, Kawashima S, Kanehisa M, Takeuchi T, Asai T Characterization of alpha-phosphoglucomutase isozymes from Toxoplasma gondii Parasitol Int. 2010 Jun;59(2):206-10. doi: 10.1016/j.parint.2010.01.007. Epub 2010 Feb 12. pubmed
Ishii N, Koike A, Yamamoto Y, Takagi T Figure classification in biomedical literature to elucidate disease mechanisms, based on pathways Artif Intell Med. 2010 Jul;49(3):135-43. doi: 10.1016/j.artmed.2010.04.005. Epub 2010 Apr 27. pubmed
Kamatani Y, Matsuda K, Kubo M, Hosono N, Daigo Y, Nakamura Y, Kamatani N A Japanese genome-wide association study of multiple hematological and biochemical traits reveals identification of 46 novel loci and replication of the majority of reported European associations Nature Genetics, in press, 2010
Kamatani Y, Wattanapokayakit S, Ochi H, Kawaguchi T, Takahashi A, Hosono N, Kubo M, Tsunoda T, Kamatani N, Kumada H, Puseenam A, Sura T, Daigo Y, Chayama K, Chantratita W, Nakamura Y, Matsuda K A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians Nat Genet. 2009 May;41(5):591-5. doi: 10.1038/ng.348. Epub 2009 Apr 6. pubmed
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M KEGG for representation and analysis of molecular networks involving diseases and drugs Nucleic Acids Research 38:D355-D360, 2010. pubmed
Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N, Wada H Domain shuffling and the evolution of vertebrates Genome Research 19:1393-403, 2009. pubmed
Kinoshita K, Obayashi T Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis Bioinformatics. 25: 2677-2684, 2009. pubmed
Kubo A, Suzuki N, Yuan X, Nakai K, Satoh N, Imai KS, Satou Y Genomic cis-regulatory networks in the early Ciona intestinalis embryo Development. 2010 May;137(10):1613-23. doi: 10.1242/dev.046789. Epub 2010 Apr 14. pubmed
Kuroshu RM, Watanabe J, Sugano S, Morishita S, Suzuki Y, Kasahara M Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly PLoS One. 2010 May 7;5(5):e10517. doi: 10.1371/journal.pone.0010517. pubmed
Li C, Nagasaki M, Saito A, Miyano S Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram BMC Syst Biol. 2010 Apr 1;4:39. doi: 10.1186/1752-0509-4-39. pubmed
Li C, Nagasaki M, Ueno K, Miyano S Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension BMC Syst Biol. 2009 Apr 27;3:42. doi: 10.1186/1752-0509-3-42. pubmed
Maeda MH, Kinoshita K Development of new indices to evaluate protein-protein interfaces: assembling space volume, assembling space distance, and global shape descriptor J Mol Graph Model. 2009 Feb;27(6):706-11. doi: 10.1016/j.jmgm.2008.11.002. Epub 2008 Nov 8. 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
Maruyama S, Sugahara J, Kanai A, Nozaki H Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes Mol Biol Evol. 2010 May;27(5):1070-6. doi: 10.1093/molbev/msp313. Epub 2009 Dec 18. pubmed
Maruyama F, Kobata M, Kurokawa K, Nishida K, Sakurai A, Nakano K, Nomura R, Kawabata S, Ooshima T, Nakai K, Hattori M, Hamada S, Nakagawa I Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content BMC Genomics. 2009 Aug 5;10:358. doi: 10.1186/1471-2164-10-358. 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
Miyakawa C, Sugii M, Matsuno H, Miyano S Computational predictions for functional proteins working after cleaved in apoptotic pathway Proc. Second International Workshop on Intelligent Informatics in Biology and Medicine, IEEE Computer Society Press, 807-812, 2009
Miyano S, Yamaguchi R, Tamada Y, Nagasaki M, Imoto S Gene networks viewed through two models Lecture Notes in Computer Science Vol.5462, 54-66, 2009. (Proc. First International Conference on Bioinformatics and Computational Biology (BICoB)). doi: 10.1007/978-3-642-00727-9_8
Mizuno H, Kitada K, Nakai K, Sarai A PrognoScan: a new database for meta-analysis of the prognostic value of genes BMC Med Genomics. 2009 Apr 24;2:18. doi: 10.1186/1755-8794-2-18. pubmed
Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S Cell Illustrator 4.0 A computational platform for systems biology. 10:0002.
Nakamura K, Yoshida R, Nagasaki M, Miyano S, Higuchi T Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing Pac Symp Biocomput. 2009:227-38. pubmed
Ng CC, Yew PY, Puah SM, Krishnan G, Yap LF, Teo SH, Lim PV, Govindaraju S, Ratnavelu K, Sam CK, Takahashi A, Kubo M, Kamatani N, Nakamura Y, Mushiroda T A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma J Hum Genet. 2009 Jul;54(7):392-7. doi: 10.1038/jhg.2009.49. Epub 2009 May 29. pubmed
Nikolova DN, Doganov N, Dimitrov R, Angelov K, Low SK, Dimova I, Toncheva D, Nakamura Y, Zembutsu H Genome-wide gene expression profiles of ovarian carcinoma: Identification of molecular targets for the treatment of ovarian carcinoma Mol Med Rep. 2009 May-Jun;2(3):365-84. doi: 10.3892/mmr_00000109. pubmed
Nishida K, Frith MC, Nakai K Pseudocounts for transcription factor binding sites Nucleic Acids Res. 2009 Feb;37(3):939-44. doi: 10.1093/nar/gkn1019. Epub 2008 Dec 23. 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
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K ATTED-II provides coexpressed gene networks for Arabidopsis Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91. doi: 10.1093/nar/gkn807. Epub 2008 Oct 25. pubmed
Obayashi T, Kinoshita K Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression DNA Res. 2009 Oct;16(5):249-60. doi: 10.1093/dnares/dsp016. Epub 2009 Sep 18. pubmed
Onuki R, Shibuya T, Kanehisa M New kernel methods for phenotype prediction from genotype data Genome Inform. 2010 Jan;22:132-41. pubmed
Oshima D, Hirosawa A, Yamashita R, Akiyama T, Inoue J Possible co-operation of distinct signal transduction pathways and transcription factors in formation of thymic microenvironments required for self-tolerance 第32回日本分子生物学会年会
Oyama M, Kozuka-Hata H, Tasaki S, Semba K, Hattori S, Sugano S, Inoue J, Yamamoto T Temporal perturbation of tyrosine phosphoproteome dynamics reveals the system-wide regulatory networks Mol Cell Proteomics. 2009 Feb;8(2):226-31. doi: 10.1074/mcp.M800186-MCP200. Epub 2008 Sep 24. pubmed
Oyama M Comprehensive description of signal transduction networks by quantitative proteomics and systems biology Current Bioinformatics, 4, 149-153, 2009
Ozaki K, Sato H, Inoue K, Tsunoda T, Sakata Y, Mizuno H, Lin TH, Miyamoto Y, Aoki A, Onouchi Y, Sheu SH, Ikegawa S, Odashiro K, Nobuyoshi M, Juo SH, Hori M, Nakamura Y, Tanaka T SNPs in BRAP associated with risk of myocardial infarction in Asian populations Nat Genet. 2009 Mar;41(3):329-33. doi: 10.1038/ng.326. Epub 2009 Feb 8. pubmed
Sasaki NV, Sato N CyanoClust: comparative genome resources of cyanobacteria and plastids Database (Oxford). 2010;2010:bap025. doi: 10.1093/database/bap025. Epub 2010 Jan 8. pubmed
The 12th International Conference on Genome Informatics, Yokohama, Japan, (December 2009)
Sasaki NV, Sato N Detection of mosaic structure of syntenic segments in marine cyanobacterial genomes The 12th International Conference on Genome Informatics, Yokohama, Japan, (December 2009)
Sasaki NV, Sato N Elucidating genome structure evolution by analysis of isoapostatic gene clusters using statistics of variance of gene distances Genome Biol Evol. 2009 Dec 18;2:1-12. doi: 10.1093/gbe/evp051. pubmed
Sathira N, Yamashita R, Tanimoto K, Kanai A, Arauchi T, Kanematsu S, Nakai K, Suzuki Y, Sugano S Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer DNA Res. 2010 Jun;17(3):169-83. doi: 10.1093/dnares/dsq007. Epub 2010 Apr 17. 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
Shigemizu D, Araki M, Okuda S, Goto S, Kanehisa M Extraction and analysis of chemical modification patterns in drug development J Chem Inf Model. 2009 Apr;49(4):1122-9. doi: 10.1021/ci8003804. pubmed
Shimamura T, Imoto S, Yamaguchi R, Fujita A, Nagasaki M, Miyano S Recursive regularization for inferring gene networks from time-course gene expression profiles BMC Syst Biol. 2009 Apr 22;3:41. doi: 10.1186/1752-0509-3-41. pubmed
Shirota M, Ishida T, Kinoshita K Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials Protein Sci. 2009 Sep;18(9):1906-15. doi: 10.1002/pro.201 pubmed
Shirota M, Ishida T, Kinoshita K Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression Genome Inform. 2009 Oct;23(1):149-58. pubmed
Sierro N, Li S, Suzuki Y, Yamashita R, Nakai K Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis Gene. 2009 Feb 1;430(1-2):44-9. doi: 10.1016/j.gene.2008.10.002. Epub 2008 Oct 21. pubmed
Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H SeSAW: balancing sequence and structural information in protein functional mapping Bioinformatics. 2010 May 1;26(9):1258-9. doi: 10.1093/bioinformatics/btq116. Epub 2010 Mar 17. pubmed
Takarabe M, Shigemizu D, Kotera M, Goto S, Kanehisa M Characterization and classification of adverse drug interactions Genome Inform. 2010 Jan;22:167-75. pubmed
Tamada Y, Araki H, Imoto S, Nagasaki M, Doi A, Nakanishi Y, Tomiyasu Y, Yasuda K, Dunmore B, Sanders D, Humphreys S, Print C, Charnock-Jones DS, Tashiro K, Kuhara S, Miyano S Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks Pac Symp Biocomput. 2009:251-63. pubmed
Tanaka M, Moriya Y, Goto S, Kanehisa M Analysis of a lipid biosynthesis protein family and phospholipid structural variations Genome Inform. 2010 Jan;22:191-201. pubmed
Tanaka Y, Yoshimura I, Nakai K Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin Chromosoma. 2010 Aug;119(4):391-404. doi: 10.1007/s00412-010-0264-y. Epub 2010 Mar 12. pubmed
Tanaka Y, Nakai K An assessment of prediction algorithms for nucleosome positioning Genome Inform. 2009 Oct;23(1):169-78. pubmed
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto S, Matsushima K, Mizushima-Sugano J, Yamashita R, Nakai K, Bentley D, Esumi H, Sugano S Massive transcriptional start site analysis of human genes in hypoxia cells Nucleic Acids Res. 2009 Apr;37(7):2249-63. doi: 10.1093/nar/gkp066. Epub 2009 Feb 22. pubmed
Tsuchiya Y, Kanamori E, Nakamura H, Kinoshita K Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction Adv Appl Bioinform Chem. 2009;2:79-100. Epub 2009 Sep 22. pubmed
Tsujita K, Itoh T, Kondo A, Oyama M, Kozuka-Hata H, Irino Y, Hasegawa J, Takenawa T Proteome of acidic phospholipid-binding proteins: spatial and temporal regulation of Coronin 1A by phosphoinositides J Biol Chem. 2010 Feb 26;285(9):6781-9. doi: 10.1074/jbc.M109.057018. Epub 2009 Dec 22 pubmed
Vandenbon A, Nakai K Modeling tissue-specific structural patterns in human and mouse promoters Nucleic Acids Res. 2010 Jan;38(1):17-25. doi: 10.1093/nar/gkp866. Epub 2009 Oct 22. pubmed
Watanabe-Fukuda Y, Yamamoto M, Miura N, Fukutake M, Ishige A, Yamaguchi R, Nagasaki M, Saito A, Imoto S, Miyano S, Takeda J, Watanabe K Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine J Gastroenterol. 2009;44(5):380-9. doi: 10.1007/s00535-009-0005-2. Epub 2009 Mar 25. pubmed
Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggstrom JZ, Goto S Systems biology approaches and pathway tools for investigating cardiovascular disease Mol Biosyst. 2009 Jun;5(6):588-602. doi: 10.1039/b902356a. Epub 2009 Apr 27. pubmed
Wijaya E, Frith MC, Suzuki Y, Horton P Recount: expectation maximization based error correction tool for next generation sequencing data Genome Inform. 2009 Oct;23(1):189-201. pubmed
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
Yamamoto T, Miyano S, Nagasaki M, Bannai H Better decomposition heuristics for the maximum-weight connected graph problem using betweenness centrality Lecture Notes in Artificial Intelligence. In press.
Yamanishi Y, Hattori M, Kotera M, Goto S, Kanehisa M E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs Bioinformatics. 2009 Jun 15;25(12):i179-86. doi: 10.1093/bioinformatics/btp223. pubmed
Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K DBTSS provides a tissue specific dynamic view of Transcription Start Sites Nucleic Acids Res. 2010 Jan;38(Database issue):D98-104. doi: 10.1093/nar/gkp1017. Epub 2009 Nov 12. pubmed
Yamayoshi S, Yamashita Y, Li J, Hanagata N, Minowa T, Takemura T, Koike S Scavenger receptor B2 is a cellular receptor for enterovirus 71 Nat Med. 2009 Jul;15(7):798-801. doi: 10.1038/nm.1992. Epub 2009 Jun 21. pubmed
Yashiro Y, Bannai H, Minowa T, Yabiku T, Miyano S, Osawa M, Iwama A, Nakauchi H Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing Int J Hematol. 2009 Jan;89(1):24-33. doi: 10.1007/s12185-008-0212-2. Epub 2008 Dec 3. pubmed
Yoshikawa N, Nagasaki M, Sano M, Tokudome S, Ueno K, Shimizu N, Imoto S, Miyano S, Suematsu M, Fukuda K, Morimoto C, Tanaka H Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism Am J Physiol Endocrinol Metab. 2009 Jun;296(6):E1363-73. doi: 10.1152/ajpendo.90767.2008. Epub 2009 Mar 17. pubmed
Zembutsu H, Suzuki Y, Sasaki A, Tsunoda T, Okazaki M, Yoshimoto M, Hasegawa T, Hirata K, Nakamura Y Predicting response to docetaxel neoadjuvant chemotherapy for advanced breast cancers through genome-wide gene expression profiling Int J Oncol. 2009 Feb;34(2):361-70. 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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