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 2010

AuthorTitleJournal/Book
Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, Boroevich KA, Nagasaki M, Yamaguchi R, Shibuya T, Kubo M, Miyano S, Nakamura Y, Tsunoda T Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing Nat Genet. 2010 Nov;42(11):931-6. doi: 10.1038/ng.691. Epub 2010 Oct 24. pubmed
Patil A, Kinoshita K, Nakamura H Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network Protein Sci. 2010 Aug;19(8):1461-8. doi: 10.1002/pro.425. pubmed
Patil A, Kinoshita K, Nakamura H Hub promiscuity in protein-protein interaction networks Int J Mol Sci. 2010 Apr 26;11(4):1930-43. doi: 10.3390/ijms11041930. pubmed
Patil A, Nakai K, Nakamura H HitPredict: a database of quality assessed protein-protein interactions in nine species Nucleic Acids Res. 2011 Jan;39(Database issue):D744-9. doi: 10.1093/nar/gkq897. Epub 2010 Oct 14. 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
Schonbach C, Nakai K, Tan TW, Ranganathan S InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010 BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S1. doi: 10.1186/1471-2105-11-S7-S1 pubmed
Kawaki H, Kubota S, Aoyama E, Fujita N, Hanagata H, Miyauchi A, Nakai K, Takigawa M Design and utility of CCN2 anchor peptide aptamers Biochimie. 2010 Aug;92(8):1010-5. doi: 10.1016/j.biochi.2010.04.021. Epub 2010 May 8. pubmed
Imai K, Nakai K Prediction of subcellular locations of proteins: where to proceed? Proteomics. 2010 Nov;10(22):3970-83. doi: 10.1002/pmic.201000274. Epub 2010 Nov 2. pubmed
Okamura K, Matsumoto KA, Nakai K Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S2. doi: 10.1186/1471-2105-11-S7-S2. 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
Khare P, Mortimer SI, Cleto CL, Okamura K, Suzuki Y, Kusakabe T, Nakai K, Meedel TH, Hastings KE Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene Nucleic Acids Res. 2011 Apr;39(7):2638-48. doi: 10.1093/nar/gkq1151. Epub 2010 Nov 24. pubmed
Yamashita R, Sathira NP, Kanai A, Tanimoto K, Arauchi T, Tanaka Y, Hashimoto S, Sugano S, Nakai K, Suzuki Y Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis Genome Res. 2011 May;21(5):775-89. doi: 10.1101/gr.110254.110. Epub 2011 Mar 3. 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
Ranganathan S, Schonbach C, Nakai K, Tan TW Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010) BMC Genomics. 2010 Dec 2;11 Suppl 4:S1. doi: 10.1186/1471-2164-11-S4-S1 pubmed
Teraguchi S, Patil A, Standley DM Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S7. doi: 10.1186/1471-2105-11-S7-S7. pubmed
Park SJ, Nakai K A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S50. doi: 10.1186/1471-2105-12-S1-S50. pubmed
Satoh T, Takeuchi O, Vandenbon A, Yasuda K, Tanaka Y, Kumagai Y, Miyake T, Matsushita K, Okazaki T, Saitoh T, Honma K, Matsuyama T, Yui K, Tsujimura T, Standley DM, Nakanishi K, Nakai K, Akira S The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection Nat Immunol. 2010 Oct;11(10):936-44. doi: 10.1038/ni.1920. Epub 2010 Aug 22. pubmed
Irie T, Park SJ, Yamashita R, Seki M, Yada T, Sugano S, Nakai K, Suzuki Y Predicting promoter activities of primary human DNA sequences Nucleic Acids Res. 2011 Jun;39(11):e75. doi: 10.1093/nar/gkr173. Epub 2011 Apr 12. 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, Yamashita R, Suzuki Y, Nakai K Effects of Alu elements on global nucleosome positioning in the human genome BMC Genomics. 2010 May 17;11:309. doi: 10.1186/1471-2164-11-309. pubmed
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novere N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD The BioPAX community standard for pathway data sharing Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. 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
Yoshida S, Maruyama S, Nozaki H, Shirasu K Horizontal gene transfer by the parasitic plant Striga hermonthica Science. 2010 May 28;328(5982):1128. doi: 10.1126/science.1187145. pubmed
Maruyama S, Suzaki T, Weber AP, Archibald JM, Nozaki H Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids BMC Evol Biol. 2011 Apr 18;11:105. doi: 10.1186/1471-2148-11-105 pubmed
Ishii N Automatic image classification and annotation methods towards comprehensive human brain database Doctor thesis, Graduate School of Frontier Sciences, The University of Tokyo, December 2010
Sato N Phylogenomic and structural modeling analyses of the PsbP superfamily reveal multiple small segment additions in the evolution of photosystem II-associated PsbP protein in green plants Mol Phylogenet Evol. 2010 Jul;56(1):176-86. doi: 10.1016/j.ympev.2009.11.021. Epub 2009 Nov 26. pubmed
Konaka Y, Fukuzaki M, Yoshida M, Shimizu K, Ogura A, Sese J Gene duplication detection with frequent pattern analysis IPSJ SIG Technical Report, Vol.2010-BIO-23 No.18, 2010
Hino N, Oyama M, Sato A, Mukai T, Iraha F, Hayashi A, Kozuka-Hata H,Yamamoto T, Yokoyama S, and Sakamoto K Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells J. Mol. Biol., 406: 343-353, 2011. pubmed
Oyama M, Nagashima T, Suzuki T, Kozuka-Hata H, Yumoto N, Shiraishi Y, Ikeda K, Kuroki Y, Gotoh N, Ishida T, Inoue S, Kitano H, Okada-Hatakeyama M Integrated quantitative analysis of the phosphoproteome and transcriptome in amoxifen-resistant breast cancer J. Biol. Chem., 286: 818-829, 2011 pubmed
Matsumura T, Oyama M, Kozuka-Hata H, Ishikawa K, Inoue T, Muta T, Semba K, Inoue J Identification of BCAP-(L) as a negative regulator of the TLR signaling-induced production of IL-6 and IL-10 in macrophages by tyrosine phosphoproteomics Biochem. Biophys. Res. Commun., 400: 265-270, 2010 pubmed
Fujita T, Kozuka-Hata H, Uno Y, Nishikori K, Morioka M, Oyama M, and Kubo T Functional analysis of the honeybee (Apis mellifera L.) salivary system using proteomics Biochem. Biophys. Res. Commun., 397: 740-744, 2010 pubmed
Oyama M, Tasaki S, Kozuka-Hata H Tyrosine-Phosphoproteome Dynamics In Systems Biology for Signaling Networks (ed. Choi, S) Springer, 447-454, 2010 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., 285: 6781-6789, 2010 pubmed
Tasaki S, Nagasaki M, Kozuka-Hata H, Semba K, Gotoh N, Hattori S, Inoue J, Yamamoto T, Miyano S, Sugano S, Oyama M Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling PLoS One, 5: e13926, 2010 pubmed
Arii J, Goto H, Suenaga T, Oyama M, Kozuka-Hata H, Imai T, Minowa A, Akashi H, Arase H, Kawaoka Y, Kawaguchi Y Non-muscle myosin IIA is a functional entry receptor for herpes simplex virus 1 Nature, 467: 859-862, 2010 pubmed
Obayashi T, Nishida K, Kasahara K, Kinoshita K ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants Plant Cell Physiol, 52, 213-9 (2011) pubmed
Obayashi T, Kinoshita K COXPRESdb: a database to compare gene coexpression in seven model animals Nucleic Acids Res, 39, D1016-22 (2011) pubmed
大林 武, 木下 賢吾 共発現情報から見る遺伝子機能ネットワーク 化学と生物 Vol.49, 48-56, 2011
Obayashi T How to measure the similarity of gene expression patterns to identify gene function QBIC2011 Bio-Informatics Workshop (Tokyo university of science, 2011.03.11)
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 2010, PLoS ONE 5(5): e10517 pubmed
Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S SiGN-SSM: open source parallel software for estimating gene networks with state space models Bioinformatics. 27(8):1172-1173, 2011 pubmed
Tamada Y, Imoto S, Araki H, Nagasaki M, Print C, Charnock-Jones DS, Miyano S Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(3):683-697, 2011 pubmed
Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S SiGN: Large-scale gene network estimation environment for high performance computing Genome Informatics. 25(1):40-52, 2011 pubmed
Tamada Y, Imoto S, Miyano S Parallel algorithm for learning optimal Bayesian network structure Journal of Machine Learning Research. 12:2437-2459, 2011
Furuta Y, Kawai M, Yahara K, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I Birth and death of genes linked to chromosomal inversion Proc. Nat. Acad. Sci. USA,108: 1501-1506 (2011) pubmed
Yahara K, Fukuyo M, Sasaki A, Kobayashi I Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer Proc. Nat. Acad. Sci. USA, 106: 18861-18866 (2009) pubmed
福崎 睦美, 吉田 真明, 小倉 淳, 瀬々 潤 比較トランスクリプトーム向けマイクロアレイの設計 情報処理学会 バイオ情報学研究会 (SIG BIO) 第24回研究会
Imai K, Fujita N, Gromiha MM, Horton P Eukaryote-wide sequence analysis of mitochondrial beta-barrel outer membrane proteins BMC Genomics. 12(1):79, 2011 pubmed
Nemoto K, Okamura Y, Terahara T, Chiba H, Fujibuchi W, Takeyama H DIVERSITY ANALYSIS OF L-ARABINOSE METABOLIC ENZYME GENES IN SOIL METAGENOME TOWARDS BIOETHANOL PRODUCTION CBRC2010, 2010
Satoh T, Takeuchi O, Vandenbon A, Yasuda K, Tanaka Y, Kumagai Y, Miyake T, Matsushita K, Okazaki T, Saitoh T, Honma K, Matsuyama T, Yui K, Tsujimura T, Standley DM, Nakanishi K, Nakai K, Akira S The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection Nat Immunol. 2010 Oct;11(10):936-44. doi: 10.1038/ni.1920. Epub 2010 Aug 22. pubmed
Pessiot JF, Chiba H, Hyakkoku H, Taniguchi T, Fujibuchi W PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs PLoS One. 2010 Aug 27;5(8):e11881. doi: 10.1371/journal.pone.0011881. pubmed
Wijaya E, Pessiot JF, Frith MC, Fujibuchi W, Asai K, Horton P In Search of True Reads: A Classification Approach to Next Generation Sequencing Data Selection In Proc 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Next Generation Sequencing Workshop, 561-566, 2010
Chiba H, Tanaka T, Miyake M, Fujibuchi W Prediction of novel effeicient induers for mesenchymal stem cell differentiation CBRC2010, Tokyo, Japan, Jul. 2010
Kim H, Kato T, Mogushi K, Tanaka H, Fujibuchi W Detection of common pathways activated by anticancer drugs using regularized kernel canonical correlation analysis CBRC2010, Tokyo, Japan, Jul. 2010
Kim H, Kato T, Mogushi K, Tanaka H, Fujibuchi W Detection of common pathways activated by anticancer drugs using regularized kernel canonical correlation analysis CBI Annual Meeting 2010, Tokyo, Japan, Sept. 2010
金 �瀘�, 加藤 毅, 茂櫛 薫, 田中 博, 藤渕 航 正則化正準相関解析を用いた抗がん剤の影響による共通パスウェイ解析 IPSJ SIG Technical Report, 2010-BIO-20(vol.9), 2010
Hongyan W, Saito TL, Morishita S Accelerating Path-free XML Queries in RDBMS IPSJ Online Transactions Vol.3, 206-217, 2010
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. 7;5(5):e10517 (2010) pubmed
Sato K, Kato Y, Hamada M, Akutsu T, Asai K IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming Bioinformatics (Proc. of ISMB/ECCB 2011), in press (2011) pubmed
Shirota M, Ishida T, Kinoshita K Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states Proteins. 2011 May;79(5):1550-63. doi: 10.1002/prot.22982. Epub 2011 Mar 1. pubmed
Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M SAHG, a comprehensive database of predicted structures of all human proteins Nucleic Acids Res. 2011 Jan;39(Database issue):D487-93. doi: 10.1093/nar/gkq1057. Epub 2010 Nov 3. pubmed
Kasahara K, Kinoshita K, Takagi T Ligand-binding site prediction of proteins based on known fragment-fragment interactions Bioinformatics. 2010 Jun 15;26(12):1493-9. doi: 10.1093/bioinformatics/btq232. Epub 2010 May 13. pubmed
Nunomura W, Kinoshita K, Parra M, Gascard P, An X, Mohandas N, Takakuwa Y Similarities and differences in the structure and function of 4.1G and 4.1R135, two protein 4.1 paralogues expressed in erythroid cells Biochem J. 2010 Dec 1;432(2):407-16. doi: 10.1042/BJ20100041. pubmed
Obayashi T, Kinoshita K Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways J Plant Res. 2010 May;123(3):311-9. doi: 10.1007/s10265-010-0333-6. Epub 2010 Apr 10. 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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