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 2011

AuthorTitleJournal/Book
Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N Using the Acropora digitifera genome to understand coral responses to environmental change Nature. 2011 Jul 24;476(7360):320-3. doi: 10.1038/nature10249. pubmed
大島 大輔, 市川 一寿 核内NF-κBの振動とその制御の数理モデル 実験医学増刊号 Vol.30 No.5, 49-55, 2012
Furukawa Y, Koga R, Nariai N, Yasuda K Acceleration of Quantum Chemistry and Chemical Similarity calculations on GPGPU architecture towards faster virtual screening International Conference on Rare Diseases & Orphan Drugs 2012, Poster Presentation.
Okamura K, Yamashita R, Takimoto N, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K Profiling ascidian promoters as the primordial type of vertebrate promoter BMC Genomics. 2011 Nov 30;12 Suppl 3:S7. doi: 10.1186/1471-2164-12-S3-S7. Epub 2011 Nov 30. pubmed
Kiryu H, Asai K Rchange: Algorithms for computing the energy changes of RNA secondary structures in response to base mutations Bioinformatics doi: 10.1093/bioinformatics/bts097, 2012 pubmed
Kiryu H Sufficient statistics and expectation maximization algorithms in phylogenetic tree models Bioinformatics 27:2346-2353, 2011 pubmed
Kiryu H, Terai G, Imamura O, Yoneyama H, Suzuki K, Asai K A detailed investigation of accessibilities around target sites of siRNAs and miRNAs Bioinformatics 27:1788-1797, 2011 pubmed
E Wijaya, M. C. Frith, Asai K, P. Horton RecountDB: a database of mapped and count corrected transcribed sequences Nucleic Acids Research. 40: D1089-92, 2012 pubmed
Hamada M, E Wijaya, M. C. Frith, Asai K Probabilistic alignments with quality scores: An application to short-read mapping toward accurate SNP/indel detection Bioinformatics. 27:3085-3092, 2011 pubmed
Yang Y, Maruyama S, Sekimoto H, Sakayama H, Nozaki H An extended phylogenetic analysis reveals ancient origin of "non-green phosphoribulokinase genes from two lineages of "green" secondar photosynthetic eukaryotes: Euglenophyta and Chlorarachniophyta BMC Research Notes. 4:330, 2011 pubmed
Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T INOH: ontology-based highly structured database of signal transduction pathways Oxford Database. Vol.2011:bar052, 2011 pubmed
Onuki R, Yamada R, Yamaguchi R, Kanehisa M, Shibuya T Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering J.Compt.Biol. 19(1):55-67, 2012 pubmed
Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator Pacific Symposium on Biocomputing. 17:164-175, 2012 pubmed
Patil A, Nakai K, Kinoshita K Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks BMC Genomics. 12(Suppl 3):S19, 2011 pubmed
田中 義章, 山下 理宇 転写制御のために有用な公共データベースとツールの紹介 実験医学増刊号 Vol.29 No.15, 76-83, 2011
Fukuyo M, Sasaki A, Kobayashi I Success of a suicidal defense strategy against infection in a structured habitat Scientific Reports, 2:238, 2012 pubmed
Furuta Y, Yahara K, Hatakeyama M, Kobayashi I Evolution of cagA oncogene of Helicobacter pylori through recombination PLoS ONE. 6(8):e23499, 2011 pubmed
Furuta Y, Kawai M, Yahara K, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T Hattori M, Uchiyama I and Kobayashi I. Birth and death of genes linked to chromosomal inversion. Proc Nat Acad Sci USA. 108:1501-1506, 2011 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. 11:105, 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 tamoxifen-resistant breast cancer J Biol Chem. 286:818-829, 2011 pubmed
Hino N, Oyama M, Sato A, Mukai T, Iraha F, Hayashi A, Kozuka-Hata H, Yamamoto T, Yokoyama S, 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
Abe S, Nagasaka K, Hirayama Y, Kozuka-Hata H, Oyama M, Aoyagi Y, Obuse C, Hirota T The initial phase of chromosome condensation requires Cdk1-mediated phosphorylation of the CAP-D3 subunit of condensin II Genes Dev. 25:863-874, 2011 pubmed
Suzuki T, Kim M, Kozuka-Hata H, Watanabe M, Oyama M, Tsumoto K, Yamamoto T Monoubiquitination of Tob/BTG family proteins competes with degradation-targeting polyubiquitination Biochem Biophys Res Commun. 409:70-74, 2011 pubmed
Katsumata Y, Kawaguchi Y, Baba S, Hattori S, Tahara K, Ito K, Iwasaki T, Yamaguchi N, Oyama M, Kozuka-Hata H, Hattori H, Nagata K, Yamanaka H, Hara M Identification of three new autoantibodies associated with systemic lupus erythematosus using two proteomic approaches Mol Cell Proteomics. 10:M110.005330, 2011 pubmed
Suzuki M, Kiga K, Kersulyte D, Cok J, Hooper CC, Mimuro H, Sanada T, Suzuki S, Oyama M, Kozuka-Hata H, Kamiya S, Zou QM, Gilman RH, Berg DE, Sasakawa C Attenuated CagA oncoprotein in Helicobacter pylori from Amerindians in Peruvian Amazon J Biol Chem. 286:29964-29972, 2011 pubmed
Huang M, Sato H, Hagiwara K, Watanabe A, Sugai A, Ikeda F, Kozuka-Hata H, Oyama M, Yoneda M, Kai C Determination of a phosphorylation site in Nipah virus nucleoprotein and its involvement in virus transcription J Gen Virol. 92:2133-2141, 2011 pubmed
Iwasa A, Halfmann P, Noda T, Oyama M, Kozuka-Hata H, Watanabe S, Shimojima M, Watanabe T, Kawaoka Y Contribution of Sec61α to the life cycle of Ebola virus J Infect Dis. 204:S919-S926, 2011 pubmed
Kozuka-Hata H, Tasaki S, Oyama M Phosphoproteomics-based systems analysis of signal transduction networks Front Physiol. 2:113, 2011 pubmed
Gorai T, Goto H, Noda T, Watanabe T, Kozuka-Hata H, Oyama M, Takano R, Neumann G, Watanabe S, Kawaoka Y F1Fo-ATPase, F-type proton-translocating ATPase, at the plasma membrane is critical for efficient influenza virus budding Proc Natl Acad Sci U S A. 109:4615-4620, 2012 pubmed
Ao-Kondo H, Kozuka-Hata H, and Oyama M Emergence of the Diversified Short ORFeome by Mass Spectrometry-Based Proteomics InTech, 2011
Yamamoto T, Saito M, Kumazawa K, Doi A, Matsui A, Takebe S, Amari T, Oyama M, Semba K ErbB2/HER2: Its Contribution to Basic Cancer Biology and the Development of Molecular Targeted Therapy In Breast Cancer Carcinogenesis Cell Growth and Signalling Pathways InTech, 2011
尾山 大明 Phos-tagを使った定量プロテオミクスによるリン酸化シグナルネットワークの統合システム解析 生物物理化学 Vol.56, s29-s32, 2012
Obayashi T, Nishida K, Kasahara K, Kinoshita K ATTED-II updates: condition-specific gene coexpression to extend coexpression analyse 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
Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S Frequent pathway mutations of splicing machinery in myelodysplasia Nature. 478(7367):64-9, 2011 pubmed
Watanabe Y, Seno S, Takenaka Y, Matsuda H An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems BMC Genomics. 13(Suppl 1):S12, 2012 pubmed
Nakayama T, Seno S, Takenaka Y, Matsuda H Inference of S-system models of gene regulatory networks using immune algorithm J Bioinform Comput Biol. 9(Suppl 1):75-86, 2011 pubmed
Takenaka Y, Seno S, Matsuda H Perfect Hamming code with a hash table for faster genome mapping BMC Genomics. 12(Suppl 3):S3, 2011 pubmed
吉澤 陽志, 瀬尾 茂人, 竹中 要一, 松田 秀雄 細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法 情報処理学会論文誌 数理モデル化と応用 Vol.4 No.4, 59-68, 2011
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. 12(Suppl 1): S50, 2011 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. 39(7):2638-2648, 2011 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. 21(5):775-789, 2011 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. 39(11):e75, 2011 pubmed
Ohshima D, Qin J, Konno H, Hirosawa A, Shiraishi T, Yanai H, Shimo Y, Shinzawa M, Akiyama N, Yamashita R, Nakai K, Akiyama T, Inoue J RANK signaling induces interferon-stimulated genes in the fetal thymic stroma Biochem Biophys Res Commun. 408(4):530-536, 2011 pubmed
Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernandez JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications J Biomed Semantics. 2:4, 2011 pubmed
Kimura K, Koike A, Nakai K. Seed-set construction by equi-entropy partitioning for efficient and sensitive short-read mapping Algorithms in Bioinformatics in (T.M.Przytycka and M.-F. Sagot ed.) Lecture Notes in Computer Science, 6833, 151-162, 2011
Yamashita R, Sugano S, Suzuki Y, Nakai K DBTSS: DataBase of Transcriptional Start Sites progress report in 2012 Nucleic Acids Res. 40(Database Issue):D150-154, 2012 pubmed
Kimura K, Koike A, Nakai K A Bit-parallel dynamic programming algorithm suitable for DNA sequence alignment J Bioinform Comput Biol. 2012 Aug;10(4):1250002. doi: 10.1142/S0219720012500023. Epub 2012 Jun 22. pubmed
Sasakura Y, Sierro N, Nakai K, Inaba K, Kusakabe TG Genome structure, functional genomics and proteomics in ascidians Genome Mapping and Genomics in Laboratory Animals, Vol.4, 87-132, 2012
Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612. Epub 2012 Oct 11. 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, 79(5):1550-1563, 2011 pubmed
Wang L, Hurley D, Watkins W, Araki H, Tamada Y, Muthukaruppan A, Ranjard L, Derkac E, Imoto S, Miyano S, Crampin E, and Print CG Cell cycle gene networks are associated with melanoma prognosis PLoS One. 2012;7(4):e34247. doi: 10.1371/journal.pone.0034247. Epub 2012 Apr 20. pubmed
Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, J Crampin EJ, and Print CG Gene network inference and visualization tools for biologists: application to new human transcriptome datasets Nucleic Acids Res. 2012 Mar;40(6):2377-98. doi: 10.1093/nar/gkr902. Epub 2011 Nov 24. 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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