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Results Achieved by Using the Supercomputer (Published Papers)
Published Papers List in 2011

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 2011

Author	Title	Journal/Book
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
Ao-Kondo H, Kozuka-Hata H, and Oyama M	Emergence of the Diversified Short ORFeome by Mass Spectrometry-Based Proteomics	InTech, 2011
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
Fukuyo M, Sasaki A, Kobayashi I	Success of a suicidal defense strategy against infection in a structured habitat	Scientific Reports, 2:238, 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.
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
Furuta Y, Yahara K, Hatakeyama M, Kobayashi I	Evolution of cagA oncogene of Helicobacter pylori through recombination	PLoS ONE. 6(8):e23499, 2011
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
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
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
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
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.
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
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
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
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
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
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.
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
Kiryu H	Sufficient statistics and expectation maximization algorithms in phylogenetic tree models	Bioinformatics 27:2346-2353, 2011
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
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
Kozuka-Hata H, Tasaki S, Oyama M	Phosphoproteomics-based systems analysis of signal transduction networks	Front Physiol. 2:113, 2011
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
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
Obayashi T, Kinoshita K	COXPRESdb: a database to compare gene coexpression in seven model animals	Nucleic Acids Res. 39:D1016-22, 2011
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
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
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.
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
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
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
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
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
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.
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.
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
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
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
Takenaka Y, Seno S, Matsuda H	Perfect Hamming code with a hash table for faster genome mapping	BMC Genomics. 12(Suppl 3):S3, 2011
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.
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
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
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
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
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
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
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
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
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
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
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
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