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Published Papers List in 2010

Supercomputer

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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

Author	Title	Journal/Book
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
Chiba H, Tanaka T, Miyake M, Fujibuchi W	Prediction of novel effeicient induers for mesenchymal stem cell differentiation	CBRC2010, Tokyo, Japan, Jul. 2010
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.
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.
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
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)
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.
Hongyan W, Saito TL, Morishita S	Accelerating Path-free XML Queries in RDBMS	IPSJ Online Transactions Vol.3, 206-217, 2010
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
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.
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.
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
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.
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.
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.
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
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
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.
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
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)
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.
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
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
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.
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
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.
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)
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.
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 analyses and applications to a broad range of flowering plants	Plant Cell Physiol, 52, 213-9 (2011)
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.
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
Oyama M, Tasaki S, Kozuka-Hata H	Tyrosine-Phosphoproteome Dynamics In Systems Biology for Signaling Networks (ed. Choi, S)	Springer, 447-454, 2010
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.
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.
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.
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.
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.
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
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.
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)
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.
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.
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.
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
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.
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
Tamada Y, Imoto S, Miyano S	Parallel algorithm for learning optimal Bayesian network structure	Journal of Machine Learning Research. 12:2437-2459, 2011
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
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
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.
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.
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
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.
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
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
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)
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.
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.
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.
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
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
金蕙鈴, 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