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 2012

AuthorTitleJournal/Book
Sutheeworapong S, Ota M, Ohta H, Kinoshita K A novel biclustering approach with iterative optimization to analyze gene expression data Adv Appl Bioinform Chem. 2012;5:23-59. doi: 10.2147/AABC.S32622. Epub 2012 Sep 7. pubmed
Kasahara K, Shirota M, Kinoshita K Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions J Chem Inf Model. 2013 Jan 28;53(1):241-8. doi: 10.1021/ci300377f. Epub 2012 Dec 18. pubmed
Obayashi T, Okamura Y, Ito S, Tadaka S, Motoike IN, Kinoshita K COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals Nucleic Acids Res. 2013 Jan;41(Database issue):D1014-20. doi: 10.1093/nar/gks1014. Epub 2012 Nov 29. pubmed
Tsuchiya Y, Kinoshita K, Endo S, Wako H Dynamic features of homodimer interfaces calculated by normal-mode analysis Protein Sci. 2012 Oct;21(10):1503-13. doi: 10.1002/pro.2140. Epub 2012 Sep 17. pubmed
Kasahara K, Shirota M, Kinoshita K Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel PLoS One. 2013;8(2):e56342. doi: 10.1371/journal.pone.0056342. Epub 2013 Feb 13. pubmed
嶋田 透, 勝間 進, 大門 高明, 藤井 告, 木内 隆史 カイコとその近縁種における寄主植物選択機構の進化 COMPLEX ADAPTIVE TRAITS. Newsletter. 平成23年度研究成果報告 新学術領域研究 「複合適応形質進化の遺伝子基盤解明」. Vol.2 No.10, 2011
Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S Identifying gene pathways associated with cancer characteristics via sparse statistical methods IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):966-72. doi: 10.1109/TCBB.2012.48. pubmed
Matsumoto H, Kiryu H. MixSIH: a mixture model for single individual haplotyping BMC Genomics. 2013;14 Suppl 2:S5. doi: 10.1186/1471-2164-14-S2-S5. Epub 2013 Feb 15. pubmed
Wijaya E, Frith MC, Horton P, Asai K Finding protein-coding genes through human polymorphisms PLoS One. 2013;8(1):e54210. doi: 10.1371/journal.pone.0054210. Epub 2013 Jan 22. pubmed
Makita Y, Nakai K Chapter 8: Bacillus subtilis transcriptional network M. Madan Babu ed.) Bacterial Gene Regulation and Transcriptional Networks, Caister Academic Press. ISBN: 978-1-908230-14-0, 2013
Moesa HA, Wakabayashi S, Nakai K, Patil A. Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification Mol Biosyst. 2012 Oct 30;8(12):3262-73. doi: 10.1039/c2mb25202c. pubmed
Morita S, Takahashi RU, Yamashita R, Toyoda A, Horii T, Kimura M, Fujiyama A, Nakai K, Tajima S, Matoba R, Ochiya T, Hatada I. Genome-Wide Analysis of DNA Methylation and Expression of MicroRNAs in Breast Cancer Cells Int J Mol Sci. 2012;13(7):8259-72. doi: 10.3390/ijms13078259. Epub 2012 Jul 3. pubmed
Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A. Sequence- and species-dependence of proteasomal processivity ACS Chem Biol. 2012 Aug 17;7(8):1444-53. doi: 10.1021/cb3001155. Epub 2012 Jun 28. 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
Yamashita R, Sugano S, Suzuki Y, Nakai K. DBTSS: DataBase of Transcriptional Start Sites progress report in 2012 Nucleic Acids Res. 2012 Jan;40(Database issue):D150-4. doi: 10.1093/nar/gkr1005. Epub 2011 Nov 15. 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 Pac Symp Biocomput. 2012;17:164-175. pubmed
Ozawa M, Sakatani M, Yao J, Shanker S, Yu F, Yamashita R, Wakabayashi S, Nakai K, Dobbs KB, Sudano MJ, Farmerie WG, Hansen PJ Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst BMC Dev Biol. 2012 Nov 6;12:33. doi: 10.1186/1471-213X-12-33. pubmed
Kunishima S, Okuno Y, Yoshida K, Shiraishi Y, Sanada M, Muramatsu H, Chiba K, Tanaka H, Miyazaki K, Sakai M, Ohtake M, Kobayashi R, Iguchi A, Niimi G, Otsu M, Takahashi Y, Miyano S, Saito H, Kojima S, Ogawa S ACTN1 Mutations Cause Congenital Macrothrombocytopenia Am J Hum Genet. 2013 Mar 7;92(3):431-8. doi: 10.1016/j.ajhg.2013.01.015. Epub 2013 Feb 21. pubmed
Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data Nucleic Acids Res. 2013 Mar 6. [Epub ahead of print] pubmed
Saida S, Watanabe KI, Sato-Otsubo A, Terui K, Yoshida K, Okuno Y, Toki T, Wang R, Shiraishi Y, Miyano S, Kato I, Morishima T, Fujino H, Umeda K, Hiramatsu H, Adachi S, Ito E, Ogawa S, Ito M, Nakahata T, Heike T Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome Blood. 2013 Mar 12. [Epub ahead of print] pubmed
Maeda K, Minamida H, Yoshida K, Kurata H Flux module decomposition for parameter estimation in a multiple-feedback loop model of biochemical networks Bioprocess Biosyst Eng. 2013 Mar;36(3):333-44. doi: 10.1007/s00449-012-0789-y. Epub 2012 Jul 22. pubmed
Maeda K, Kurata H A symmetric dual feedback system provides a robust and entrainable oscillator PLoS One. 2012;7(2):e30489. doi: 10.1371/journal.pone.0030489. Epub 2012 Feb 20. pubmed
Yasuda T, Suzuki S, Nagasaki M, Miyano S ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs BMC Bioinformatics. 2012 Oct 30;13:279. doi: 10.1186/1471-2105-13-279. pubmed
Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S XiP: a computational environment to create, extend and share workflows Bioinformatics. 2013 Jan 1;29(1):137-9. doi: 10.1093/bioinformatics/bts630. Epub 2012 Oct 25. pubmed
Koso H, Takeda H, Yew CC, Ward JM, Nariai N, Ueno K, Nagasaki M, Watanabe S, Rust AG, Adams DJ, Copeland NG, Jenkins NA Transposon mutagenesis identifies genes that transform neural stem cells into glioma-initiating cells Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):E2998-3007. doi: 10.1073/pnas.1215899109. Epub 2012 Oct 8. pubmed
Yamauchi M, Yamaguchi R, Nakata A, Kohno T, Nagasaki M, Shimamura T, Imoto S, Saito A, Ueno K, Hatanaka Y, Yoshida R, Higuchi T, Nomura M, Beer DG, Yokota J, Miyano S, Gotoh N Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma PLoS One. 2012;7(9):e43923. doi: 10.1371/journal.pone.0043923. Epub 2012 Sep 19. pubmed
Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators Nat Genet. 2012 May 27;44(7):760-4. doi: 10.1038/ng.2291. pubmed
Affara M, Sanders D, Araki H, Tamada Y, Dunmore BJ, Humphreys S, Imoto S, Savoie C, Miyano S, Kuhara S, Jeffries D, Print C, Charnock-Jones DS Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis BMC Genomics. 2013 Jan 16;14:23. doi: 10.1186/1471-2164-14-23. pubmed
Bowe A, Onoder T, Sadakane K, Shibuya T Succinct de Bruijn graphs The 12th Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science. 7534: 225-235, 2012
Fujimori S, Hino K, Saito A, Miyano S, Miyamoto-Sato E PRD: A protein-RNA interaction database Bioinformation. 2012;8(15):729-30. doi: 10.6026/97320630008729. Epub 2012 Aug 3. pubmed
Fujimori S, Hirai N, Masuoka K, Oshikubo T, Yamashita T, Washio T, Saito A, Nagasaki M, Miyano S, Miyamoto-Sato E IRView: a database and viewer for protein interacting regions Bioinformatics. 2012 Jul 15;28(14):1949-50. doi: 10.1093/bioinformatics/bts289. Epub 2012 May 15. pubmed
Fujita A, Severino P, Kojima K, Sato JR, Patriota AG, Miyano S Functional clustering of time series gene expression data by Granger causality BMC Syst Biol. 2012 Oct 30;6:137. doi: 10.1186/1752-0509-6-137. 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, Crampin EJ, 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
Ishimaru S, Mimori K, Yamamoto K, Inoue H, Imoto S, Kawano S, Yamaguchi R, Sato T, Toh H, Iinuma H, Maeda T, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka J, Kudo SE, Sugihara K, Hase K, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Barnard GF, Miyano S, Mori M Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24 Ann Surg Oncol. 2012 Sep;19(9):2853-8. doi: 10.1245/s10434-012-2278-6. Epub 2012 Mar 21. pubmed
Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S Symbolic hierarchical clustering for pain vector Intelligent Decision Technologies, 16, 17-124, 2012
Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S Connection between traditional medicine and disease ACM SIGHIT Record, 2(1), 21-21, 2012
Kojima K, Imoto S, Yamaguchi R, Fujita A, Yamauchi M, Gotoh N, Miyano S Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing BMC Genomics. 2012;13 Suppl 1:S6. doi: 10.1186/1471-2164-13-S1-S6. Epub 2012 Jan 17. pubmed
Komatsu M, Yoshimaru T, Matsuo T, Kiyotani K, Miyoshi Y, Tanahashi T, Rokutan K, Yamaguchi R, Saito A, Imoto S, Miyano S, Nakamura Y, Sasa M, Shimada M, Katagiri T Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis Int J Oncol. 2013 Feb;42(2):478-506. doi: 10.3892/ijo.2012.1744. Epub 2012 Dec 18. pubmed
Mimura I, Nangaku M, Kanki Y, Tsutsumi S, Inoue T, Kohro T, Yamamoto S, Fujita T, Shimamura T, Suehiro J, Taguchi A, Kobayashi M, Tanimura K, Inagaki T, Tanaka T, Hamakubo T, Sakai J, Aburatani H, Kodama T, Wada Y Dynamic change of chromatin conformation in response to hypoxia enhances the expression of GLUT3 (SLC2A3) by cooperative interaction of hypoxia-inducible factor 1 and KDM3A Mol Cell Biol. 2012 Aug;32(15):3018-32. doi: 10.1128/MCB.06643-11. Epub 2012 May 29. pubmed
Niida A, Imoto S, Shimamura T, Miyano S. Bioinformatics. 2012 Jun 15;28(12):i115-20. doi: 10.1093/bioinformatics/bts203 Statistical model-based testing to evaluate the recurrence of genomic aberrations. pubmed
Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S Computational gene network analysis reveals TNF-induced angiogenesis BMC Syst Biol. 2012;6 Suppl 2:S12. doi: 10.1186/1752-0509-6-S2-S12. Epub 2012 Dec 12. pubmed
Okayama H, Kohno T, Ishii Y, Shimada Y, Shiraishi K, Iwakawa R, Furuta K, Tsuta K, Shibata T, Yamamoto S, Watanabe S, Sakamoto H, Kumamoto K, Takenoshita S, Gotoh N, Mizuno H, Sarai A, Kawano S, Yamaguchi R, Miyano S, Yokota J Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas Cancer Res. 2012 Jan 1;72(1):100-11. doi: 10.1158/0008-5472.CAN-11-1403. Epub 2011 Nov 11. pubmed
Onuki R, Yamada R, Yamaguchi R, Kanehisa M, Shibuya T Population model-based inter-diplotype similarity measure for accurate diplotype clustering J Comput Biol. 2012 Jan;19(1):55-67. doi: 10.1089/cmb.2010.0227. Epub 2011 Dec 9. pubmed
Sahli M, Shibuya T Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes BMC Res Notes. 2012 May 16;5:243. doi: 10.1186/1756-0500-5-243. pubmed
Sahli M, Shibuya T Max-Shift BM and Max-Shift Horspool: practical fast exact string matching algorithms J Information Processing, 20(2), 419-425, 2012
Sahli M, Shibuya T Argan - an artificial sequencing tool for simulated data and experimental Proc. The 4th International Conference on Bioinformatics and Biomedical Technology (ICBBT 2012), 29, 196-199, 2012
Sahli M, Shibuya T An algorithm for classifying DNA reads Proc. International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2012), 31, 59-63, 2012
Sahli M, Shibuya T Qamar - A more accurate DNA sequencing error correcting algorithm Proc. International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2012), 31, 53-58, 2012
Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T Identifiability of local transmissibility parameters in agent-based pandemic simulation Proc. 15th International Conference on Information Fusion. IEEE Computer Society Press, 2466-2471, 2012
Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T Parallel agent-based simulator for influenza pandemic Lecture Notes in Computer Science, 7068, 361-370, 2012
Sharma A, Imoto S, Miyano S A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data Current Bioinformatics, 7(3), 289-294, 2012
Sharma A, Imoto S, Miyano S A between-class overlapping filter-based method for transcriptome data analysis J Bioinform Comput Biol. 2012 Oct;10(5):1250010. doi: 10.1142/S0219720012500102. Epub 2012 Jun 22. pubmed
Sharma A, Imoto S, Miyano S A top-r feature selection algorithm for microarray gene expression data IEEE/ACM Trans Comput Biol Bioinform. 2012 May-Jun;9(3):754-64. doi: 10.1109/TCBB.2011.151. pubmed
Sharma A, Imoto S, Miyano S, Sharma Null space based feature selection method for gene expression dat International Journal of Machine Learning and Cybernetics, 3(4), 269-276, 2012
Takatsuno Y, Mimori K, Yamamoto K, Sato T, Niida A, Inoue H, Imoto S, Kawano S, Yamaguchi R, Toh H, Iinuma H, Ishimaru S, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka J, Kudo SE, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Miyano S, Sugihara K, Mori M The rs6983267 SNP Is Associated with MYC Transcription Efficiency, Which Promotes Progression and Worsens Prognosis of Colorectal Cancer Ann Surg Oncol. 2013 Apr;20(4):1395-402. doi: 10.1245/s10434-012-2657-z. Epub 2012 Sep 14. pubmed
Tamura T, Sone M, Nakamura Y, Shimamura T, Imoto S, Miyano S, Okazawa H A restricted level of PQBP1 is needed for the best longevity of Drosophila Neurobiol Aging. 2013 Jan;34(1):356.e11-20. doi: 10.1016/j.neurobiolaging.2012.07.015. Epub 2012 Aug 15. pubmed
Terashi G, Shibuya T, Takeda-Shitaka M LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value. J Comput Biol. 2012 May;19(5):493-503. doi: 10.1089/cmb.2011.0230. Epub 2012 Apr 17 pubmed
Wang L, Hurley DG, Watkins W, Araki H, Tamada Y, Muthukaruppan A, Ranjard L, Derkac E, Imoto S, Miyano S, Crampin EJ, 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
Yamaguchi R, Imoto S, Kami M, Watanabe K, Miyano S, Yuji K Does twitter trigger bursts in signature collections? PLoS One. 2013;8(3):e58252. doi: 10.1371/journal.pone.0058252. Epub 2013 Mar 6 pubmed
Yamamoto M, Yamaguchi R, Munakata K, Takashima K, Nishiyama M, Hioki K, Ohnishi Y, Nagasaki M, Imoto S, Miyano S, Ishige A, Watanabe K BMC Genomics. 2012 Jul 23;13:335. doi: 10.1186/1471-2164-13-335 A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. pubmed
Yuji K, Imoto S, Yamaguchi R, Matsumura T, Murashige N, Kodama Y, Minayo S, Imai K, Kami M Forecasting Japan's physician shortage in 2035 as the first full-fledged aged society PLoS One. 2012;7(11):e50410. doi: 10.1371/journal.pone.0050410. Epub 2012 Nov 30. pubmed
Sato N, Moriyama T, Toyoshima M, Mizusawa M, Tajima N The all0458/lti46.2 gene encodes a low temperature-induced Dps protein homologue in the cyanobacteria Anabaena sp. PCC 7120 and Anabaena variabilis M3 Microbiology. 2012 Oct;158(Pt 10):2527-36. Epub 2012 Jul 26. pubmed
田島 直幸, 佐藤 修正, 丸山 史人, 黒川 顕, 太田 啓之, 田畑 哲之, 関根 康介, 森山 崇, 佐藤 直樹 単細胞紅藻チノリモ(Porphyridium purpureum)の葉緑体ゲノム解析 光合成研究22, 156-159, 2013
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. 2012 Mar 20;109(12):4615-20. doi: 10.1073/pnas.1114728109. Epub 2012 Mar 5. pubmed
Abe R, Caaveiro JM, Kozuka-Hata H, Oyama M, Tsumoto K Mapping ultra-weak protein-protein interactions between heme transporters of Staphylococcus aureus J Biol Chem. 2012 May 11;287(20):16477-87. doi: 10.1074/jbc.M112.346700. Epub 2012 Mar 14. pubmed
Oikawa T, Oyama M, Kozuka-Hata H, Uehara S, Udagawa N, Saya H, Matsuo K Tks5-dependent formation of circumferential podosomes/invadopodia mediates cell-cell fusion J Cell Biol. 2012 May 14;197(4):553-68. doi: 10.1083/jcb.201111116. pubmed
Narita K, Kozuka-Hata H, Nonami Y, Ao-Kondo H, Suzuki T, Nakamura H, Yamakawa K, Oyama M, Inoue T, Takeda S Proteomic analysis of multiple primary cilia reveals a novel mode of ciliary development in mammals Biol Open. 2012 Aug 15;1(8):815-25. doi: 10.1242/bio.20121081. Epub 2012 Jun 29. pubmed
Nilsson CL, Dillon R, Devakumar A, Shi SD, Greig M, Rogers JC, Krastins B, Rosenblatt M, Kilmer G, Major M, Kaboord BJ, Sarracino D, Rezai T, Prakash A, Lopez M, Ji Y, Priebe W, Lang FF, Colman H, Conrad CA Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1alpha signaling network: an initial study in GSC11 glioblastoma stem cells J Proteome Res. 2010 Jan;9(1):430-43. doi: 10.1021/pr9007927. pubmed
Kozuka-Hata H, Nasu-Nishimura Y, Koyama-Nasu R, Ao-Kondo H, Tsumoto K, Akiyama T, Oyama M Phosphoproteome of human glioblastoma initiating cells reveals novel signaling regulators encoded by the transcriptome PLoS One. 2012;7(8):e43398. doi: 10.1371/journal.pone.0043398. Epub 2012 Aug 17. pubmed
Shuo T, Koshikawa N, Hoshino D, Minegishi T, Ao-Kondo H, Oyama M, Sekiya S, Iwamoto S, Tanaka K, Seiki M Detection of the heterogeneous O-glycosylation profile of MT1-MMP expressed in cancer cells by a simple MALDI-MS method PLoS One. 2012;7(8):e43751. doi: 10.1371/journal.pone.0043751. Epub 2012 Aug 22. pubmed
Shibata Y, Oyama M, Kozuka-Hata H, Han X, Tanaka Y, Gohda J, Inoue J p47 negatively regulates IKK activation by inducing the lysosomal degradation of polyubiquitinated NEMO Nat Commun. 2012;3:1061. doi: 10.1038/ncomms2068. pubmed
Fujita T, Kozuka-Hata H, Ao-Kondo H, Kunieda T, Oyama M, Kubo T Proteomic analysis of the royal jelly and characterization of the functions of its derivation glands in the honeybee J Proteome Res. 2013 Jan 4;12(1):404-11. doi: 10.1021/pr300700e. Epub 2012 Nov 29. pubmed
Koyama-Nasu R, Takahashi R, Yanagida S, Nasu-Nishimura Y, Oyama M, Kozuka-Hata H, Haruta R, Manabe E, Hoshino-Okubo A, Omi H, Yanaihara N, Okamoto A, Tanaka T, Akiyama T PLoS One. 2013;8(1):e53710. doi: 10.1371/journal.pone.0053710. Epub 2013 Jan 10 The cancer stem cell marker CD133 interacts with plakoglobin and controls desmoglein-2 protein levels. pubmed
Hirano A, Yumimoto K, Tsunematsu R, Matsumoto M, Oyama M, Kozuka-Hata H, Nakagawa T, Lanjakornsiripan D, Nakayama KI, Fukada Y Cell. 2013 Feb 28;152(5):1106-18. doi: 10.1016/j.cell.2013.01.054 FBXL21 Regulates Oscillation of the Circadian Clock through Ubiquitination and Stabilization of Cryptochromes. pubmed
Kozuka-Hata H, Goto Y, Oyama M Phosphoproteomics-based characterization of cancer cell signaling networks In Oncogenomics and Cancer Proteomic Novel Approaches in Biomarkers Discovery and Therapeutic Targets in Cancer (ed. Elena Arechaga-Ocampo and Cesar Lopez-Camarillo), InTech, 2013
尾山 大明, 秦 裕子 高精度定量プロテオミクスによる翻訳後修飾シグナルの包括的動態解 実験医学 Vol.30, 681-685, 2012
Maehara K, Odawara J, Harada A, Yoshimi T, Nagao K, Obuse C, Akashi K, Tachibana T, Sakata T, Ohkawa Y A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples Nucleic Acids Res. 2013 Jan 7;41(1):54-62. doi: 10.1093/nar/gks1010. Epub 2012 Nov 3. pubmed
Kumamaru H, Ohkawa Y, Saiwai H, Yamada H, Kubota K, Kobayakawa K, Akashi K, Okano H, Iwamoto Y, Okada S Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells Nat Commun. 2012;3:1140. doi: 10.1038/ncomms2132. pubmed
Fujii Y, Shiota M, Ohkawa Y, Baba A, Wanibuchi H, Kinashi T, Kurosaki T, Baba Y Surf4 modulates STIM1-dependent calcium entry Biochem Biophys Res Commun. 2012 Jun 15;422(4):615-20. doi: 10.1016/j.bbrc.2012.05.037. Epub 2012 May 15. pubmed
Harada A, Okada S, Konno D, Odawara J, Yoshimi T, Yoshimura S, Kumamaru H, Saiwai H, Tsubota T, Kurumizaka H, Akashi K, Tachibana T, Imbalzano AN, Ohkawa Y Chd2 interacts with H3.3 to determine myogenic cell fate EMBO J. 2012 May 8;31(13):2994-3007. doi: 10.1038/emboj.2012.136. pubmed
Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure in samples of limited cell number Methods Mol Biol. 2012;798:531-42. doi: 10.1007/978-1-61779-343-1_32. pubmed
Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays Methods Mol Biol. 2012;798:517-30. doi: 10.1007/978-1-61779-343-1_31. pubmed
Kumamaru H, Saiwai H, Ohkawa Y, Yamada H, Iwamoto Y, Okada S Age-related differences in cellular and molecular profiles of inflammatory responses after spinal cord injury J Cell Physiol. 2012 Apr;227(4):1335-46. doi: 10.1002/jcp.22845. pubmed
中西 由紀子, 中村 博, 土井 淳 多様なマイクロアレイデータから推定された遺伝子間相互作用のデータベース;遺伝子ネットワークデータベース (GNDB) 第35回日本分子生物学会年会
Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I Chromosome painting in silico in a bacterial species reveals fine population structure Mol Biol Evol. 2013 Mar 16. [Epub ahead of print] pubmed
Yahara K, Kawai M, Furuta Y, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species Genome Biol Evol. 2012 Jan;4(5):628-40. doi: 10.1093/gbe/evs043. Epub 2012 Apr 25. pubmed
Araki R, Seno S, Takenaka Y, Matsuda H An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles Gene. 2013 Apr 10;518(1):17-25. doi: 10.1016/j.gene.2012.11.090. Epub 2012 Dec 21. pubmed
Tani H, Imamachi N, Salam KA, Mizutani R, Ijiri K, Irie T, Yada T, Suzuki Y, Akimitsu N Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability RNA Biol. 2012 Nov;9(11):1370-9. doi: 10.4161/rna.22360. Epub 2012 Oct 12. pubmed
秋光 信佳 ゲノムワイドなRNA分解測定 細胞工学別冊 次世代シークエンサー目的別アドバンストメソッド, 100-108, 2012
Furukawa Y, Koga R, Yasuda K, Nariai N. Acceleration of Quantum Chemistry and Chemical Similarity calculations on GPGPU architecture towards faster virtual screening 第3回CBI学会FMO研究会, 2012
Matsumae H, Hamada M, Fujie M, Niimura Y, Tanaka H, Kawashima T. A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis Gene. 2013 Apr 25;519(1):82-90. doi: 10.1016/j.gene.2013.01.042. Epub 2013 Feb 4. pubmed
Nakao S, Higuchi T Weight adjustment of the particle filter on distributed computing systems Proc. 15th International Conference on Information Fusion. 2012
Kusakabe R, Tani T, Nishitsuji K, Shindo M, Okamura K, Miyamoto Y, Nakai K, Suzuki Y, Kusakabe TG, Inoue K Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues Gene Expr Patterns. 2013 Jan-Feb;13(1-2):43-50. doi: 10.1016/j.gep.2012.11.001. Epub 2012 Nov 16pubmed
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
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