論　文（誌上発表：2013年）

  • Umemura, M., Koike, H., Nagano, N., Ishii, T., Kawano, J., Yamane, N., Kozone I., Horimoto, K., Shin-ya, K., Asai, K., Yu, J., Bennett, JW., Machida, M.; "MIDDAS-M: Motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data.", PLoS ONE, 8(12) e84028 (2013).
  • Umemura, M., Koike, H., Kawano, J., Ishii, T., Miyamura, Y., Ikegami, T., Terai, G., Kumagai, T., Takeda, I., Tamano, K., Horimoto, K., Yu, J., Asai, K., Machida, M.; "Genomic platform for efficient identification of fungal secondary metabolism genes.", Proceeding of Asian Mycological Congress 2013, S3pp. 34-35 (2013).
  • Konstantin Tretyakov, Tatyana Goldberg, Victor X Jin and Paul Horton.: "Summary of talks and papers at ISCB-Asia/SCCG 2012",BMC Genomics 14 (2), (2013).
  • Minoru Sugihara and Ana-Nicoleta Bondar.: "Influence of the Retinal Methyl Groups on Retinal Structure and Dynamics", Current Physical Chemistry 3(2): 211-218 (2013)
  • Yokobori T, Iinuma H, Shimamura T, Imoto S, Sugimachi K, Ishii H, Iwatsuki M, Ota D, Ohkuma M, Iwaya T, Nishida N, Kogo R, Sudo T, Tanaka F, Shibata K, Toh H, Sato T, Barnard GF, Fukagawa T, Yamamoto S, Nakanishi H, Sasaki S, Miyano S, Watanabe T, Kuwano H, Mimori K, Pantel K, Mori M.: "Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis.", Cancer Res.73(7):2059 -69. doi: 10.1158/0008-5472.CAN-12-0326.(2013)
  • Jean-Francois Pessiot, Pui Shan Wong, Toru Maruyama, Ryoko Morioka, Sachiyo Aburatani, Michihiro Tanaka, Wataru Fujibuchi.: "The impact of collapsing data on microarray analysis and DILI prediction", Systems Biomedicine, pp137 - 143(2013)
  • Atsushi Hirano, Tomoshi Kameda, Daisuke Shinozaki, Tsutomu Arakawa and Kentaro Shiraki.: "Molecular Dynamics Simulation of the Arginine-Assisted Solubilization of Caffeic Acid: Intervention in the Interaction", J. Phys. Chem. B, 117 (25):7518?7527(2013)
  • Hirose S, Noguchi T.: "ESPRESSO: a system for estimating protein expression and solubility in protein expression systems", Proteomics. 13(9):1444-56(2013).
  • Sachiyo Aburatani, Wataru Fujibuchi, Junko Yamane, Satoshi Imanishi, Reiko Nagano, Hideko Sone, Seiichiroh Ohsako.: "Inference of Gene Regulatory Networks to Detect Toxicity-Specific Effects in Human Embryonic Stem Cells", International Journal On Advances in Life Sciences, (1) and(2):103-14 (2013).
  • 富井健太郎: "大規模ヒトゲノムデータから探 る自然選択の痕跡", 実験医学, 31(11):1750-1(2013)
  • Kawamura S, Unno Y, Tanaka M, Sasaki T, Yamano A, Hirokawa T, Kameda T, Asai A, Arisawa M, Shuto S.: "Investigation of the noncovalent binding mode of covalent proteasome inhibitors around the transition state by combined use of cyclopropylic strain-based conformational restriction and computational modeling", J Med Chem., 56(14):5829-42(2013).
  • Kuraku S, Zmasek CM, Nishimura O, Katoh K.: "aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity", Nucleic Acids Res. 4, W22-28(2013).
  • Hiroto SAIGO, Hisashi KASHIMA, Koji TSUDA.: "Fast Iterative Mining Using Sparsity-Inducing Loss Functions", IEICE TRANSACTIONS on Information and Systems E96-D(8):1766-1773(2013)
  • Chuan Xiao, Jianbin Qin, Wei Wang, Yoshiharu Ishikawa, Koji Tsuda, Kunihiko Sadakane.: "Efficient error-tolerant query autocompletion", Proceedings of the VLDB Endowment, 6(6): 373-384 (2013)
  • Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda and Jun Sese.: "Statistical significance of combinatorial regulations", PNAS, 110(32): 12996-13001(2013)
  • Iwakiri J, Kameda T, Asai K, Hamada M.: "Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions", Bioinformatics, 29(20):2524-8(2013)
  • Duverle DA, Takeuchi I, Murakami-Tonami Y, Kadomatsu K, Tsuda K.: "Discovering combinatorial interactions in survival data", Bioinformatics, 29(23):3053-9(2013).
  • Chun Fang, Tamotsu Noguchi, Daisuke Tominaga and Hayato Yamana.: "MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation", BMC Bioinformatics, 14pp.300(2013) Bioinformatics.29(8):965-72.(2013).
  • Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda and Jun Sese.: "Statistical significance of combinatorial regulations", Proc Natl Acad Sci., 110(32): 12996?13001(2013)
  • Teruyuki Ueda, Masao Honda, Katsuhisa Horimoto, Sachiyo Aburatani, Shigeru Saito, Taro Yamashita, Yoshio Sakai, Mikiko Nakamura, Hajime Takatori, Hajime Sunagozaka, Shuichi Kaneko.: "Gene expression profiling of hepatitis B- and hepatitis C-related hepatocellular carcinoma using graphical Gaussian modeling", Genomics, 101(4): 238?248 (2013)
  • Katoh K., Standley DM.,:"MAFFT multiple sequence alignment software version 7: improvements in performance and usability.", Mol Biol Evol. 30(4):772-80.(2013). headAbstract
  • Shrestha AM., Frith MC.,:"An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome.", Bioinformatics. 29(8):965-72.(2013). headAbstract
  • Wijaya E., Frith MC, Horton P., Asai K.,:"Finding protein-coding genes through human polymorphisms.", PLoS One. 8(1):e54210.(2013). headAbstract
  • Tsuzuki T., Sakaguchi N., Kudoh T., Takano S., Uehara M., Murayama T., Sakurai T., Hashii M., Higashida H., Weber K., Guse AH., Kameda T., Hirokawa T., Kumaki Y., Potter BV., Fukuda H., Arisawa M., Shuto S.,:"Design and Synthesis of Cyclic ADP-4-Thioribose as a Stable Equivalent of Cyclic ADP-Ribose, a Calcium Ion-Mobilizing Second Messenger.", Angew Chem Int Ed Engl. doi: 10.1002/anie.201302098.(2013). headAbstract
  • Kitazawa S., Kameda T., Yagi-Utsumi M., Sugase K., Baxter NJ., Kato K., Williamson MP., Kitahara R.,:"Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin.", Biochemistry; 52(11):1874-85. doi: 10.1021/bi301420m.(2013). headAbstract
  • Hitaoka Seiji, Shibata Yuto, Matoba Hiroshi, Kawano Akihiro, Harada Masataka, Rahman Motiur M, Daisuke Tsuji, Hirokawa Takatsugu, Kouji Itou, Tatsusada Yoshida and Hiroshi Chuman,:"Modeling of Human Neuraminidase-1 and Its Validation by LERE-Correlation Analysis", Chem-Bio Informatics Journal, Vol.13, pp.30-40(2013). headAbstract
  • Ueda T., Tominaga D., Araki N., Yoshikawa T.,:"Estimate hidden dynamic profiles of siRNA effect on apoptosis.", BMC Bioinformatics, 14:97. doi: 10.1186/1471-2105-14-97.(2013). headAbstract
  • Tsuyuzaki K., Tominaga D., Kwon Y., Miyazaki S.,:"Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset.", BMC Genomics 14 Suppl 2:S9. doi: 10.1186/1471-2164-14-S2-S9.(2013). headAbstract
  • Tamura Y., Harada Y., Nishikawa SI., Yamano K., Kamiya M., Shiota T., Kuroda T., Kuge O., Sesaki H., Imai K., Tomii K., Endo T.:"Tam41 Is a CDP-Diacylglycerol Synthase Required for Cardiolipin Biosynthesis in Mitochondria", Cell Metabolism, in press.(2013). headAbstract
  • Nishino T., Rago F., Hori T., Tomii K., Cheeseman IM., Fukagawa T.:"CENP-T provides a structural platform for outer kinetochore assembly.", The EMBO Journa, 6;32(3), pp.424-36.(2013). headAbstract
  • Kimura M., Kose S., Okumura N., Imai K., Furuta M., Sakiyama N., Tomii K., Horton P., Takao T., Imamoto N.:"Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics.", Mol Cell Proteomics.,12(1), pp145-57(2013). headAbstract
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