論　文（誌上発表：2014年）

  • Kazuhiro Sakamaki, Kouhei Shimizu, Hiroaki Iwata, Kenichiro Imai, Yutaka Satou, Noriko Funayama, Masami Nozaki, Mamiko Yajima, Osamu Nishimura, Mayura Higuchi, Kumiko Chiba, Michi Yoshimoto, Haruna Kimura, Andrew Y. Gracey, Takashi Shimizu, Kentaro Tomii, Osamu Goto, Koji Akasaka, Tatsuya Sawasaki and David J. Miller.: "The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution", Molecular and Biology Evolution, 2014 Sep 3. [Online Ahead of Print] headAbstract
  • Sheetlin SL, Park Y, Frith MC, Spouge JL.: “Frameshift alignment: statistics and post-genomic applications.", Bioinformatics, 2014 Aug 28. pii: btu576. [Epub ahead of print] headAbstract
  • Szu-Chin Fu, Kenichiro Imai, Tatsuya Sawasaki and Kentaro Tomii (2014): "ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites", PROTEOMICS, Volume 14, Issue 17-18, pages 2042–2046, September 2014. headAbstract
  • 富井健太郎: “進化情報を考慮した疾患関連SNPsの新しい同定法”, 実験医学, ,32(13):2112-3(2014).
  • Marumo, K., Nakada-Tsukui, K., Tomii, K., Nozaki, T.; "Ligand heterogeneity of the cysteine protease binding protein family in the parasitic protist Entamoeba histolytica.", International Journal for Parasitology, S0020-7519(14)pp. 120-129 (2014). headAbstract
  • Gotoh, O., Morita, M., Nelson, DR.; "Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment.", BMC Bioinformatics, 15pp. 189 (2014). headAbstract
  • 花岡悟一郎, 大畑幸矢, 松田隆宏, 縫田光司, Nuttapong Attrapadung; "モジュール化に基づく高機能暗号の設計　〜実社会への高機能暗号の導入における障壁の低減に向けて〜.", シンセシオロジー, 7(2) pp. 93-104 (2014). headAbstract
  • Umemura, M., Nagano, N., Koike, H., Kawano, J., Ishii, T., Miyamura, Y., Kikuchi, M., Tamano, K., Yu, J., Shin-Ya, K., Machida, M.; "Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus.", Fungal Genetics and Biology, 6823-30 (2014). headAbstract
  • Hirano, A., Tanaka, T., Kataura, H., Kameda, T.; "Arginine Side Chains as a Dispersant for Individual Single-Wall Carbon Nanotubes.", Chemistry-A European Journal, 20(17) pp. 4922-4930 (2014). headAbstract
  • Hirano, A., Arakawa, T., Kameda, T.; "Interaction of Arginine with Capto MMC in Multimodal Chromatography.", Journal of Chromatography A, 1338 pp. 58-66 (2014). headAbstract
  • Ohmiya, H., Vitezic, M., Frith, MC., Itoh, M., Carninci, P., Forrest, ARR., Hayashizaki, Y., Lassmann, T., the FANTOM Consortium.; "RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).", BMC Genomics, 15pp. 269 (2014). headAbstract
  • Frith, MC., the FANTOM Consortium.; "Explaining the correlations among properties of mammalian promoters.", Nucleic Acids Research, 42(8) pp. 4823-4832 (2014). headAbstract
  • 富井健太郎:x "がんゲノムにおける変異の共通 性と特異性", 実験医学, 32(3):418-9(2014)
  • Shrestha, AM., Frith, MC., Horton, P.; "A bioinformatician’s guide to the forefront of suffix array construction algorithms.", Briefings in Bioinformatics (2014). headAbstract
  • Yamasaki, S., Hirokawa, T., Asai, K., Fukui, K.; "Tertiary structure prediction of RNA-RNA complexes using secondary structure and fragment based method.", Journal of Chemical Information and Modeling, 54(2) pp. 672-682 (2014). headAbstract
  • Soichiro Kitazawa, Tomoshi Kameda, Ayumi Kumo, Maho Yagi-Utsumi, Nicola J. Baxter, Koichi Kato, Mike P. Williamson and Ryo Kitahara: "Close Identity between Alternatively Folded State N2 of Ubiquitin and the Conformation of the Protein Bound to the Ubiquitin-Activating Enzyme", Biochemistry 53 (3):447-449(2014)
  • Toda E, Terashima Y, Esaki K, Yoshinaga S, Sugihara M, Kofuku Y, Shimada I, Suwa M, Kanegasaki S, Terasawa H, Matsushima K.: "Identification of a binding element for the cytoplasmic regulator FROUNT in the membrane-proximal C-terminal region of chemokine receptors CCR2 and CCR5", Biochem J., 457(2):313-22. doi: 10.1042/BJ20130827 (2014)
  • Masayuki Sakurai, Hiroki Ueda, Takanori Yano, Shunpei Okada, Hideki Terajima, Toutai Mitsuyama, Atsushi oyoda, Asao Fujiyama, Hitomi Kawabata and Tsutomu Suzuki: ""4A biochemical landscape of A-to-I RNA editing in the human brain transcriptome", Genome Res., 3pp.522-534, doi: 10.1101/gr.162537.113 (2014).
  • Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi : "Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests", PLOS ONE, 9(1):e84623(2014)
  • Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh: "Tetrahedral Gray Code for Visualization of Genome Information", PLOS ONE, 9 (1):e86133(2014)
  • Horton P.: "Next-generation Bioinformatics: connecting bases to genes, networks and disease", Brief Bioinform, 15 (2): 137 (2014)
  • Nagano, N., Koike, H., Ishii, T., Kawano, J., Tamano, K., Yu, J., Shin-ya, K., Machida, M.; "The first ribosomal peptide synthase pathway in filamentous fungi.", Proceedings of ECFG12, CS6.5 (2014).
  • Takeda, I., Tamano, K., Yamane, N., Ishii T., Miura, A. Umemura, M., Terai, G., Baker, SE., Koike, H., Machida, M.; "Genome Sequence of the Mucoromycotina Fungus Umbelopsis isabellina, an Effective Producer of Lipids.", Genome announcements, 2(1) e00071-14 (2014). headAbstract
  • Seko, A., Maekawa, T., Tsuda, K., Tanaka, I.; "Machine learning with systematic density-functional theory calculations: Application to melting temperatures of single- and binary-component solids.", Physical Review B, 89pp. 54303 (2014). headAbstract
  • Itsuki, A., Aburatani, S.; "Comparative Analysis of Enzyme Activities Concerned in Decomposition of Toluene.", Proceeding of World Academy of Science, Engineering and Technology , 86pp. 126-129 (2014).
  • S Aburatani and H Toh: "Network inference of AP pattern formation system in D. melanogaster by structural equation modeling", J. Phys.: Conf. Ser. 490 012145 doi:10.1088/1742-6596/490/1/012145 (2014)
  • Inoue, T., Takano, K., Watanabe, T., Kawahara, J., Yoshinaka, R., Kishimoto, A., Tsuda, K., Minato, S.-I., Hayashi, Y.: "Distribution Loss Minimization With Guaranteed Error Bound", IEEE Transactions on Smart Grid 5(1):102 - 111(2014)
  • Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y.: "Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3)", Biochim Biophys Acta., 1844 (3):585-92(2014).
  • Yoshinori Fukasawa, Ross KK Leung, Stephen KW Tsui & Paul Horton,:"Plus ca change − evolutionary sequence divergence predicts protein subcellular localization signals", BMC Genomics, 15:46, doi:10.1186/1471-2164-15-46, (2014). headAbstract
  • Anish Man Singh Shrestha, Martin C. Frith & Paul Horton,:"A Bioinformatician's Guide to the Forefront of Suffix Array Construction Algorithms", Briefings in Bioinformatics, Jan 10, 2014. [Epub ahead of print](2014). headFull Text
  • Yutaka Saito, Junko Tsuji, Toutai Mituyama,:"Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions", Nucl. Acids Res., doi: 10.1093/nar/gkt1373, (2014). headAbstract
  • Kazunori Yamada and Kentaro Tomii:"Revisiting amino acid substitution matrices for identifying distantly related proteins.", Bioinformatics, 30 (3): pp.317-325.(2014). headAbstract
  • Martin C. Frith and Laurent Noe,:"Improved search heuristics nd 20,000 new alignments between human and mouse genomes", Nucl. Acids Res., doi: 10.1093/nar/gku104, (2014). headAbstract
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