論文

• Sarel J. Fleishman, Timothy A. Whitehead, Eva-Maria Strauch, Jacob E. Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C. Mitchell, Omar N. A. Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jerome Aze, Seren Soner, Sefik Kerem Oval., Pemra Ozbek, Nir Ben Tal, Turkan Haliloglu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Perez-Cano, Carles Pons, Juan Fernandez-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H. Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Patapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita, Camden M. Driggers, Robert G. Hall, Jessica L. Morgan, Victor L. Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Weiyi Zhang, Carlos J. Camacho, Krishna P. Kilambi, Aroop Sircar, Jeffrey J. Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodriguez, Daisuke Kihara, P. Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J. Wodak, Joel Janin, David Baker. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology, Journal of Molecular Biology, ScienceDirect, Volume 414, Issue 2, pp. 289-302, Nov. 2011.  公式リンク  
  
• Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita. Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states, Proteins, Vol. 79, p. 1550-63, May 2011.
• Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita. ATTED-II provides coexpressed gene networks for Arabidopsis, Nucleic Acids Research, Vol. 37, DB issue, pp. D987-D991, Jan. 2009.
• Miho Higurashi, Takashi Ishida, Kengo. PiSite: a database of protein interaction sites using multiple binding states in the PDB., Nucleic Acid Research, Vol. 37, Page 360-364, 2009.
• Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita. Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials, Protein science, Vol. 18, Page 1906-15, 2009.
• Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita. COXPRESdb: a database of coexpressed gene networks in mammals, Nucleic Acids Research, Vol. 36, DB issue, pp. D77-D82, Jan. 2008.
• Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis, Nucleic Acids Research, Vol. 35, DB Issue, pp. D863-D869, Jan. 2007.

国際会議発表 (査読有り)

• Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita. Development of a New Meta-Score for Protein Structure Prediction from Seven All-Atom Distance Dependent Potentials Using Support Vector Regression, Genome Informatics, Vol. 23, pp. 149-158, Dec. 2009.  公式リンク  
  

国際会議発表 (査読なし・不明)

• Takashi Ishida, Kengo Kinoshita. Development of prediction servers for protein disorder, BIOINFO 2009 CBI-KSBSB Joint Conference, Proc. BIOINFO 2009 CBI-KSBSB Joint Conference, Nov. 2009.

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