Research Keywords 【 display / non-display

  • Computational Bilogy, Bioinformatics, Biophysics, Molecular Evolution, protein-DNA/RNA interactions

Research Pursuits 【 display / non-display

  • Our laboratory studies the following themes making good use of both calculation ability of a computer owned in the laboratory as well as the infinite spirit and imagination of the students and teachers. The theme group is composed of two axes. The first axis has its base on the biological questions, and it aims to solve the mystery by applying the existing methods. In the case that the existing methods do not fit, we might develop new methods by ourselves. Another axis has its base on the technical questions and aims drastic improvement of the existing computational biology’s methods as well as development of new methods. In fact, single themes have both aspects, but they tend to have a main axis out of two. Each researcher’s preference determines which axis they focus on. Professor has his base on the biological questions and sometimes develops new technologies, if necessary.

Educational Pursuits 【 display / non-display

  • For the education of computational Biology, The following lectures are delivered. Introduction to Bioinformatics, Computational Biology, Biostatistics, Molecular Structural Biology, Bioinformatics Programing, Advanced Computational Biology, Practice for Computational Biology, Advanced Information Science for Biology, Practice for Information Science for Biology, Predictive Biology, Academic Presentation in English, Career Development, Biophysics.

Academic 【 display / non-display

  • Waseda University, Department of Science and Engineering, Applied Physics, University, 1988/03, Graduated, JAPAN

  • Waseda University Graduate School, School of Science and Engineering, Physics and Applied Physics, Graduate School(Master's Course), 1990/03, Completed, JAPAN

  • Nagoya University Graduate School, Faculty of Science, Department of Biology, Graduate School(Doctor's Course), 1993/03, Accomplished credits for doctoral program, JAPAN

Degree 【 display / non-display

  • PhD in Science, 1999/03

Campus Career 【 display / non-display

  • Graduate School of Humanities and Sciences, Research Organization, the Core Section The Natural/Applied Sciences Division, Professor

  • Faculty of Core Research Natural Science Division, Professor

  • Graduate School of Humanities and Sciences, Education Organization, Doctral Program Life Sciences, Professor

  • Graduate School of Humanities and Sciences, Education Organization, Doctral Program Life Sciences, Professor

  • Graduate School of Humanities and Sciences, Education Organization, Master's Program Life Sciences, Professor

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External Career 【 display / non-display

  • , Research Associate, 1993.04 - 1996.03

  • , Research Associate, 1996.04 - 2001.12

  • National Institute of Genetics, Project Professor, 2013.10 - 2017.03

  • Waseda University School of Advanced Science and Engineering, Professor, 2017.04 -

Research Field 【 display / non-display

 

Books 【 display / non-display

  • Prediction of Protein Structures, Functions, and Interactions

    Prediction of molecular interactions from 3D-structures: from small ligands to large protein complexes, Wiley and Sons, 2008.12, Kinoshita, K., Kono, H., Yura, K., Bujnicki, J.M., Textbook, 159-186

  • Proceedings of the International Symposium on Frontiers of Computational Science 2005 (ISFCS2005)

    Contribution of computational biology and structural genomics to understand genome and transcriptome, Springer, 2007.04, Go, M., Yura, K., Shionyu, M., Kaneda, Y., Kawamura, H., Sasai, M., Book, 75-80

  • 生物物理学ハンドブック

    ドメイン,モチーフ,モジュール, 朝倉書店, 2007.04, 由良 敬, 石渡信一、桂 勲、桐野 豊、美宅成樹, Dictionary, 51-53

  • 食品の科学

    ビタミン、ミネラルのかたち, 東京化学同人, 2005.03, 由良 敬, 上野川 修一、田之倉 優, Research Book, 87-95

  • パリティ 2013年6月号

    Intrinsically disordered proteins, Physics Today 68(8), Maruzen, American Institute of Physics, 2013.06, 2012, Kei Yura, Peter Tompa, Kyou-Hoon Han, Research Book, 45-47

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Papers 【 display / non-display

  • Characteristics and prediction of RNA editing sites in transcripts of the moss Takakia lepidozioides chloroplast

    DNA Research, vol.15(5)(p.309 - 321), 2008.12, Yura, K., Miyata, Y., Arikawa, T., Higuchi, M., Sugita, M., Original, Research paper (scientific journal), Capital Author

  • Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal mode analysis

    Biophysical Journal, vol.95(6)(p.2895 - 2908), 2008.09, Matsumoto, A., Kamata, T., Takagi, J., Iwasaki, K., Yura, K., Original, Research paper (scientific journal), Coauthor

  • Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue

    Biophysical Journal, vol.94(6)(p.2194 - 2203), 2008.03, Miyazawa, Y., Nishioka, H., Yura, K., Yamato, T., Original, Research paper (scientific journal), Coauthor

  • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

    Nucleic Acids Research, vol.36(DataBase Issue)(p.D793 - D799), 2008.01, Genome Information Integration Project and H-Invitational 2 consortium, Original, Research paper (scientific journal), Coauthor

  • coliSNP database server mapping nsSNPs on protein structures

    Nucleic Acids Research, vol.36(DataBase Issue)(p.D409 - D413), 2008.01, Kono, H., Yuasa, T., Nishiue, S., Yura, K., Original, Research paper (scientific journal), Coauthor

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Presentations 【 display / non-display

  • プリン生合成系の成り立ち—全酵素の俯瞰的な構造比較から—

    塩生 真史、郷 通子、由良 敬 , Domestic, 2016.12, 第39 回日本分子生物学会年会, Yokohama, 日本分子生物学会, Invited, Main Speaker

  • タンパク質複合体界面における「からまった」構造は何を意味するのか?

    YURA Kei, NAKAGAWA Mariko, HAYWARD Steven, Domestic, 2016.09, 日本生化学会大会, Sendai, 日本生化学会, Invited, Main Speaker

  • ラン藻プロテオームの立体構造は どこまでわかったか?

    IWASAKI Ai, YURA Kei, Domestic, 2016.06, ラン藻ゲノム交流会2016, 東京大学駒場キャンパス、東京, ラン藻ゲノム交流会, Invited, Main Speaker

  • 配列から機能まで、統合解析のためのVapRoS

    由良 敬, Domestic, 2016.03, 日本農芸化学会2016年度大会, 札幌, 日本農芸化学会, Invited, Main Speaker

  • Improvement in the prediction of RNA interface in RNA-binding protein

    YURA Kei, Domestic, 2015.09, The 53rd Annual Meeting of the Biophysical Society of Japan, Kanazawa University, Kanazawa, Japan, the Biophysical Society of Japan, Invited, Main Speaker

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Prize for Research Activities 【 display / non-display

  • BIOPHYSICS論文賞

    Shoichi Metsugi, “Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile” BIOPHYSICS vol. 1, pp.33-43 (2005), 2013.10, Domestic