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2016 Fiscal Year Research-status Report

文字列の非可換位相半群上の確率・統計理論とそれらの環境再生生物工学への応用

Research Project

Project/Area Number 16KT0020
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

小谷野 仁  国立研究開発法人理化学研究所, 生命システム研究センター, 研究員 (10570989)

Co-Investigator(Kenkyū-buntansha) 緒方 博之  京都大学, 化学研究所, 教授 (70291432)
矢野 孝次  京都大学, 理学研究科, 准教授 (80467646)
林田 守広  京都大学, 化学研究所, 助教 (40402929)
Project Period (FY) 2016-07-19 – 2019-03-31
Keywords文字列 / 確率論 / 統計学 / 計算生物学 / 環境再生
Outline of Annual Research Achievements

研究プロジェクトの初年度である昨年度は、まず、理論モデルの構築とそれを用いた数値解析で必要になる極限定理の整備とアルゴリズムの準備を行った。これらの研究の結果の一部は、既に Koyano, H., Hayashida, M., and Akutsu, T., Maximum margin classifier working in a set of strings, Proceedings of the Royal Society A, 472(2187), 2016、Hayashida, M. and Koyano, H., Integer linear programming approach to median and center strings for a probability distribution on a set of strings, Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, 3, 35-41, 2016 及び Hayashida, M. and Koyano, H., Finding median and center strings for a probability distribution on a set of strings under Levenshtein distance based on integer linear programming, Communications in Computer and Information Science, 690, to appear の論文にまとめて発表した。
次に、理論モデルの構築に着手した。モデルの定式化を終え、現在その性質を数学的に調べている。
更に、モデルに含まれるパラメーターの推定方法を開発する研究を行った。モデルの構築よりこの研究の方が先に終わり、論文にまとめて学術誌に投稿され、現在査読されているところである。arXiv では、プレプリント Koyano, H., Hayashida, M., and Akutsu, T., Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings, arXiv:1411.6471[math.ST] が既に公開されている。

Current Status of Research Progress
Current Status of Research Progress

3: Progress in research has been slightly delayed.

Reason

昨年度は勤務先の異動があり、それに多くの時間を取られてしまったことと、定式化した理論モデルの数学的な解析が、予想以上に多くの予備的な定理や方法の準備を必要としたため、研究の進行が当初の計画より少し遅れている。

Strategy for Future Research Activity

しかし、上の研究実績の概要の欄でも述べたように、今年度に行う予定であった研究のうち昨年度に実行できた部分もあるため、今年度は研究の環境を整備して、遅れを取り戻したい。

Causes of Carryover

学術誌に投稿していた原稿が昨年度中に受理に至らず、その掲載費として計上していた予算を執行できなかった。また、研究結果の発表を目指して応募した 1 月の国際会議において応募原稿が受理されず、その旅費として計上していた予算を執行できなかった。

Expenditure Plan for Carryover Budget

今年度に論文の出版費と国際会議で研究発表を行うための旅費として使用する予定である。

  • Research Products

    (30 results)

All 2018 2017 2016

All Journal Article (27 results) (of which Int'l Joint Research: 17 results,  Peer Reviewed: 23 results,  Open Access: 1 results) Presentation (3 results) (of which Int'l Joint Research: 3 results)

  • [Journal Article] Euler string-based compression of tree-structured data and its application to analysis of RNAs2018

    • Author(s)
      Liu, L., Mori, T., Zhao, Y., Hayashida, M., and Akutsu, T.
    • Journal Title

      Current Bioinformatics

      Volume: 13 Pages: 25–33

    • DOI

      10.2174/1574893611666160608102231

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Finding median and center strings for a probability distribution on a set of strings under Levenshtein distance based on integer linear programming2017

    • Author(s)
      Hayashida, M. and Koyano, H.
    • Journal Title

      Communications in Computer and Information Science

      Volume: 690 Pages: 108-121

    • Peer Reviewed
  • [Journal Article] Weak convergence of h-transforms for one-dimensional diffusions2017

    • Author(s)
      Yano, K., Yano, Y., and Yen, J.-Y.
    • Journal Title

      Statistics and Probability Letters

      Volume: 122 Pages: 152-156

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Type III polyketide synthases: functional classification and phylogenomics2017

    • Author(s)
      Shimizu, Y., Ogata, H., and Goto, S.
    • Journal Title

      ChemBioChem

      Volume: 18 Pages: 50-65

    • Peer Reviewed
  • [Journal Article] Environmental viral genomes shed new light on virus-host interactions in the ocean2017

    • Author(s)
      Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., Sullivan, M.B., Goto, S., Ogata, H., and Yoshida, T.
    • Journal Title

      mSphere

      Volume: 2 Pages: e00459-16

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Discriminating the reaction types of plant type III polyketide synthases2017

    • Author(s)
      Shimizu, Y., Ogata, H., and Goto, S.
    • Journal Title

      Bioinformatics

      Volume: 33 Pages: 1937-1943

    • Peer Reviewed
  • [Journal Article] ViPTree: the viral proteomic tree server2017

    • Author(s)
      Nishimura, Y., Yoshida, T., Kuronishi, M., Uehara, H., Ogata, H., and Goto, S.
    • Journal Title

      Bioinformatics

      Volume: 33 Pages: 2379-2380

    • Peer Reviewed
  • [Journal Article] Maximum margin classifier working in a set of strings2016

    • Author(s)
      Koyano, H., Hayashida, M., and Akutsu, T.
    • Journal Title

      Proceedings of the Royal Society A

      Volume: 472 Pages: 印刷中

    • DOI

      10.1098/rspa.2015.0551

    • Peer Reviewed
  • [Journal Article] Integer linear programming approach to median and center strings for a probability distribution on a set of strings2016

    • Author(s)
      Hayashida, M. and Koyano, H.
    • Journal Title

      Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies

      Volume: 3 Pages: 35-41

    • DOI

      10.5220/0005666400350041

    • Peer Reviewed
  • [Journal Article] Critical evaluation of in silico methods for prediction of coiled-coil regions in proteins2016

    • Author(s)
      Li, C., Chang, C. C. H., Porebski, B. T., Hayashida, M., Akutsu, T., Song, J., and Buckle, A. M.
    • Journal Title

      Briefings in Bioinformatics

      Volume: 17 Pages: 270-282

    • DOI

      https://doi.org/10.1093/bib/bbv047

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order2016

    • Author(s)
      Jindalertudomdee, J., Hayashida, M., Zhao, Y., and Akutsu, T.
    • Journal Title

      BMC Bioinformatics

      Volume: 17 Pages: 113

    • DOI

      10.1186/s12859-016-0962-4

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Enumeration method for structural isomers containing user-defined structures based on breadth-first search approach2016

    • Author(s)
      Jindalertudomdee, J., Hayashida, M., and Akutsu, T.
    • Journal Title

      Journal of Computational Biology

      Volume: 23 Pages: 625-640

    • DOI

      10.1089/cmb.2016.0056

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length2016

    • Author(s)
      Bao, Y., Hayashida, M., and Akutsu, T.
    • Journal Title

      BMC Bioinformatics

      Volume: 17 Pages: 487

    • DOI

      10.1186/s12859-016-1353-6

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems2016

    • Author(s)
      An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G., ithgow, T., and Song, J.
    • Journal Title

      Scientific Reports

      Volume: 7 Pages: 41031

    • DOI

      10.1038/srep41031

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 文字列の集合上の確率分布における中央文字列および中心文字列に対する整数計画問題2016

    • Author(s)
      林田守広、小谷野仁
    • Journal Title

      IPSJ SIG Technical Report

      Volume: 2016-MPS-108 Pages: 7

  • [Journal Article] Grammar-based compression for unrooted trees and subclass of plane graphs using integer linear programming2016

    • Author(s)
      Hayashida, M., Cao, Y., and Zhao, Y.
    • Journal Title

      IPSJ SIG Technical Report

      Volume: 2016-MPS-108 Pages: 11

  • [Journal Article] Improving accuracy for predicting heterodimeric protein complexes using combination kernels2016

    • Author(s)
      Ruan, P., Hayashida, M., Akutsu, T., and Vert, J.-P.
    • Journal Title

      IPSJ SIG Technical Report

      Volume: 2016-MPS-108 Pages: 12

  • [Journal Article] Complex network-based approaches to biomarker discovery2016

    • Author(s)
      Hayashida, M. and Akutsu, T.
    • Journal Title

      Biomarkers in Medicine

      Volume: 10 Pages: 621-632

    • DOI

      10.2217/bmm-2015-0047

  • [Journal Article] Benthic protists: the under-charted majority2016

    • Author(s)
      Forster, D., Dunthorn, M., Mahe, F., Dolan, J.R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R., Claverie, J.-M., Decelle, J., Edvardsen, B., Egge, E., Eikrem, W., Gobet, A., Kooistra, W.H.C.F., Logares, R., Massana, R., Montresor, M., Not, F., Ogata, H. et al.
    • Journal Title

      FEMS Microbiology Ecology

      Volume: 92 Pages: fiw129

    • DOI

      10.1093/femsec/fiw120

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A Ralstonia solanacearum phage phiRP15 is closely related to Viunalikeviruses and encodes 19 tRNA-related sequences2016

    • Author(s)
      Mihara, T., Nasr-Eldin, M.A., Chatchawankanphanich, O., Bhunchoth, A., Phironrit, N., Kawasaki, T., Nakano, M., Fujie, M., Ogata, H., and Yamada, T
    • Journal Title

      Virology Reports

      Volume: 6 Pages: 61-73

    • DOI

      https://doi.org/10.1016/j.virep.2016.07.001

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Two Asian jumbo phages, phiRSL2 and phiRSF1, infect Ralstonia solanacearum and show common features of phiKZ-related phages2016

    • Author(s)
      Bhunchoth, A., Blanc-Mathieu, R., Mihara, T., Nishimura, Y, Askora, A., Phironrit, N., Leksomboon, C., Chatchawankanphanich, O., Kawasaki, T., Nakano, M., Fujie, M., Ogata, H., and Yamada, Y.
    • Journal Title

      Virology

      Volume: 494 Pages: 56-66

    • DOI

      10.1016/j.virol.2016.03.028

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] DNA repair genes in the Megavirales pangenome2016

    • Author(s)
      Blanc-Mathieu, R. and Ogata, H.
    • Journal Title

      Current Opinion in Microbiology

      Volume: 31 Pages: 94-100

    • DOI

      10.1016/j.mib.2016.03.011

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Linking virus genomes with host taxonomy2016

    • Author(s)
      Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.
    • Journal Title

      Viruses

      Volume: 8 Pages: 66

    • DOI

      10.3390/v8030066

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Plankton networks driving carbon export in the oligotrophic ocean2016

    • Author(s)
      Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J., Ogata, H. et al.
    • Journal Title

      Nature

      Volume: 532 Pages: 465-70

    • DOI

      10.1038/nature16942

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages2016

    • Author(s)
      Lescot, M., Hingamp, P., Kojima, K.K., Villar, E., Romac, S., Veluchamy, A., Boccara, M., Jaillon, O., Iudicone, D., Bowler, C., Wincker, P., Claverie, J.-M., and Ogata, H
    • Journal Title

      ISME Journal

      Volume: 10 Pages: 1134-1146

    • DOI

      10.1038/ismej.2015.192

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Identification of a new oat beta-amylase by functional proteomics2016

    • Author(s)
      Ben Halima, N., Khemakhem, B., Fendri, I., Ogata, H., Baril, P., Pichon, C., and Abdelkafi, S.
    • Journal Title

      Biochimica et Biophysica Acta

      Volume: 10 Pages: 1134-1146

    • DOI

      10.1016/j.bbapap.2015.10.001

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses2016

    • Author(s)
      Roux, S., Brum, J.R., Dutilh, B.E., Sunagawa, S., Duhaime, M.B., Loy, A., Poulos, B.T., Solonenko, N., Lara, E., Poulain, J., Tara Oceans Coordinators including Ogata, H. et al.
    • Journal Title

      Nature

      Volume: 537 Pages: 689-693

    • DOI

      10.1038/nature19366

    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Optimal string clustering based on a statistical theory on a topological monoid of strings2017

    • Author(s)
      Koyano, H., Hayashida, M., and Akutsu, T.
    • Organizer
      13th Workshop on Stochastic Models, Statistics and Their Applications
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2017-02-24 – 2017-02-24
    • Int'l Joint Research
  • [Presentation] Host-pathogen protein interaction prediction based on local topology structures of a protein interaction network2016

    • Author(s)
      Jindalertudomdee, J., Hayashida, M., Song, J., and Akutsu. T.
    • Organizer
      IEEE 16th International Conference on Bioinformatics and BioEngineering
    • Place of Presentation
      Taichung, Taiwan
    • Year and Date
      2016-10-31 – 2016-10-31
    • Int'l Joint Research
  • [Presentation] Integer linear programming approach to median and center strings for a probability distribution on a set of strings2016

    • Author(s)
      Hayashida M. and Koyano, H.
    • Organizer
      15th European Conference on Computational Biology
    • Place of Presentation
      The Hague, Netherlands
    • Year and Date
      2016-09-03 – 2016-09-03
    • Int'l Joint Research

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Published: 2018-01-16  

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