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2017 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 InstitutionTokyo Institute of Technology

Principal Investigator

小谷野 仁  東京工業大学, 生命理工学院, 特任助教 (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  松江工業高等専門学校, その他部局等, 准教授 (40402929)
Project Period (FY) 2016-07-19 – 2019-03-31
Keywords微生物の群集 / ダイナミクス / 推定 / 予測 / 制御 / 文字列の位相半群 / 環境再生
Outline of Annual Research Achievements

研究プロジェクトの 2 年目である昨年度は、理論モデルの構築と第 1 段階の数値解析を行った。これらの研究成果の一部は、既に論文 Hayashida, M., Kamada, M., and Koyano, H., Improving conditional random field model for prediction of protein-RNA Residue-base contacts, Quantitative Biology, to appear と Mihara, T., Koyano, H., Hingamp, P., Grimsley, N., Goto, S., and Ogata, H., Taxon richness of ``Megaviridae'' exceeds those of Bacteria and Archaea in the ocean, Microbes and Environments, to appear にまとめて発表し、国際会議において、発表 Hayashida, M., Koyano, H., and Akutsu, T., Grammar-based compression for directed and undirected generalized series-parallel graphs using integer linear programming, Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies, Volume 4: Bioinformatics, 105-111, 2018 を行った。また、論文 Koyano, H., Hayashida, M., and Akutsu, T., Optimal string clustering based on a Laplacelike mixture and EM algorithm on a set of strings, arXiv:1411.6471 [math.ST] を、学術誌からの査読報告に基づいて現在改訂している。更に、論文 Koyano, H. and Yano, K., Evolutionary model of a population of DNA sequences through the interaction with an environment and its application to speciation analysis, arXiv:1706.01182 [q-bio.PE] をプレプリントとして公開した。現在、微生物群集から抽出された配列の環境標本を用いて、構築してきた理論モデルの実証研究と解析方法の応用研究に取り組んでいる。この後、微生物群集のダイナミクスの制御理論の構築とソフトウェアへの実装を行う。

Current Status of Research Progress
Current Status of Research Progress

3: Progress in research has been slightly delayed.

Reason

昨年度は、一昨年度に続き、2 年連続で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

現在の研究室は研究に多くの時間を使えるため、今年度に遅れを取り戻したい。

Causes of Carryover

(理由)学術誌に投稿していた原稿が昨年度内に受理に至らず、その掲載費として計上していた予算を執行出来なかったため。また、研究成果の発表を目指して応募していた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出来なかったため。

(使用計画)今年度に論文の出版費と国際会議において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

    (44 results)

All 2018 2017

All Journal Article (21 results) (of which Int'l Joint Research: 13 results,  Peer Reviewed: 19 results) Presentation (23 results) (of which Int'l Joint Research: 12 results)

  • [Journal Article] Taxon richness of ``Megaviridae'' exceeds those of Bacteria and Archaea in the ocean2018

    • Author(s)
      Mihara, T., Koyano, H., Hingamp, P., Grimsley, N., Goto, S., and Ogata, H.
    • Journal Title

      Microbes and Environments

      Volume: 33(2) Pages: 162-171

    • DOI

      10.1264/jsme2.ME17203

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Determining the minimum number of protein-protein interactions required to support known protein complexes2018

    • Author(s)
      Nakajima, N., Hayashida, M., Jansson, J., Maruyama, O., and Akutsu, T.
    • Journal Title

      PLoS ONE

      Volume: 13(4) Pages: e0195545

    • DOI

      10.1371/journal.pone.0195545

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Improving prediction of heterodimeric protein complexes using combination with pairwise kernel2018

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

      BMC Bioinformatics

      Volume: 19(1) Pages: 39

    • DOI

      10.1186/s12859-018-2017-5

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] On optimal periodic dividend strategies for Levy risk processes2018

    • Author(s)
      Noba, K., Perez, J.-L., Yamazaki, K., and Yano, K.
    • Journal Title

      Insurance: Mathematics and Economics

      Volume: 80 Pages: 29-44

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice2018

    • Author(s)
      Nishiyama, H., Nagai, T., Kudo, M., Okazaki, Y., Azuma, Y., Watanabe, T., Susumu, G., Ogata, H., and Sakurai, T.
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 495 Pages: 273-279

    • DOI

      10.1016/j.bbrc.2017.10.130

    • Peer Reviewed
  • [Journal Article] Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes2018

    • Author(s)
      Yoshikawa, G., Askora, A., Blanc-Mathieu, R., Kawasaki, T., Li, Y., Nakano, M., Ogata, H., and Yamada, T.
    • Journal Title

      Scientific Report

      Volume: 8 Pages: 4486

    • DOI

      10.1038/s41598-018-22239-3

  • [Journal Article] Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan2018

    • Author(s)
      Yoshida, T., Nishimura, Y., Watai, H., Haruki, N., Morimoto, D., Kaneko, H., Honda, T., Yamamoto, K., Hingamp, P., Sako, Y., Goto, S., and Ogata, H.
    • Journal Title

      ISME Journal

      Volume: 12 Pages: 1287-1295

    • DOI

      10.1038/s41396-018-0052-x

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Improving conditional random field model for prediction of protein-RNA Residue-base contacts2018

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

      Quantitative Biology

      Volume: 印刷中 Pages: 印刷中

    • Peer Reviewed
  • [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

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Local time penalizations with various clocks for one-dimensional diffusions2018

    • Author(s)
      Profeta, C., Yano., K., and Yano, Y.
    • Journal Title

      Journal of the Mathematical Society of Japan

      Volume: 印刷中 Pages: 印刷中

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A global ocean atlas of eukaryotic genes2018

    • Author(s)
      Carradec, Q., Pelletier, E., Da Silva, C., Ogata, H., et al.
    • Journal Title

      Nature Communications

      Volume: 9 Pages: 373

    • 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] Online regression algorithm with nonlinear transformation and its application to prediction of protein-protein interaction strengths2017

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

      IPSJ SIG Technical Report

      Volume: 2017-MPS-114 Pages: 1-4

  • [Journal Article] SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems2017

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

      Scientific Reports

      Volume: 7 Pages: 41031

    • Peer Reviewed / Int'l Joint Research
  • [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] Replications of two closely related groups of jumbo phages show different level of dependence on host-encoded RNA polymerase2017

    • Author(s)
      Matsui, T., Yoshikawa, G., Mihara, T., Chatchawankanphanich, O., Kawasaki, T., Nakano, M., Fujie, M., Ogata, H., and Yamada, T.
    • Journal Title

      Frontiers in Microbiology

      Volume: 8 Pages: 1010

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition2017

    • Author(s)
      Alberti, A., Poulain, J., Engelen, S., Ogata, H., et al.
    • Journal Title

      Scientific Data

      Volume: 4 Pages: 170093

    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Grammar-based compression for directed and undirected generalized series-parallel graphs using integer linear programming2018

    • Author(s)
      Hayashida, M., Koyano, H., and Akutsu, T.
    • Organizer
      9th International Conference on Bioinformatics Models, Methods and Algorithms
    • Int'l Joint Research
  • [Presentation] DNA 配列の集団の時間発展を記述する偏微分方程式とその種分化の分 析への応用2018

    • Author(s)
      小谷野仁
    • Organizer
      情報処理学会第 80 回全国大会
  • [Presentation] ncRNA-disease association prediction based on sequence information and tripartite network2018

    • Author(s)
      Mori, T., Ngouv, H., Hayashida, M., Akutsu, T., and Nacher, J.
    • Organizer
      16th Asia Pacific Bioinformatics Conference
    • Int'l Joint Research
  • [Presentation] Improving prediction of heterodimeric protein complexes using combination with pairwise kernel2018

    • Author(s)
      Ruan, P., Hayashida, M., Akutsu, T., and Vert, J.-P.
    • Organizer
      28th International Conference on Genome Informatics
    • Int'l Joint Research
  • [Presentation] Actors of the biological pump: are viruses involved in the process?2018

    • Author(s)
      Blanc-Mathieu, R., 遠藤寿, 緒方博之
    • Organizer
      第12回日本ゲノム微生物学会年会
  • [Presentation] Network analysis reveals the relationship between eukaryotic viruses and the biological carbon pump2018

    • Author(s)
      Velazquez, R. H., Blanc-Mathieu, R., 遠藤寿, 緒方博之
    • Organizer
      第12回日本ゲノム微生物学会年会
  • [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
      2017 13th Workshop on Stochastic Models, Statistics and Their Applications
    • Int'l Joint Research
  • [Presentation] Predicting strengths of protein-protein interactions through online regression algorithms2017

    • Author(s)
      Hayashida, M., Kamada, M., and Koyano, H.
    • Organizer
      2017 International Conference on Parallel and Distributed Processing Techniques and Applications
    • Int'l Joint Research
  • [Presentation] Improving conditional random field model for prediction of protein-RNA Residue-base contacts2017

    • Author(s)
      Hayashida, M., Okada, M., Kamada, M., and Koyano, H.
    • Organizer
      11th International Conference on Computational Systems Biology
    • Int'l Joint Research
  • [Presentation] Biodiversity of marine plankton revealed by Tara Oceans’ eco-systems approach2017

    • Author(s)
      Ogata, H.
    • Organizer
      Tara Coral Conference
    • Int'l Joint Research
  • [Presentation] Towards unveiling pivotal roles of viruses in marine ecosystems2017

    • Author(s)
      Ogata, H., Blanc-Mathieu, R., Hingamp, P., Nishimura, Y., Li, Y., and Yoshida, T.
    • Organizer
      73rd Fujihara Seminar, International Conference “Molecular Life of Diatoms”
    • Int'l Joint Research
  • [Presentation] Comparison of giant virus diversity across ecosystem2017

    • Author(s)
      Li, Y., Hingamp, P., Watai, H., Blanc-Mathieu, R., Yoshida, T., and Ogata, H.
    • Organizer
      17th International Workshop on Bioinformatics and Systems Biology
    • Int'l Joint Research
  • [Presentation] マルチオミクス解析が明らかにする海洋ウイルスの多様性と存在意義2017

    • Author(s)
      緒方博之, Blanc-Mathieu, R., Hingamp, P., 西村陽介, 李岩沢, 吉田天士
    • Organizer
      日本進化学会第19回大会
  • [Presentation] Characterizing the diversity of Megaviridae2017

    • Author(s)
      Li, Y., Hingamp, P., Watai, H., Blanc-Mathieu, R., Yoshida, T., and Ogata, H.
    • Organizer
      2017年度日本微生物生態学会環境ウイルス研究部会
  • [Presentation] ウイルス分類体系のゲノム類似性指標による評価2017

    • Author(s)
      黒西愛, Blanc-Mathieu, R., 五斗進, 緒方博之
    • Organizer
      2017年度日本微生物生態学会環境ウイルス研究部会
  • [Presentation] カンキツかいよう病菌に感染するファージ XacN1 のゲノム解析2017

    • Author(s)
      吉川元貴, Blanc-Mathieu, R., 緒方博之, 山田隆
    • Organizer
      2017年度日本微生物生態学会環境ウイルス研究部会
  • [Presentation] 巨大ウイルス群 NCLDV に属する新規ウイルス OV のゲノム解析2017

    • Author(s)
      吉川元貴, Blanc-Mathieu, R., 望月智弘, Song C., 村田和義, 緒方博之, 武村政春
    • Organizer
      環境微生物系学会合同大会2017
  • [Presentation] 温泉の底質泥から分離した新規巨大ウイルスについて2017

    • Author(s)
      武村政春, Song, C., 望月智弘, 吉川元貴, Blanc-Mathieu, R., 緒方博之, 村田和義
    • Organizer
      環境微生物系学会合同大会2017
  • [Presentation] 何故に今頃ネオウイルス学?2017

    • Author(s)
      緒方博之
    • Organizer
      環境微生物系学会合同大会2017
  • [Presentation] Multi-omics approach to assess viral impact on marine plankton2017

    • Author(s)
      Ogata, H.
    • Organizer
      KAUST Global Ocean Genome Workshop
    • Int'l Joint Research
  • [Presentation] Diversity and biogeography of marine giruses and their association with the biological carbon pump2017

    • Author(s)
      Blanc-Mathieu, R., Li, Y., Kaneko, H., Endo, H., and Ogata, H.
    • Organizer
      3rd Ringberg Symposium on Giant Virus Biology
    • Int'l Joint Research
  • [Presentation] Diversity and ecological role of giant viruses in the sunlit ocean2017

    • Author(s)
      Blanc-Mathieu, R., Kaneko, H., Yoshikawa, G., and Ogata, H.
    • Organizer
      ConBio2017, The Dawn of Giant Virus Biology
    • Int'l Joint Research
  • [Presentation] 海洋ウイルス:どこから来て、何をしているのか?2017

    • Author(s)
      緒方博之
    • Organizer
      第33回国際生物学賞記念シンポジウム

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Published: 2018-12-17  

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