Probability theory and statistics on a noncommutative topological monoid of strings and their application to bioremediation

2018 Fiscal Year Annual Research Report

• Project/Area Number: 16KT0020
• Research Institution: Tokyo 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, 電気情報工学科, 准教授 (40402929)
• Project Period (FY): 2016-07-19 – 2019-03-31
• Keywords: 文字列の位相半群 / 制御理論 / 確率・統計 / バイオインフォマティクス / 数理生物学

Outline of Annual Research Achievements

アルファベット A 上の文字列の非可換位相半群 A* には、これまで実数の集合 R 上の正規分布や自然数の集合 N 上の 2 項分布のようなパラメトリックな分布は導入されていなかった。Koyano, H., Hayashida, M., and Akutsu, T., arXiv:1411.6471 [math.ST] では、その混合モデルを用いて、ある環境中の DNA 配列の集団にその環境から掛かる淘汰圧の分布を表すよう設計された Laplace 様分布という確率分布を A* 上に導入し、その基本的な性質を調べることから始めて、その混合モデルのパラメーターを推定する方法を開発し、それに対して数理的基礎付けを与え、数値実験を行ってその有効性を確かめた。
また、上述の研究の結果と、拡散方程式をモチーフにして、A* 上で、1 つの環境中の生物群集が持つ DNA 配列の集団が、配列中に確率的に起こる突然変異と、周囲の環境から掛かる淘汰圧の下で時間発展していく様子、すなわち DNA 配列の集団の進化を記述する偏微分方程式を導出した Koyano, H. and Yano, K., arXiv:1406.0597 [q-bio.PE] の結果を組み合わせて、アブラナ科の植物の周辺環境中の微生物群集から収集された 16S リボソーム RNA 遺伝子配列の環境標本を用いたシミュレーション研究に取り組み、1 つの環境中の生物群集が持つ配列の集団のダイナミクスをコンピューターの中で徐々に再現できるようになってきた。
これらの研究の結果に基づき、現在、1 つの環境中の微生物群集のダイナミクスを、それが持つ配列の集団に掛かる淘汰圧を人工的に変化させることにより、集団が各時刻で（例えば、汚染物質の分解という点で）最適な組成を持つように制御する理論を構築する研究に取り組んでいる。

Research Products

• [Journal Article] Multiray generalization of the arcsine laws for occupation times of infinite ergodic transformations (2019)
  • Author(s): Sera, T. and Yano, K.
  • Journal Title: Transactions of the American Mathematical Society Volume: 印刷中 Pages: 印刷中
  • Peer Reviewed
• [Journal Article] Generalized refracted Levy process and its application to exit problem (2019)
  • Author(s): Noba, K. and Yano, K.
  • Journal Title: Stochastic Processes and their Applications Volume: 129(5) Pages: 1697-1725
  • Peer Reviewed
• [Journal Article] Local time penalizations with various clocks for one-dimensional diffusions (2019)
  • Author(s): Profeta, C., Yano, K., and Yano, Y.
  • Journal Title: Journal of the Mathematical Society of Japan Volume: 71(1) Pages: 203-233
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Medusavirus a novel large DNA virus discovered from hot spring water (2019)
  • Author(s): Yoshikawa G., Blanc-Mathieu R., Song C., Kayama Y., Mochizuki T., Murata K., Ogata H., and Takemura M.
  • Journal Title: Journal of Virology Volume: 93 Pages: e02130-18
  • DOI: 10.1128/JVI.02130-18
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Structural and phylogenetic diversity of anaerobic carbon-monoxide dehydrogenases (2019)
  • Author(s): Inoue, M., Nakamoto, I., Omae, K., Oguro, T., Ogata, H., Yoshida, T., and Sako, Y.
  • Journal Title: Frontiers in Microbiology Volume: 9 Pages: 3353
  • DOI: 10.3389/fmicb.2018.03353
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Community-level responses to iron availability in open ocean planktonic ecosystems (2019)
  • Author(s): Caputi, L., Carradec, Q., Eveillard, D., Kirilovsky, A., Pelletier, P. et al.
  • Journal Title: Global Biogeochemical Cycles Volume: 印刷中 Pages: 印刷中
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Minimum Information about Uncultivated Virus Genomes (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses (2019)
  • Author(s): Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M. et al.
  • Journal Title: Nature Biotechnology Volume: 37 Pages: 29–37
  • DOI: 10.1038/nbt.4306
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Taxon richness of ``Megaviridae'' exceeds those of Bacteria and Archaea in the ocean (2018)
  • 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] Analysis of critical and redundant vertices in controlling directed complex networks using feedback vertex sets. (2018)
  • Author(s): Bao, Y. , Hayashida, M. , Liu, P. , Ishitsuka, M. , Nacher, J. C., and Akutsu, T.
  • Journal Title: Journal of Computational Biology Volume: 25(10) Pages: 625-640
  • DOI: 10.1089/cmb.2018.0019
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Improving conditional random field model for prediction of protein-RNA residue-base contacts (2018)
  • Author(s): Hayashida, M., Okada, N., Kamada, M., and Koyano, H.
  • Journal Title: Quantitative Biology Volume: 6(2) Pages: 155-162
  • Peer Reviewed
• [Journal Article] Determining the minimum number of protein-protein interactions required to support known protein complexes (2018)
  • 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] ncRNA-disease association prediction based on sequence information and tripartite network (2018)
  • Author(s): Mori, T., Ngouv, H., Hayashida, M., Akutsu, T., and Nacher, J. C.
  • Journal Title: BMC Systems Biology Volume: 12(Suppl 1) Pages: 37
  • DOI: 10.1186/s12918-018-0527-4
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors (2018)
  • Author(s): Wang, J., Yang, B., Leier, A., Marquez-Lago, T. T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K.-C., Strugnell, R. A., Song, J., and Lithgow, T.
  • Journal Title: Bioinformatics Volume: 34(15) Pages: 2546–2555
  • DOI: 10.1093/bioinformatics/bty155
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Improving prediction of heterodimeric protein complexes using combination with pairwise kernel (2018)
  • 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] Euler string-based compression of tree-structured data and its application to analysis of RNAs (2018)
  • 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] On optimal periodic dividend and capital injection strategies for spectrally negative Levy models (2018)
  • Author(s): Noba, K., Perez, J.-L., Yamazaki, K., and Yano, K.
  • Journal Title: Journal of Applied Probability Volume: 55(4) Pages: 1272-1286
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] On optimal periodic dividend strategies for Levy risk processes (2018)
  • 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] Multiray generalization of the arcsine laws for occupation times of infinite ergodic transformations. Infinitely divisible processes and related topics (2018)
  • Author(s): Sera, T. and Yano, K.
  • Journal Title: The Institute of Statistical Mathematics Cooperative Research Report Volume: 402(22) Pages: 9-14
• [Journal Article] Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice (2018)
  • 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] Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans (2018)
  • Author(s): Seeleuthner, Y., Mondy, S., Lombard, V., Carradec, Q., Pelletier, E. et al.
  • Journal Title: Nature Communications Volume: 9 Pages: 310
  • DOI: 10.1038/s41467-017-02235-3
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Diatom diversity through HTS-metabarcoding in coastal European seas (2018)
  • Author(s): Piredda, R., Claverie, J.-M., Decelle, J., de Vargas, C., Dunthorn, M., Edvardsen, B., Eikrem, W., Forster, D., Kooistra, W. H. C. F., Logares, R., Massana, R., Montresor, M., Not, F., Ogata, H., Pawlowski, J., Romac, S., Sarno, D., Stoeck, T., and Zingone, A.
  • Journal Title: Scientific Report Volume: 8 Pages: 18059
  • DOI: 10.1038/s41598-018-36345-9
• [Journal Article] Degenerate PCR primers to reveal the diversity of giant viruses in coastal waters (2018)
  • Author(s): Li, Y., Hingamp, P., Watai, H., Endo, H., Yoshida, T., and Ogata, H.
  • Journal Title: Viruses Volume: 10 Pages: 496
  • DOI: 10.3390/v10090496
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean (2018)
  • Author(s): Endo, H., Ogata, H., and Suzuki, K.
  • Journal Title: Scientific Report Volume: 8 Pages: 10916
  • DOI: 10.1038/s41598-018-29039-9
  • Peer Reviewed
• [Journal Article] Habitat alterations by viruses: strategies by tupanviruses and others (2018)
  • Author(s): Ogata, H.
  • Journal Title: Microbes and Environments Volume: 33 Pages: 117-119
  • DOI: 10.1264/jsme2.ME3302rh
  • Peer Reviewed
• [Journal Article] MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes (2018)
  • Author(s): Arai, W., Taniguchi, T., Goto, S., Moriya, Y., Uehara, H., Takemoto, K., Ogata, H., and Takami, H.
  • Journal Title: Bioscience, Biotechnology, and Biochemistry Volume: 82 Pages: 1515-1517
  • DOI: 10.1080/09168451.2018.1476122
  • Peer Reviewed
• [Journal Article] Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes (2018)
  • 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 Japan (2018)
  • 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] A global ocean atlas of eukaryotic genes (2018)
  • Author(s): Carradec, Q., Pelletier, E., Da Silva, C., Alberti, A., Seeleuthner, Y. et al.
  • Journal Title: Nature Communications Volume: 9 Pages: 373
  • DOI: 10.1038/s41467-017-02342-1
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Artificial neural network approach to prediction of protein--RNA residue-base contacts (2019)
  • Author(s): Hayashida, M. and Koyano, H.
  • Organizer: The 12th International Joint Conference on Biomedical Engineering Systems and Technologies
  • Int'l Joint Research
• [Presentation] Classification of modes of indigenous food inventions and strategies for new food development (2019)
  • Author(s): Koyano, H., Yamamoto, N., Sawada, K., Yago, H., and Yamada, T.
  • Organizer: 2019 Food and Society International Coference
  • Int'l Joint Research
• [Presentation] Factors to modify traditional preserved foods (2019)
  • Author(s): Sawada, K., Yamamoto, N., Koyano, H., Yago, H., and Yamada, T.
  • Organizer: 2019 Food and Society International Coference
  • Int'l Joint Research
• [Presentation] 微生物群集のダイナミクスの数理モデリングと数値解析 (2019)
  • Author(s): 小谷野 仁, 澤田 和典, 山本 希, 山田 拓司
  • Organizer: 情報処理学会第 81 回全国大会
• [Presentation] ゲノム解析による Aspergilllus luchuensis 変異株の遺伝子変異の検出 (2019)
  • Author(s): 山本 希, 渡来 直生, 小谷野 仁, 澤田 和典, 山田 拓司
  • Organizer: 日本農芸化学会 2019 年度大会
• [Presentation] 地球規模海洋オミクスデータに基づく巨大ウイルスと生物炭素ポンプの関係の解明 (2019)
  • Author(s): 緒方 博之
  • Organizer: 第 2 回感染症診断と治療におけるゲノム解析
• [Presentation] 大規模観測とメタゲノム解析による海洋微生物の多様性研究 (2019)
  • Author(s): 遠藤 寿
  • Organizer: メタオミクスワークショップ in 京都 2019
• [Presentation] Global distribution of nucleocytoplasmic large DNA viruses in the ocean (2019)
  • Author(s): Endo, H., Li, Y., Blanc-Mathieu, R., and Ogata, H.
  • Organizer: ASLO 2019 Aquatic Sciences Meeting
  • Int'l Joint Research
• [Presentation] Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles (2018)
  • Author(s): Matsubara, T., Ochiai, T., Hayashida, M., Akutsu, T., and Nacher, J.
  • Organizer: The 18th IEEE International Conference on Bioinformatics and BioEngineering
  • Int'l Joint Research
• [Presentation] Analyzing order of domains in grammar-based compression of proteomes (2018)
  • Author(s): Hayashida, M., Ishibashi, K., and Koyano, H.
  • Organizer: The 24th International Conference on Parallel and Distributed Processing Techniques and Applications
  • Int'l Joint Research
• [Presentation] Grammar-based compression for directed and undirected generalized series-parallel graphs using integer linear programming (2018)
  • Author(s): Hayashida, M., Koyano, H., and Akutsu, T.
  • Organizer: The 9th International Conference on Bioinformatics Models, Methods and Algorithms
  • Int'l Joint Research
• [Presentation] ncRNA-disease association prediction based on sequence information and tripartite network (2018)
  • Author(s): Mori, T., Ngouv, H., Hayashida, M., Akutsu, T., Nacher, J.
  • Organizer: The 16th Asia Pacific Bioinformatics Conference
  • Int'l Joint Research
• [Presentation] 環境との相互作用の下での DNA 配列の集団 の進化のモデル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] 文字列の非可換位相半群上の偏微分方程式と生物群集の動態解析 (2018)
  • Author(s): 小谷野 仁, 澤田 和典, 山本 希, 山田 拓司
  • Organizer: 日本応用数理学会 2018 年度年会
• [Presentation] 配列類似性に基づいたウイルスゲノム自動分類法 (2018)
  • Author(s): 黒西 愛, Blanc-Mathieu, R., 遠藤 寿, 五斗 進, 緒方 博之
  • Organizer: 環境ウイルス研究集会
• [Presentation] Regression analysis using global ocean metagenomes revealed the contribution of eukaryotic viruses to carbon export (2018)
  • Author(s): Kaneko, H., Blanc-Mathieu, R., Endo, H., and Ogata, H.
  • Organizer: Workshop on Environmental Viruses
  • Int'l Joint Research
• [Presentation] Prymnesium kappa Virus RF01: A deep branching Mimiviridae encoding a large number of metabolic genes (2018)
  • Author(s): Blanc-Mathieu, R., Dahle, H., Brandt, D., Ogata, H., and Sandaa, R.-A.
  • Organizer: Workshop on Environmental Viruses
  • Int'l Joint Research
• [Presentation] アカントアメーバに感染する新規ウイルス Medusavirus のゲノム解析 (2018)
  • 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: 環境ウイルス研究集会
• [Presentation] Genomic characterization of Medusavirus, a new giant virus infecting Acanthamoeba (2018)
  • Author(s): Yoshikawa, G., Blanc-Mathieu, R., Song, C., Mochizuki, T., Murata, K., Ogata, H., and Takemura, M.
  • Organizer: International Workshop on Bioinformatics and Systems Biology 2018
  • Int'l Joint Research
• [Presentation] Development of viral genome classification method based on sequence similarity (2018)
  • Author(s): Kuronishi, M., Blanc-Mathieu, R., Endo, H., Goto, S., and Ogata, H.
  • Organizer: International Workshop on Bioinformatics and Systems Biology 2018
  • Int'l Joint Research
• [Presentation] Diversity of marine prymnesioviruses and their strategies for stable co-existence with their phytoplankton hosts (2018)
  • Author(s): Sandaa, R.-A., Lawrence, J., Blanc-Mathieu, R., Dahle, H., Steen, I. H., and Ogata, H.
  • Organizer: EMBO Workshop Viruses of Microbes 2018
  • Int'l Joint Research
• [Presentation] A giant virus from a freshwater environment with a full set of histone genes (2018)
  • Author(s): Ogata, H., Yoshikawa, G., Chihong, S., Blanc-Mathieu, R., Mochizuki, T., Murata, K., and Takemura, M.
  • Organizer: The 9th Aquatic Virus Workshop
  • Int'l Joint Research
• [Presentation] Reluctant affaires-algal virus-haptophyte relatioship in the ocean (2018)
  • Author(s): Sandaa, R.-A., Lawrence, J., Blanc-Mathieu, R., Dahle, H., Steen, I. H., and Ogata, H.
  • Organizer: The 9th Aquatic Virus Workshop
  • Int'l Joint Research
• [Presentation] Viruses of the eukaryotic plankton: insight into their diversity, host range and role in carbon export (2018)
  • Author(s): Blanc-Mathieu, R., Kaneko, H., Velazquez, R. H., Endo, H., and Ogata, H.
  • Organizer: 2018 JSME annual meeting
  • Int'l Joint Research
• [Presentation] Eukaryotic viruses in Tara Oceans samples: insight into their diversity and role in carbon export (2018)
  • Author(s): Blanc-Mathieu, R., Kaneko, H., Velazquez, R. H., Endo, H., and Ogata, H.
  • Organizer: Rinkai Hackathon 2018
  • Invited
• [Presentation] Actors of the biological pump: are viruses involved in the process? (2018)
  • Author(s): Blanc-Mathieu, R., 金子 博人, Velazquez, R. H., 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 pump (2018)
  • Author(s): 金子 博人, 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