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

• Project/Area Number: 16KT0020
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Multi-year Fund
• Section: 特設分野
• Research Field: Mathematical Sciences in Search of New Cooperation
• Research Institution: Tokyo Institute of Technology (2017-2018); Institute of Physical and Chemical Research (2016)
• Principal Investigator: Koyano Hitoshi 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
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000); Fiscal Year 2018: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2017: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2016: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
• Keywords: 文字列の位相半群 / DNA 配列の集団 / ダイナミクス / 統計的推定 / 制御 / バイオレメディエーション / 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 / 微生物の群集 / 推定 / 予測 / 環境再生 / 文字列 / 確率論 / 統計学 / 計算生物学 / 確率 / 統計 / 計算生物

Outline of Final Research Achievements

In this research project, we constructed a theory of a partial differential equation that describes the evolution of DNA sequences in an environment on the noncommutative topological monoid A* of strings on an alphabet A = {a, c, g, t}. Moreover, we introduced on A* a probability distribution named the Laplace-like distribution, which was designed to represent a population distribution of gene sequences in an environment using the mixture model of the distributions, and developed a theory for estimating the parameters of the mixture model. Furthermore, we developed a statistical method to analyze the dynamics of a population of DNA sequences in an environment and applied it to environmental samples of microbial sequences collected from surrounding environments of plants to demonstrate its usefulness.

Academic Significance and Societal Importance of the Research Achievements

1990 年代の前半に微生物を利用する環境浄化技術の研究が始まり、2000 年代半ばに、微生物によるバイオレメディエーション利用指針が制定された。このガイドラインでは、1 つの環境中の生物群集の時間発展を長期先まで予測することが求められているが、現在の数理・情報科学的技術では、このことを忠実に実行することは出来ない。本研究により、1 つの環境中の微生物群集の時間発展をコンピューターで計算することが出来るようになってきた。また、微生物群集のダイナミクスの特徴を抽出することも可能になった。今後は、本研究の結果を基礎にして、環境再生微生物工学の立案と制御のための体系的な技術の開発を目指す。

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
  • 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
  • NAID: 130007557117
  • 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, Takemura M
  • Journal Title: J Virol Volume: 93 Issue: 8 Pages: 1-24
  • DOI: 10.1128/jvi.02130-18
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases (2019)
  • Author(s): Inoue Masao、Nakamoto Issei、Omae Kimiho、Oguro Tatsuki、Ogata Hiroyuki、Yoshida Takashi、Sako Yoshihiko
  • Journal Title: Frontiers in Microbiology Volume: 9 Pages: 3353-3353
  • DOI: 10.3389/fmicb.2018.03353
  • NAID: 120006629159
  • Peer Reviewed / Open Access / 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
  • 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 EM, Dutilh BE, Koonin EV, et al
  • Journal Title: Nat Biotechnol Volume: 37 Issue: 1 Pages: 29-37
  • DOI: 10.1038/nbt.4306
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean (2018)
  • Author(s): Mihara Tomoko、Koyano Hitoshi、Hingamp Pascal、Grimsley Nigel、Goto Susumu、Ogata Hiroyuki
  • Journal Title: Microbes and Environments Volume: 33 Issue: 2 Pages: 162-171
  • DOI: 10.1264/jsme2.ME17203
  • NAID: 130007393740
  • ISSN: 1342-6311, 1347-4405
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Analysis of critical and redundant vertices in controlling directed complex networks using feedback vertex sets (2018)
  • Author(s): Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose Nacher, Tatsuya Akutsu
  • Journal Title: Journal of Computational Biology Volume: 25 Issue: 10 Pages: 1071-1090
  • 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): Natsu Nakajima, Morihiro Hayashida, Jesper Jansson, Osamu Maruyama, Tatsuya Akutsu
  • Journal Title: PLOS ONE Volume: 13 Issue: 4 Pages: e0195545-e0195545
  • DOI: 10.1371/journal.pone.0195545
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ncRNA-disease association prediction based on sequence information and tripartite network (2018)
  • Author(s): T. Mori, H. Ngouv, M. Hayashida, T. Akutsu and J. C. Nacher
  • Journal Title: BMC Systems Biology Volume: 12 Issue: S1 Pages: 1-1
  • DOI: 10.1186/s12918-018-0527-4
  • Peer Reviewed / Open Access / 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) Issue: 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 Peiying、Hayashida Morihiro、Akutsu Tatsuya、Vert Jean-Philippe
  • Journal Title: BMC Bioinformatics Volume: 19 Issue: S1 Pages: 39-39
  • DOI: 10.1186/s12859-018-2017-5
  • NAID: 120006537092
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Euler string-based compression of tree-structured data and its application to analysis of RNAs (2018)
  • Author(s): L. Liu, T. Mori, Y. Zhao, M. Hayashida and T. Akutsu
  • Journal Title: Current Bioinformatics Volume: 13 Issue: 1 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, Goto S, Ogata H, Sakurai T.
  • Journal Title: Biochem Biophys Res Commun Volume: 495 Issue: 1 Pages: 273-279
  • DOI: 10.1016/j.bbrc.2017.10.130
  • NAID: 120006377721
  • Peer Reviewed / Open Access
• [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 Issue: 1 Pages: 310-310
  • 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 Issue: 1 Pages: 18059-18059
  • 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, Ogata H.
  • Journal Title: Viruses Volume: 10 Issue: 9 Pages: 496-511
  • DOI: 10.3390/v10090496
  • Peer Reviewed / Open Access / 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 Issue: 1 Pages: 10916-10916
  • DOI: 10.1038/s41598-018-29039-9
  • NAID: 120006517794
  • 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 Issue: 2 Pages: 117-119
  • DOI: 10.1264/jsme2.ME3302rh
  • NAID: 130007393720
  • ISSN: 1342-6311, 1347-4405
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes (2018)
  • Author(s): Arai Wataru、Taniguchi Takeaki、Goto Susumu、Moriya Yuki、Uehara Hideya、Takemoto Kazuhiro、Ogata Hiroyuki、Takami Hideto
  • Journal Title: Bioscience, Biotechnology, and Biochemistry Volume: 82 Issue: 9 Pages: 1515-1517
  • DOI: 10.1080/09168451.2018.1476122
  • Peer Reviewed / Open Access
• [Journal Article] Xanthomonas citri Jumbo Phage XacN1 Exhibits a Wide Host Range and High Complement of tRNA Geness (2018)
  • Author(s): Genki Yoshikawa, Ahmed Askora, Romain Blanc-Mathieu, Takeru Kawasaki, Yanze, Li, Miyako Nakano, Hiroyuki Ogata, and Takashi Yamada
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 4486-4486
  • DOI: 10.1038/s41598-018-22239-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [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 Takashi, Nishimura Yosuke, Watai Hiroyasu, Haruki Nana, Morimoto Daichi, Kaneko Hiroto, Honda Takashi, Yamamoto Keigo, Hingamp Pascal, Sako Yoshihiko, Goto Susumu, Ogata Hiroyuki
  • Journal Title: The ISME Journal Volume: 印刷中 Issue: 5 Pages: 1287-1295
  • DOI: 10.1038/s41396-018-0052-x
  • Peer Reviewed / Open Access / 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, Blanc-Mathieu R, Lima-Mendez G,
  • Journal Title: Nat. Commun. Volume: 9 Issue: 1 Pages: 373-373
  • DOI: 10.1038/s41467-017-02342-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Improving conditional random field model for prediction of protein-RNA Residue-base contacts (2018)
  • Author(s): Hayashida, M., Kamada, M., and Koyano, H.
  • Journal Title: Quantitative Biology Volume: 印刷中
  • Peer Reviewed
• [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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Local time penalizations with various clocks for one-dimensional diffusions (2018)
  • Author(s): Profeta, C., Yano., K., and Yano, Y.
  • Journal Title: Journal of the Mathematical Society of Japan Volume: 印刷中
  • NAID: 130007557117
  • 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., Ogata, H., et al.
  • Journal Title: Nature Communications Volume: 9 Pages: 373-373
  • NAID: 120006551767
  • 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 programming (2017)
  • 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 strengths (2017)
  • 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 systems (2017)
  • 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: 41031-41031
  • NAID: 120005997781
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Weak convergence of h-transforms for one-dimensional diffusions (2017)
  • Author(s): Yano, K., Yano, Y., and Yen, J.-Y.
  • Journal Title: Statistics and Probability Letters Volume: 122 Pages: 152-156
  • NAID: 120006323765
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Type III polyketide synthases: functional classification and phylogenomics (2017)
  • 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 ocean (2017)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Discriminating the reaction types of plant type III polyketide synthases (2017)
  • 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 server (2017)
  • Author(s): Nishimura, Y., Yoshida, T., Kuronishi, M., Uehara, H., Ogata, H., and Goto, S.
  • Journal Title: Bioinformatics Volume: 33 Pages: 2379-2380
  • NAID: 120006329212
  • Peer Reviewed
• [Journal Article] Replications of two closely related groups of jumbo phages show different level of dependence on host-encoded RNA polymerase (2017)
  • 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: 1010-1010
  • NAID: 120006331975
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition (2017)
  • Author(s): Alberti, A., Poulain, J., Engelen, S., Ogata, H., et al.
  • Journal Title: Scientific Data Volume: 4 Pages: 170093-170093
  • NAID: 120006979737
  • 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 systems (2017)
  • Author(s): Y. An, J. Wang, J. Song, C. Li, J. Revote, T. Naderer, M. Hayashida, T. Akutsu, Y. Zhang, G. I. Webb, T. Lithgow
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 41031-41031
  • DOI: 10.1038/srep41031
  • NAID: 120005997781
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Maximum margin classifier working in a set of strings (2016)
  • Author(s): H. Koyano, M. Hayashida, T. Akutsu
  • Journal Title: Proceedings of the Royal Society A Volume: 472 Issue: 2187 Pages: 20150551-20150551
  • DOI: 10.1098/rspa.2015.0551
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Integer linear programming approach to median and center strings for a probability distribution on a set of strings (2016)
  • 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
  • NAID: 120005947093
  • Peer Reviewed
• [Journal Article] Critical evaluation of in silico methods for prediction of coiled-coil regions in proteins (2016)
  • 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 Issue: 2 Pages: 270-282
  • DOI: 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 order (2016)
  • Author(s): J. Jindalertudomdee, M. Hayashida, Y. Zhao, T. Akutsu
  • Journal Title: BMC Bioinformatics Volume: 17 Issue: 1 Pages: 113-113
  • DOI: 10.1186/s12859-016-0962-4
  • NAID: 120005822781
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Enumeration method for structural isomers containing user-defined structures based on breadth-first search approach (2016)
  • Author(s): J. Jindalertudomdee, M. Hayashida, T. Akutsu
  • Journal Title: Journal of Computational Biology Volume: 23 Issue: 8 Pages: 625-640
  • DOI: 10.1089/cmb.2016.0056
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length (2016)
  • Author(s): Y. Bao, M. Hayashida, T. Akutsu
  • Journal Title: BMC Bioinformatics Volume: 17 Issue: 1 Pages: 487-487
  • DOI: 10.1186/s12859-016-1353-6
  • NAID: 120005973378
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [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: 7-7
• [Journal Article] Grammar-based compression for unrooted trees and subclass of plane graphs using integer linear programming (2016)
  • Author(s): Hayashida, M., Cao, Y., and Zhao, Y.
  • Journal Title: IPSJ SIG Technical Report Volume: 2016-MPS-108 Pages: 11-11
• [Journal Article] Improving accuracy for predicting heterodimeric protein complexes using combination kernels (2016)
  • Author(s): Ruan, P., Hayashida, M., Akutsu, T., and Vert, J.-P.
  • Journal Title: IPSJ SIG Technical Report Volume: 2016-MPS-108 Pages: 12-12
• [Journal Article] Complex network-based approaches to biomarker discovery (2016)
  • Author(s): Hayashida, M. and Akutsu, T.
  • Journal Title: Biomarkers in Medicine Volume: 10 Issue: 6 Pages: 621-632
  • DOI: 10.2217/bmm-2015-0047
  • Peer Reviewed
• [Journal Article] Benthic protists: the under-charted majority (2016)
  • 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 Issue: 8 Pages: fiw120-fiw120
  • 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 sequences (2016)
  • Author(s): Tomoko Mihara, Mohamed A. Nasr-Eldin, Orawan Chatchawankanphanich, Anjana Bhunchoth, Namthip Phironrit, Takeru Kawasaki, Miyako Nakano, Makoto Fujie, Hiroyuki Ogata, Takashi Yamada
  • Journal Title: Virology Reports Volume: 6 Pages: 61-73
  • DOI: 10.1016/j.virep.2016.07.001
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Two Asian jumbo phages, phiRSL2 and phiRSF1, infect Ralstonia solanacearum and show common features of phiKZ-related phages (2016)
  • Author(s): Anjana Bhunchoth 他12名
  • Journal Title: Virology Volume: 494 Pages: 56-66
  • DOI: 10.1016/j.virol.2016.03.028
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] DNA repair genes in the Megavirales pangenome. (2016)
  • Author(s): Blanc-Mathieu R., Ogata H.
  • Journal Title: Curr. Opin. Microbiol. Volume: 31 Pages: 94-100
  • DOI: 10.1016/j.mib.2016.03.011
  • NAID: 120005741090
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Linking virus genomes with host taxonomy. (2016)
  • Author(s): Mihara T., Nishimura Y., Shimizu Y., Nishiyama H., Yoshikawa G., Uehara H., Hingamp P., Goto S, Ogata H.
  • Journal Title: Viruses Volume: 8 Issue: 3 Pages: 66-66
  • DOI: 10.3390/v8030066
  • NAID: 120005947134
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Plankton networks driving carbon export in the oligotrophic ocean. (2016)
  • Author(s): Guidi L., Chaffron S., Bittner L., ..., Ogata H., ..., Karsenti E., Bowler C., Gorsky G.
  • Journal Title: Nature Volume: - Issue: 7600 Pages: 465-470
  • DOI: 10.1038/nature16942
  • NAID: 120005745631
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. (2016)
  • 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., Ogata H.
  • Journal Title: ISME J. Volume: 10 Issue: 5 Pages: 1134-1146
  • DOI: 10.1038/ismej.2015.192
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Identification of a new oat beta-amylase by functional proteomics (2016)
  • 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 Issue: 1 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 viruses (2016)
  • 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 Issue: 7622 Pages: 689-693
  • DOI: 10.1038/nature19366
  • 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
• [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: 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 network (2018)
  • 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 kernel (2018)
  • 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 pump (2018)
  • 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 strings (2017)
  • 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 algorithms (2017)
  • 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 contacts (2017)
  • 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 approach (2017)
  • Author(s): Ogata, H.
  • Organizer: Tara Coral Conference
  • Int'l Joint Research
• [Presentation] Towards unveiling pivotal roles of viruses in marine ecosystems (2017)
  • 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 ecosystem (2017)
  • 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 Megaviridae (2017)
  • 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 plankton (2017)
  • 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 pump (2017)
  • 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 ocean (2017)
  • 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
• [Presentation] Optimal string clustering based on a statistical theory on a topological monoid of strings (2017)
  • Author(s): Koyano, H., Hayashida, M., and Akutsu, T.
  • Organizer: 13th Workshop on Stochastic Models, Statistics and Their Applications
  • Place of Presentation: Berlin, Germany
  • Int'l Joint Research
• [Presentation] Host-pathogen protein interaction prediction based on local topology structures of a protein interaction network (2016)
  • 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
  • Int'l Joint Research
• [Presentation] Integer linear programming approach to median and center strings for a probability distribution on a set of strings (2016)
  • Author(s): Hayashida M. and Koyano, H.
  • Organizer: 15th European Conference on Computational Biology
  • Place of Presentation: The Hague, Netherlands
  • Int'l Joint Research