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Mori, Tomoya

Institute for Chemical Research (ICR) Assistant Professor

Mori, Tomoya
list
    Last Updated :2022/09/30

    Basic Information

    Affiliated programs (koza)

    • Graduate School of Informatics, 知能情報学専攻 生命システム情報学, 助教

    Professional Memberships

    • Information Processing Society of Japan
    • Japanese Society for Bioinformatics

    Academic Degree

    • Master (informatics)(Kyoto University)
    • PhD (Informatics)(Kyoto University)

    Academic Resume (Graduate Schools)

    • Kyoto University, Graduate School of Informatics, Department of Intelligence Science and Technology, 修了
    • Kyoto University, Graduate School of Informatics, Department of Intelligence Science and Technology, 修了

    Academic Resume (Undergraduate School/Majors)

    • Doshisha University, 工学部インテリジェント情報工学科, 卒業

    High School

    • High School

      学校法人ヴィアトール学園 洛星高等学校

    Research History

    • From 01 Apr. 2018
      Bioinformatics Center, Institute for Chemical Research, Kyoto University, Assistant Professor
    • From 01 Apr. 2016
      Center for iPS Cell Research and Application, Kyoto University, Researcher
    • From 01 Nov. 2015
      Center for iPS Cell Research and Application, Kyoto University, JSPS Research Fellowship for Young Scientists (PD)
    • From 01 Oct. 2015
      Bioinformatics Center, Institute for Chemical Research, Kyoto University, JSPS Research Fellowship for Young Scientists (PD)
    • From 01 Apr. 2014
      Bioinformatics Center, Institute for Chemical Research, Kyoto University, JSPS Research Fellowship for Young Scientists (DC2)
    • From 01 Apr. 2013
      Faculty of Culture and Information Science, Doshisha University, -

    Profile

    • Profile

      Tomoya Mori received his Ph.D. degree in informatics from Kyoto University, Japan, in 2015. After working in Bioinformatics Center, Institute for Chemical Research, Kyoto University and Center for iPS Cell Research and Application, Kyoto University, he joined Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan as a assistant professor in Apr. 2018. His research interests are algorithms for bioinformatics and multi-omics analysis.

    ID,URL

    Website(s) (URL(s))

    researchmap URL

    list
      Last Updated :2022/09/30

      Research

      Research Topics, Overview of the research

      • Research Topics

        Single-cell omics analysis, Bioinformatics, Algorithms for Graph Theory
      • Overview of the research

        Development of algorithms for spatial omics analysis, cell trajectory inference and comparison, and graph-structured biological data

      Research Interests

      • Single-cell omics analysis
      • Discrete algorithm
      • Bioinformatics

      Research Areas

      • Informatics, Biological, health, and medical informatics

      Papers

      • Attractor detection and enumeration algorithms for Boolean networks
        Tomoya Mori; Tatsuya Akutsu
        Computational and Structural Biotechnology Journal, May 2022, Peer-reviewed, Lead author, Corresponding author
      • Identification of periodic attractors in Boolean networks using a priori information
        Ulrike Münzner; Tomoya Mori; Marcus Krantz; Edda Klipp; Tatsuya Akutsu
        PLOS Computational Biology, Jan. 2022, Peer-reviewed
      • Comparison of pseudoknotted RNA secondary structures by topological centroid identification and tree edit distance
        Feiqi Wang; Tatsuya Akutsu; Tomoya Mori
        Journal of Computational Biology, 2020, Peer-reviewed, Last author, Corresponding author
      • Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering.
        Tomoya Mori; Haruka Takaoka; Junko Yamane; Cantas Alev; Wataru Fujibuchi
        Scientific reports, 29 Aug. 2019, Peer-reviewed
      • Euler string-based compression of tree-structured data and its application to analysis of RNAs
        Liu L; Mori T; Zhao Y; Hayashida M; Akutsu T
        Current Bioinformatics, 2018, Peer-reviewed
      • An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data
        Yuki Kato; Tomoya Mori; Kengo Sato; Shingo Maegawa; Hiroshi Hosokawa; Tatsuya Akutsu
        BIOINFORMATICS, Jan. 2017, Peer-reviewed
      • Development of enhanced reduced representation bisulfite sequencing method for single-cell methylome analysis
        Yamane J; Mori T; Taniyama N; Kobayashi K; Fujibuchi W
        Genomics and Computational Biology, 2017, Peer-reviewed
      • Development of 3D tissue reconstruction method from single-cell RNA-seq data
        Mori T; Yamane J; Kobayashi K; Taniyama N; Tano T; Fujibuchi W
        Genomics and Computational Biology, 2017, Peer-reviewed
      • Exact Identification of the Structure of a Probabilistic Boolean Network from Samples
        Xiaoqing Cheng; Tomoya Mori; Yushan Qiu; Wai-Ki Ching; Tatsuya Akutsu
        IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, Nov. 2016, Peer-reviewed
      • A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models
        Takanori Hasegawa; Atsushi Niida; Tomoya Mori; Teppei Shimamura; Rui Yamaguchi; Satoru Miyano; Tatsuya Akutsu; Seiya Imoto
        COMPUTATIONAL STATISTICS & DATA ANALYSIS, Feb. 2016, Peer-reviewed
      • Similar Subtree Search Using Extended Tree Inclusion
        Tomoya Mori; Atsuhiro Takasu; Jesper Jansson; Jaewook Hwang; Takeyuki Tamura; Tatsuya Akutsu
        2016 32ND IEEE INTERNATIONAL CONFERENCE ON DATA ENGINEERING (ICDE), 2016, Peer-reviewed
      • Similar Subtree Search Using Extended Tree Inclusion
        Tomoya Mori; Atsuhiro Takasu; Jesper Jansson; Jaewook Hwang; Takeyuki Tamura; Tatsuya Akutsu
        IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, Dec. 2015, Peer-reviewed
      • Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks
        Tomoya Mori; Max Flottmann; Marcus Krantz; Tatsuya Akutsu; Edda Klipp
        BMC SYSTEMS BIOLOGY, Aug. 2015, Peer-reviewed
      • Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks
        Takanori Hasegawa; Tomoya Mori; Rui Yamaguchi; Teppei Shimamura; Satoru Miyano; Seiya Imoto; Tatsuya Akutsu
        BMC SYSTEMS BIOLOGY, Mar. 2015, Peer-reviewed
      • An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data
        Takanori Hasegawa; Tomoya Mori; Rui Yamaguchi; Seiya Imoto; Satoru Miyano; Tatsuya Akutsu
        JOURNAL OF COMPUTATIONAL BIOLOGY, Nov. 2014, Peer-reviewed
      • A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees
        Tomoya Mori; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        JOURNAL OF COMPUTATIONAL BIOLOGY, Oct. 2012, Peer-reviewed

      Misc.

      • 根付き順序木の圧縮における分割型文法とオイラー文字列との比較
        劉立偉; 森智弥; 趙楊; 林田守広; 阿久津達也
        電子情報通信学会技術研究報告, 2015
      • Evaluating Effectiveness of Accessibility to Infer RNA-RNA Interactions
        Yuki Kato; Tomoya Mori; Kengo Sato; Shingo Maegawa; Hiroshi Hosokawa; Tatsuya Akutsu
        IPSJ SIG technical reports, 12 Sep. 2013
      • An Improved Clique-Based Method for Computing Edit Distance between Rooted Unordered Trees
        Tomoya Mori; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        IPSJ SIG technical reports, 06 Sep. 2011
      • An improved clique-based method for computing edit distance between unordered trees and its application to comparison of glycan structures
        Tatsuya Akutsu; Tomoya Mori; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu; Etsuji Tomita
        Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011, 2011, Peer-reviewed

      Presentations

      • Periodic attractor identification using a priori information in Boolean networks
        Tomoya Mori, Ulrike Münzner, Marcus Kranz, Edda Klipp, Tatsuya Akutsu
        International Conference On Intelligent Computing, 09 Aug. 2022
      • 空間トランスクリプトームの自己組織化マップクラスタリングによる三次元組織インシリコ再構築
        森 智弥
        第3回幹細胞情報学研究イニシアチブ研究会, 12 Jul. 2021, Invited
      • 分岐を考慮した時系列シングルセルデータのアラインメント
        杉原 礼一; 加藤 有己; 森 智弥; 河原 行郎
        第61回BIO研究発表会, 12 Mar. 2020
      • In silico three-dimensional reconstruction and identification of spatial discriminator genes of mouse gastrula embryo structure by self-organizing map (SOM) clustering
        Tomoya Mori
        The 42nd Annual Meeting of the Molecular Biology Society of Japan, 03 Dec. 2019
      • Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering
        Tomoya Mori
        Japan-Germany International Workshop 2019-1 The Human Cell Type Authentication Initiative, 15 May 2019, Invited
      • In silicon 3D tissue reconstruction
        Tomoya Mori
        Japan-Germany International Workshop 2018-1 The Human Cell Type Authentication Initiative, Apr. 2018
      • Development of ab initio 3D reconstruction algorithm for mid-gastrula mouse embryo from transcriptome using kernel self-organizing map
        Tomoya Mori
        Single Cell Science Symposium “Technology Meets Biology”, Jul. 2017
      • Development of 3D tissue reconstruction method from single-cell RNA-seq data
        Tomoya Mori
        2nd Challenges in Computational Biology: Gene Expression Data Analysis, Dec. 2016
      • 無順序木間の編集距離計算のための動的計画法を用いたクリークに基づく手法
        森 智弥
        生命情報科学若手の会, Oct. 2014
      • A clique-based method using dynamic programming for unordered tree edit distance problem
        Tomoya Mori
        The 12th International Workshop on Bioinformatics and Systems Biology,, Jul. 2012
      • An improved clique-based method for computing edit distance between rooted unordered trees
        Tomoya Mori
        情報処理学会バイオ情報学研究会, Sep. 2011
      • 実験医学増刊34(17):再生医療と疾患解明の鍵となる組織幹細胞
        森 智弥; 藤渕 航, Contributor, 精密細胞分類に基づく幹細胞・分化細胞の評価
        羊土社, Oct. 2016, Not refereed

      Awards

      • 2011
        SIG BIO, IPSJ SIGBIO Best Student Presentation Award
      • 2013
        Information Processing Society of Japan, IPSJ Yamashita SIG Research Award
      list
        Last Updated :2022/09/30

        Education

        Teaching subject(s)

        • From 01 Apr. 2022, To 31 Mar. 2023
          Introduction to Bioinformatics
          3159, Spring, Graduate School of Informatics, 2
        • From 01 Apr. 2022, To 31 Mar. 2023
          Bioinformatics, Adv.
          3179, Fall, Graduate School of Informatics, 2
        • From Apr. 2020, To Mar. 2021
          Introduction to Bioinformatics
          Spring, 情報学研究科
        • From Apr. 2020, To Mar. 2021
          Bioinformatics, Adv.
          Fall, 情報学研究科
        • From Apr. 2021, To Mar. 2022
          Introduction to Bioinformatics
          Spring, 情報学研究科
        • From Apr. 2021, To Mar. 2022
          Bioinformatics, Adv.
          Fall, 情報学研究科
        list
          Last Updated :2022/09/30

          Administration

          Faculty management (title, position)

          • From 01 Apr. 2019, To 31 Mar. 2020
            化学研究所広報委員会 委員
          • From 01 Apr. 2019, To 31 Mar. 2020
            化学研究所情報システム技術委員会 委員
          • From 01 Apr. 2020, To 31 Mar. 2021
            化学研究所情報システム技術委員会委員
          • From 01 Apr. 2021, To 31 Mar. 2022
            化学研究所情報システム技術委員会委員
          list
            Last Updated :2022/09/30

            Academic, Social Contribution

            Committee Memberships

            • From Apr. 2022, To Present
              Editorial Committee of IPSJ Transactions on Mathematical Modeling and Its Applications (TOM), Information Processing Society of Japan (IPSJ)
            • From Mar. 2021, To Present
              Review Editor, Frontiers in Genetics
            • From Apr. 2021, To Present
              Editorial committee of IPSJ Transactions on Bioinformatics (TBIO), Information Processing Society of Japan (IPSJ)
            • From Apr. 2019, To Present
              Steering Committee of IPSJ SIG BIO, Information Processing Society of Japan (IPSJ)

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