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

• ORCID ID

  0000-0003-3483-0056

• J-Global ID

  201801006323904398

• External link

  https://kdb.iimc.kyoto-u.ac.jp/profile_private/ja.22dad5ec779719b8.html

Website(s) (URL(s))

• http://rdb.kuicr.kyoto-u.ac.jp/researchers/view/tomoya+mori
• http://sunflower.kuicr.kyoto-u.ac.jp/~tmori/

researchmap URL

• https://researchmap.jp/7000023223

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

• Spatial omics analysis
• Single-cell omics analysis
• Discrete algorithm
• Bioinformatics

Research Areas

• Informatics, Biological, health, and medical informatics

Papers

• eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

  Tomoya Mori; Toshiro Takase; Kuan-Chun Lan; Junko Yamane; Cantas Alev; Azuma Kimura; Kenji Osafune; Jun K. Yamashita; Tatsuya Akutsu; Hiroaki Kitano; Wataru Fujibuchi

  BMC Bioinformatics, 15 Jun. 2023, Peer-reviewed, Lead author

  
• On the complexity of tree edit distance with variables

  Tatsuya Akutsu; Tomoya Mori; Naotoshi Nakamura; Satoshi Kozawa; Yuhei Ueno; Thomas N Sato

  33rd International Symposium on Algorithms and Computation (ISAAC 2022), Dec. 2022, Peer-reviewed

  
• Alignment of single-cell trajectory trees with CAPITAL

  Reiichi Sugihara; Yuki Kato; Tomoya Mori; Yukio Kawahara

  Nature Communications, 14 Oct. 2022, Peer-reviewed

  
• 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, Lead author

  
• 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, Lead author

  
• 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

  IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, Dec. 2015, Peer-reviewed, Lead author

  
• 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, Lead author

  
• 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, Lead author

  

Misc.

• 1細胞RNA-seqデータを用いた細胞状態遷移経路アラインメント法の開発

  杉原 礼一; 加藤 有己; 森 智弥; 河原 行郎

  RNA Frontier Meeting 2022, Oct. 2022

  
• CAPITALによるシングルセルデータの疑似時系列比較解析

  加藤 有己; 杉原 礼一; 森 智弥; 河原 行郎

  第43回日本分子生物学会年会, Dec. 2020

  
• Alignment of complex single-cell trajectories with CAPITAL

  Yuki Kato; Reiichi Sugihara; Tomoya Mori; Yukio Kawahara

  28th Conference on Intelligent Systems for Molecular Biology (ISMB2020), Jul. 2020

  
• 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

  

Books and Other Publications

• RNA Structure Prediction, Methods in Molecular Biology

  Feiqi Wang; Tatsuya Akutsu; Tomoya Mori, Contributor, Metrics for RNA Secondary Structure Comparison

  Humana, New York, Jan. 2023

  Find Kyoto University's collection of books :

  
• 実験医学別冊 空間オミクス解析スタートアップ実践ガイド

  Tomoya Mori; Wataru Fujibuchi, Contributor, 遺伝子発現データベースを活用した空間・発生解析

  Yodosha, Dec. 2022

  Find Kyoto University's collection of books :

  
• 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

  Find Kyoto University's collection of books :

  

Industrial Property Rights

• 特願PCT/JP2018/04 7908, 個々の細胞情報から細胞高次元情報を推定する装置・方法・プログラム

  Wataru Fujibuchi; Tomoya Mori

  
• 特許第7241406号, WO2019/131785, 特願2017-250042, 個々の細胞情報から組織高次元情報を推定する装置、方法、プログラム

  Wataru Fujibuchi; Tomoya Mori

  

Awards

• 2011

  SIG BIO, IPSJ SIGBIO Best Student Presentation Award
• 2013

  Information Processing Society of Japan, IPSJ Yamashita SIG Research Award

Education

Teaching subject(s)

• From 01 Apr. 2023, To 31 Mar. 2024

  Bioinformatics, Adv.

  3179, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Introduction to Bioinformatics

  3159, Spring, Graduate School of Informatics, 2
• 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

Administration

Faculty management (title, position)

• From 01 Apr. 2023, To 31 Mar. 2024

  化学研究所総務・教務委員会
• 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

Academic, Social Contribution

Committee Memberships

• From Jun. 2023, To Present

  論文誌ジャーナル/JIP編集委員会 小委員会（基盤グループ [Computing Group]）編集委員, Information Processing Society of Japan (IPSJ)
• 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 Mar. 2023

  Steering Committee of IPSJ SIG BIO, Information Processing Society of Japan (IPSJ)