Tomoya Mori

Profile Information

Affiliation: Assistant Professor, Institute for Chemical Research Bioinformatics Center, Kyoto University

Degree: PhD (Informatics)(Sep, 2015, Kyoto University)

ORCID ID: https://orcid.org/0000-0003-3483-0056
J-GLOBAL ID: 201801006323904398
researchmap Member ID: 7000023223

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

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.

Research Interests

Research Areas

Informatics / Biological, health, and medical informatics /

Research History

Education

Apr, 2012 - Sep, 2015

Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University
Apr, 2010 - Mar, 2012

Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University
Apr, 2006 - Mar, 2010

Doshisha University

Committee Memberships

Jun, 2023 - 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)
Apr, 2022 - Present

Editorial Committee of IPSJ Transactions on Mathematical Modeling and Its Applications (TOM), Information Processing Society of Japan (IPSJ)
Apr, 2021 - Present

Editorial committee of IPSJ Transactions on Bioinformatics (TBIO), Information Processing Society of Japan (IPSJ)
Mar, 2021 - Present

Review Editor, Frontiers in Genetics
Apr, 2019 - Mar, 2023

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

Awards

Mar, 2013

山下記念研究賞, 情報処理学会
Mar, 2012

学生奨励賞, 情報処理学会バイオ情報学研究会

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 …

BMC Bioinformatics, 24(1), Jun 15, 2023 Peer-reviewedLead author
Metrics for RNA Secondary Structure Comparison.

Feiqi Wang, Tatsuya Akutsu, Tomoya Mori

Methods in molecular biology (Clifton, N.J.), 2586 79-88, 2023
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), 248 44:1-44:14, Dec, 2022 Peer-reviewed
Alignment of single-cell trajectory trees with CAPITAL

Reiichi Sugihara, Yuki Kato, Tomoya Mori, Yukio Kawahara

Nature Communications, 13(1), Oct 14, 2022 Peer-reviewed
Attractor detection and enumeration algorithms for Boolean networks

Tomoya Mori, Tatsuya Akutsu

Computational and Structural Biotechnology Journal, 20 2512-2520, May, 2022 Peer-reviewedLead authorCorresponding 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, 18(1) e1009702, 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, 27 1-9, 2020 Peer-reviewedLast authorCorresponding 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, 9(1) 12597-12597, Aug 29, 2019 Peer-reviewedLead 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, 13(1) 25-33, 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, 33(2) 202-209, 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, 3(2) e49, 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, 3(1) e53, 2017 Peer-reviewedLead 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, 13(6) 1107-1116, 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, 94 63-74, 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, 27(12) 3360-3373, Dec, 2015 Peer-reviewedLead 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, 9(45) 9 pages, Aug, 2015 Peer-reviewedLead 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, 9(14) 13 pages, 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, 21(11) 785-798, 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, 19(10) 1089-1104, Oct, 2012 Peer-reviewedLead 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), 725, 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, 115(112) 245-246, 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, 2013(3) 1-2, Sep 12, 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, 2011(3) 1-6, Sep 6, 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, 536-540, 2011 Peer-reviewed

Books and Other Publications

RNA Structure Prediction, Methods in Molecular Biology

Feiqi Wang, Tatsuya Akutsu, Tomoya Mori (Role: Contributor, Metrics for RNA Secondary Structure Comparison)

Humana, New York, Jan, 2023 (ISBN: 9781071627679)
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 (Role: 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 (ISBN: 9784758122610)
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 (Role: 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 (ISBN: 9784758103589)

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, Aug 9, 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, Jul 12, 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, Mar 12, 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, Dec 3, 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, May 15, 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

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

Teaching Experience

Sep, 2020 - Present

Bioinformatics, Adv. (Kyoto University)
Apr, 2020 - Present

Introduction to Bioinformatics (Kyoto University)

Professional Memberships

Research Projects

空間オミクスに基づく生体組織ドメイン推定および解析法の確立

Grant-in-Aid for Scientific Research, Japan Society for the Promotion of Science, Apr, 2023 - Mar, 2026

Tomoya Mori
Development of cell trajectory inference and comparison algorithm based on single-cell omics data

Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists, Grant-in-Aid for Early-Career Scientists, Japan Society for the Promotion of Science, Apr, 2019 - Mar, 2022

Tomoya Mori
Development of detailed cell classification and cell evaluation method based on DNA methylation

Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science, Apr, 2017 - Mar, 2019

Tomoya Mori
確率ブーリアンネットワークを用いた細胞内シグナル伝達機構のモデル化とその解

Grant-in-Aid for Scientific Research, Grant-in-Aid for JSPS Research Fellows, Japan Society for the Promotion of Science, Apr, 2014 - Mar, 2016

Tomoya Mori

Industrial Property Rights

特許第7241406号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
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