森智弥

Last Update: 2020/01/08 11:24:31

Name(Kanji/Kana/Abecedarium Latinum)

森智弥/モリトモヤ/Mori, Tomoya

Primary Affiliation(Org1/Job title)

Institute for Chemical Research (ICR)/Assistant Professor

Affiliated programs (koza)

Org1	Job title
Graduate Schools Informatics	Assistant Professor

Academic Organizations You are Affiliated to in Japan

Organization name(Japanese)	Organization name(English)
日本バイオインフォマティクス学会	Japanese Society for Bioinformatics
情報処理学会	Information Processing Society of Japan

Academic Degree

Field(Japanese)	Field(English)	University(Japanese)	University(English)	Method
修士（情報学）		京都大学
博士（情報学）		京都大学

Graduate School

University(Japanese)	University(English)	Faculty(Japanese)	Faculty(English)	Major(Japanese)	Major(English)	Degree
京都大学		大学院情報学研究科修士課程知能情報学専攻				修了
京都大学		大学院情報学研究科博士後期課程知能情報学専攻				修了

Undergraduate School / Major(s)

University(Japanese)	University(English)	Faculty(Japanese)	Faculty(English)	Major(s)(Japanese)	Major(s)(English)	Degree
同志社大学		工学部インテリジェント情報工学科				卒業

High School

Highschool	Kana
学校法人ヴィアトール学園洛星高等学校

Work Experience

Period	Organization(Japanese)	Organization(English)	Job title(Japanese)	Job title(English)
2013/04/01-2014/03/31	同志社大学文化情報学部	Faculty of Culture and Information Science, Doshisha University	実習助手
2014/04/01-2015/09/30	京都大学化学研究所バイオインフォマティクスセンター	Bioinformatics Center, Institute for Chemical Research, Kyoto University	日本学術振興会特別研究員 (DC2)	JSPS Research Fellowship for Young Scientists (DC2)
2015/10/01-2015/10/31	京都大学化学研究所バイオインフォマティクスセンター	Bioinformatics Center, Institute for Chemical Research, Kyoto University	日本学術振興会特別研究員 (PD)	JSPS Research Fellowship for Young Scientists (PD)
2015/11/01-2016/03/31	京都大学 iPS細胞研究所	Center for iPS Cell Research and Application, Kyoto University	日本学術振興会特別研究員 (PD)	JSPS Research Fellowship for Young Scientists (PD)
2016/04/01-2018/03/31	京都大学 iPS細胞研究所	Center for iPS Cell Research and Application, Kyoto University	特定研究員	Researcher
2018/04/01-	京都大学化学研究所バイオインフォマティクスセンター	Bioinformatics Center, Institute for Chemical Research, Kyoto University	助教	Assistant Professor

Personal Profile

(Japanese)
2015年京都大学大学院情報学研究科博士後期課程修了。情報学博士。京都大学化学研究所バイオインフォマティクスセンター、京都大学iPS細胞研究所を経て、2018年より京都大学化学研究所バイオインフォマティクスセンター助教（情報学研究科知能情報学専攻協力講座）。専門はバイオインフォマティクスに関連するアルゴリズム開発及び細胞のマルチオミックスデータ解析である。日本バイオインフォマティクス学会及び情報処理学会の会員。
(English)
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.

Personal Website(s) (URL(s))

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

ORCID ID

https://orcid.org/0000-0003-3483-0056

researchmap URL

https://researchmap.jp/7000023223

Research Topics

(Japanese)
バイオインフォマティクス、グラフ理論に関するアルゴリズム開発、マルチオミックス解析
(English)
Bioinformatics, Algorithms for Graph Theory, Multi-omics analysis

Overview of the research

(Japanese)
1. グラフ構造データの比較アルゴリズム開発, 2. ブーリアンネットワークによるシグナル伝達ネットワークのモデル化とシミュレーション, 3. 単一細胞トランスクリプトーム及びメチローム解析
(English)
1. Algorithms for comparing graph-structured data, 2. Modeling and simulation of signaling network using Boolean network, 3. Single-cell Transcriptome/Methylome analysis

Fields of research (key words)

Key words(Japanese)	Key words(English)
バイオインフォマティクス	Bioinformatics
離散アルゴリズム	Discrete algorithm
単一細胞解析	Single-cell analysis

Published Papers

Author	Author(Japanese)	Author(English)	Title	Title(Japanese)	Title(English)	Bibliography	Bibliography(Japanese)	Bibliography(English)	Publication date	Refereed paper	Language	Publishing type	Disclose
Mori T, Takaoka H, Yamane J, Alev C, Fujibuchi W	Mori T, Takaoka H, Yamane J, Alev C, Fujibuchi W	Mori T, Takaoka H, Yamane J, Alev C, Fujibuchi W	Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering	Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering	Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering	Scientific Reports, 9, 12597	Scientific Reports, 9, 12597	Scientific Reports, 9, 12597	2019/08	Refereed	English	Research paper(scientific journal)	Disclose to all
Liu L, Mori T, Zhao Y, Hayashida M, Akutsu T	Liu L, Mori T, Zhao Y, Hayashida M, Akutsu T	Liu L, Mori T, Zhao Y, Hayashida M, Akutsu T	Euler string-based compression of tree-structured data and its application to analysis of RNAs	Euler string-based compression of tree-structured data and its application to analysis of RNAs	Euler string-based compression of tree-structured data and its application to analysis of RNAs	Current Bioinformatics, 13, 1, 25-33	Current Bioinformatics, 13, 1, 25-33	Current Bioinformatics, 13, 1, 25-33	2018	Refereed	English	Research paper(scientific journal)	Disclose to all
Mori T, Yamane J, Kobayashi K, Taniyama N, Tano T, Fujibuchi W	Mori T, Yamane J, Kobayashi K, Taniyama N, Tano T, Fujibuchi W	Mori T, Yamane J, Kobayashi K, Taniyama N, Tano T, Fujibuchi W	Development of 3D tissue reconstruction method from single-cell RNA-seq data	Development of 3D tissue reconstruction method from single-cell RNA-seq data	Development of 3D tissue reconstruction method from single-cell RNA-seq data	Genomics and Computational Biology, 3, 1, e53	Genomics and Computational Biology, 3, 1, e53	Genomics and Computational Biology, 3, 1, e53	2017	Refereed	English	Research paper(international conference proceedings)	Disclose to all
Yamane J, Mori T, Taniyama N, Kobayashi K, Fujibuchi W	Yamane J, Mori T, Taniyama N, Kobayashi K, Fujibuchi W	Yamane J, Mori T, Taniyama N, Kobayashi K, Fujibuchi W	Development of enhanced reduced representation bisulfite sequencing method for single-cell methylome analysis	Development of enhanced reduced representation bisulfite sequencing method for single-cell methylome analysis	Development of enhanced reduced representation bisulfite sequencing method for single-cell methylome analysis	Genomics and Computational Biology, 3, 2, e49	Genomics and Computational Biology, 3, 2, e49	Genomics and Computational Biology, 3, 2, e49	2017	Refereed	English	Research paper(international conference proceedings)	Disclose to all
Kato Y, Mori T, Sato K, Maegawa S, Hosokawa H, Akutsu T	Kato Y, Mori T, Sato K, Maegawa S, Hosokawa H, Akutsu T	Kato Y, Mori T, Sato K, Maegawa S, Hosokawa H, Akutsu T	An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data	An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data	An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data	Bioinformatics, 33, 2, 201-209	Bioinformatics, 33, 2, 201-209	Bioinformatics, 33, 2, 201-209	2017	Refereed	English	Research paper(scientific journal)	Disclose to all
Cheng X, Mori T, Qiu Y, Ching W-K, Akutsu T	Cheng X, Mori T, Qiu Y, Ching W-K, Akutsu T	Cheng X, Mori T, Qiu Y, Ching W-K, Akutsu T	Exact identification of the structure of a probabilistic Boolean network from sample	Exact identification of the structure of a probabilistic Boolean network from sample	Exact identification of the structure of a probabilistic Boolean network from sample	IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13, 5, 1107-1116	IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13, 5, 1107-1116	IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13, 5, 1107-1116	2016	Refereed	English	Research paper(scientific journal)	Disclose to all
Hasegawa T, Niida A, Mori T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S	Hasegawa T, Niida A, Mori T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S	Hasegawa T, Niida A, Mori T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S	A likelihood-free filtering method via approximate Bayesian computation in evaluating biologival simulation models	A likelihood-free filtering method via approximate Bayesian computation in evaluating biologival simulation models	A likelihood-free filtering method via approximate Bayesian computation in evaluating biologival simulation models	Computational Statistics and Data Analysis, 94, 63-74	Computational Statistics and Data Analysis, 94, 63-74	Computational Statistics and Data Analysis, 94, 63-74	2016	Refereed	English	Research paper(scientific journal)	Disclose to all
Mori T, Takasu A, Jansson J, Hwang J, Tamura T, Akutsu T	Mori T, Takasu A, Jansson J, Hwang J, Tamura T, Akutsu T	Mori T, Takasu A, Jansson J, Hwang J, Tamura T, Akutsu T	Similar subtree search using extended tree inclusion	Similar subtree search using extended tree inclusion	Similar subtree search using extended tree inclusion	IEEE Transactions on Knowledge and Data Engineering, 27, 12, 3360-3373	IEEE Transactions on Knowledge and Data Engineering, 27, 12, 3360-3373	IEEE Transactions on Knowledge and Data Engineering, 27, 12, 3360-3373	2015	Refereed	English	Research paper(scientific journal)	Disclose to all
Mori T, Flöttmann M, Krantz M, Akutsu T, Klipp E	Mori T, Flöttmann M, Krantz M, Akutsu T, Klipp E	Mori T, Flöttmann M, Krantz M, Akutsu T, Klipp E	Stochastic simulation of Boolean rxncon model: towards quantitative analysis of large signaling networks	Stochastic simulation of Boolean rxncon model: towards quantitative analysis of large signaling networks	Stochastic simulation of Boolean rxncon model: towards quantitative analysis of large signaling networks	BMC Systems biology, 9, 45, 9 pages	BMC Systems biology, 9, 45, 9 pages	BMC Systems biology, 9, 45, 9 pages	2015	Refereed	English	Research paper(scientific journal)	Disclose to all
Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T	Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T	Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T	Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks	Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks	Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks	BMC Systems biology, 9, 14, 13 pages	BMC Systems biology, 9, 14, 13 pages	BMC Systems biology, 9, 14, 13 pages	2015	Refereed	English	Research paper(scientific journal)	Disclose to all
Hasegawa T, Mori T, Yamaguchi T, Imoto S, Miyano S, Akutsu T	Hasegawa T, Mori T, Yamaguchi T, Imoto S, Miyano S, Akutsu T	Hasegawa T, Mori T, Yamaguchi T, Imoto S, Miyano S, Akutsu T	An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data	An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data	An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data	Journal of Computational Biology, 21, 11, 785-798	Journal of Computational Biology, 21, 11, 785-798	Journal of Computational Biology, 21, 11, 785-798	2014	Refereed	English	Research paper(scientific journal)	Disclose to all
Mori T, Tamura T, Fukagawa D, Takasu A, Tomita E, Akutsu T	Mori T, Tamura T, Fukagawa D, Takasu A, Tomita E, Akutsu T	Mori T, Tamura T, Fukagawa D, Takasu A, Tomita E, Akutsu T	A clique-based method using dynamic programming for computing edit distance between unordered trees	A clique-based method using dynamic programming for computing edit distance between unordered trees	A clique-based method using dynamic programming for computing edit distance between unordered trees	Journal of Computational Biology, 19, 10, 1089-1104	Journal of Computational Biology, 19, 10, 1089-1104	Journal of Computational Biology, 19, 10, 1089-1104	2012	Refereed	English	Research paper(scientific journal)	Disclose to all
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Misc

Author	Author(Japanese)	Author(English)	Title	Title(Japanese)	Title(English)	Bibliography	Bibliography(Japanese)	Bibliography(English)	Publication date	Refereed paper	Language	Disclose
劉立偉, 森智弥, 趙楊, 林田守広, 阿久津達也	劉立偉, 森智弥, 趙楊, 林田守広, 阿久津達也	劉立偉, 森智弥, 趙楊, 林田守広, 阿久津達也	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	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	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	電子情報通信学会技術研究報告, 115, 112, 245-246	電子情報通信学会技術研究報告, 115, 112, 245-246	電子情報通信学会技術研究報告, 115, 112, 245-246	2015		Japanese	Disclose to all
Akutsu T, Mori T, Tamura T, Fukagawa D, Takasu A, Tomita E	Akutsu T, Mori T, Tamura T, Fukagawa D, Takasu A, Tomita E	Akutsu T, Mori T, Tamura T, Fukagawa D, Takasu A, Tomita E	An improved clique-based method for computing edit distance between unordered trees and its application to comparison of glycan structures	An improved clique-based method for computing edit distance between unordered trees and its application to comparison of glycan structures	An improved clique-based method for computing edit distance between unordered trees and its application to comparison of glycan structures	Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011, 536-540	Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011, 536-540	Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011, 536-540	2011	Refereed	English	Disclose to all
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Conference Activities & Talks

Title	Title(Japanese)	Title(English)	Conference	Conference(Japanese)	Conference(English)	Date	Language	Assortment	Disclose
In silico three-dimensional reconstruction and identification of spatial discriminator genes of mouse gastrula embryo structure by self-organizing map (SOM) clustering	自己組織化マップによるマウス原腸胚構造 in silico 三次元再構築と空間識別遺伝子の同定	In silico three-dimensional reconstruction and identification of spatial discriminator genes of mouse gastrula embryo structure by self-organizing map (SOM) clustering	The 42nd Annual Meeting of the Molecular Biology Society of Japan	第42回日本分子生物学会年会	The 42nd Annual Meeting of the Molecular Biology Society of Japan	2019/12/03	Japanese	Oral presentation(general)	Disclose to all
Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering[Invited]	Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering [Invited]	Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering [Invited]	Japan-Germany International Workshop 2019-1 The Human Cell Type Authentication Initiative	Japan-Germany International Workshop 2019-1 The Human Cell Type Authentication Initiative	Japan-Germany International Workshop 2019-1 The Human Cell Type Authentication Initiative	2019/05/15	English	Symposium workshop panel(nominated)	Disclose to all
In silicon 3D tissue reconstruction	In silico 3D tissue reconstruction	In silicon 3D tissue reconstruction	Japan-Germany International Workshop 2018-1 The Human Cell Type Authentication Initiative	Japan-Germany International Workshop 2018-1 The Human Cell Type Authentication Initiative	Japan-Germany International Workshop 2018-1 The Human Cell Type Authentication Initiative	2018/04	English		Disclose to all
Development of ab initio 3D reconstruction algorithm for mid-gastrula mouse embryo from transcriptome using kernel self-organizing map	Development of ab initio 3D reconstruction algorithm for mid-gastrula mouse embryo from transcriptome using kernel self-organizing map	Development of ab initio 3D reconstruction algorithm for mid-gastrula mouse embryo from transcriptome using kernel self-organizing map	Single Cell Science Symposium “Technology Meets Biology”	Single Cell Science Symposium “Technology Meets Biology”	Single Cell Science Symposium “Technology Meets Biology”	2017/07	English	Oral presentation(general)	Disclose to all
Development of 3D tissue reconstruction method from single-cell RNA-seq data	Development of 3D tissue reconstruction method from single-cell RNA-seq data	Development of 3D tissue reconstruction method from single-cell RNA-seq data	2nd Challenges in Computational Biology: Gene Expression Data Analysis	2nd Challenges in Computational Biology: Gene Expression Data Analysis	2nd Challenges in Computational Biology: Gene Expression Data Analysis	2016/12	English	Oral presentation(general)	Disclose to all
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	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	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	生命情報科学若手の会	生命情報科学若手の会		2014/10	Japanese	Oral presentation(general)	Disclose to all
A clique-based method using dynamic programming for unordered tree edit distance problem	A clique-based method using dynamic programming for unordered tree edit distance problem	A clique-based method using dynamic programming for unordered tree edit distance problem	The 12th International Workshop on Bioinformatics and Systems Biology,	The 12th International Workshop on Bioinformatics and Systems Biology,	The 12th International Workshop on Bioinformatics and Systems Biology,	2012/07	English	Oral presentation(general)	Disclose to all
An improved clique-based method for computing edit distance between rooted unordered trees	An improved clique-based method for computing edit distance between rooted unordered trees	An improved clique-based method for computing edit distance between rooted unordered trees	情報処理学会バイオ情報学研究会	情報処理学会バイオ情報学研究会	情報処理学会バイオ情報学研究会	2011/09	English	Oral presentation(general)	Disclose to all
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Books etc

Author	Author(Japanese)	Author(English)	Title	Title(Japanese)	Title(English)	Publisher	Publisher(Japanese)	Publisher(English)	Publication date	Language	Type	Disclose
森智弥, 藤渕航	森智弥, 藤渕航	森智弥, 藤渕航	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	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	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	羊土社	羊土社	羊土社	2016/10		Contributor	Disclose to all
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Awards

Title(Japanese)	Title(English)	Organization name(Japanese)	Organization name(English)	Date
バイオ情報学研究会学生奨励賞	IPSJ SIGBIO Best Student Presentation Award	情報処理学会バイオ情報学研究会	SIG BIO	2011
情報処理学会山下記念研究賞	IPSJ Yamashita SIG Research Award	情報処理学会	Information Processing Society of Japan	2013

External funds: competitive funds and Grants-in-Aid for Scientific Research (Kakenhi)

Type	Position	Title(Japanese)	Period
特別研究員奨励費	Representative	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シミュレーション	2014/04/01-2016/03/31
若手研究B	Representative	DNAメチル化情報に基づく細胞の詳細な分類と評価手法の開発	2017/04/01-2019/03/31
若手研究	Representative	単一細胞オミックスデータに基づく細胞系譜推定および比較アルゴリズムの開発	2019/04/01-2022/03/31

Faculty management (title, position)

Title	Period
化学研究所広報委員会委員	2019/04/01-2020/03/31
化学研究所情報システム技術委員会委員	2019/04/01-2020/03/31

Academic organizaions (conference administrator)

Organization name	Group name	Title	Period
情報処理学会	バイオ情報学研究会（SIG BIO）	運営委員	2019/04/01-2021/03/31

Experience of living abroad

Organization	Department	Research theme	Country	Period
フンボルト大学（Humboldt University）	Theoretical biophysics laboratory	確率ブーリアンネットワークを用いたシグナル伝達ネットワークの数理モデル化	ドイツ	2012/12/-2013/03/

森 智弥

森智弥