Hideto Mori, Ph.D.

Education

• 2023.03 Ph.D., Systems Biology Program, Keio University, Tokyo, Japan

• 2018.03 Master of Media and Governance, Systems Biology Program, Keio University, Tokyo, Japan

• 2016.03 Bachelor of Arts in Environment and Information, Keio University, Tokyo, Japan.

Work Experience

• 2023.04-Today Specially Appointed Associate Professor (Full-Time), Premium Research Institute for Human Metaverse Medicine (PRIMe), Osaka University

• 2021.04-2023.03 Research Assistant (TTCK Fellow), Institute for Advanced Biosciences, Keio University   

• 2016.09-2021.03 Research Assistant, Research Center for Advanced Science and Technology, The University of Tokyo

• 2018.04-2020.03 Research Associate (Fixed term/Research incentive), Graduate School of Media and Governance, Keio University  

• 2014.04-2018.03 Research Assistant (TTCK Fellow), Institute for Advanced Biosciences, Keio University

Research Experiences

• 2021-2023 Exploring the mechanism for species-specific fusion of male and female gametes.
  @Ikawa laboratory, The Institute of Medical Science, The University of Tokyo 

• 2019-2021 Screening of new genome editing tools.
  @Yachie laboratory, Research Center for Advanced Science and Technology, The University of Tokyo

• 2019-2021 Development of a novel hierarchical DNA assembly method.
  @Yachie laboratory, Research Center for Advanced Science and Technology, The University of Tokyo

• 2016-Today Development of software tools to accelerate the development of genome editing tools and their applications.
  @Yachie laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Premium Research Institute for Human Metaverse Medicine (PRIMe), Osaka University

  • 2016-2018 A software tool to screen new genome editing-associated gene candidates (https://github.com/yachielab/SPADE).  

  • 2018-Today A universal platform to analyze genome editing outcomes.

  • 2018-2020 A machine learning model to predict base editing outcomes (https://github.com/yachielab/base-editing-prediction).

  • 2020-Today A framework to efficiently describe and share reproducible DNA construction protocols. (https://github.com/yachielab/QUEEN)

• 2013-2016, Development of a web-based biological model simulation environment.
  @Naito laboratory, Institute for Advanced Biosciences, Keio University

Preprints

1. Yamauchi-Ishikawa Y,  Emori C, Mori H, Endo T, Kobayashi K,  Watanabe Y, Sagara H, Nagata T,  Motooka D, Ninomiya A, Ozawa M, Ikawa M
   Age-associated aberrations of cumulus-oocyte interaction and microfilamentous structure in the zona pellucida decline female fertility
   bioRxiv. 2023 Dec 30, doi:https://doi.org/10.1101/2023.12.30.573680

2. Ishiguro S†, Ishida K†, Sakata RC†, Mori H, Takana M, King S, Bashth O, Ichiraku M, Masuyama N, Takimoto R, Kijima Y, Adel A, Toyoshima H, Seki M, Oh JH, Archambault AS, Nishida K, Kondo A, Kuhara S, Aburatani H, Klein Geltink RI, Takashima Y, Shakiba N, Yachie N.
   A multi-kingdom genetic barcoding system for precise target clone isolation.
   bioRxiv. 2023 Jan 19, doi: https://doi.org/10.1101/2023.01.18.524633
   †These authors equally contributed to this work.

Peer-reviewed articles

1. Ozawa M, Mori H, Endo T, Ishikawa-Yamauchi Y, Motooka D, Emori C, & Ikawa M. 
   Age-related decline in spermatogenic activity accompanied with endothelial cell senescence in male mice.
   iScience, 2023, 108456. https://doi.org/10.1016/j.isci.2023.108456 ​

2. Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O.
   An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
   Cell. 2023 Sep 22:S0092-8674(23)00963-7. doi: 10.1016/j.cell.2023.08.031. 

3. Oura S, Mori H, Ikawa M.
   Genome editing in mice and its application to the study of spermatogenesis.
   Gene and Genome Editing. 2022 Dec;3-4:100014. doi:10.1016/j.ggedit.2022.100014. 

4. Mori H, Yachie N.
   A framework to efficiently describe and share reproducible DNA materials and construction protocols.
   Nature Communications. 2022 May 24;13(1):2894. doi: 10.1038/s41467-022-30588-x. PMID: 35610233; PMCID: PMC9130275.

5. Nakagawa R, Ishiguro S, Okazaki S, Mori H, Tanaka M, Aburatani H, Yachie N, Nishimasu H, Nureki O.
   Engineered Campylobacter jejuni Cas9 variant with enhanced activity and broader targeting range.
   Communications Biology. 2022 Mar 8;5(1):211. doi: 10.1038/s42003-022-03149-7. PMID: 35260779; PMCID:PMC8904486.

6. Konno N, Kijima Y†, Watano K†, Ishiguro S†, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W, Yachie N.
   Deep distributed computing to reconstruct extremely large lineage trees.
   Nature Biotechnology. 2022 Apr;40(4):566-575. doi: 10.1038/s41587-021-01111-2. Epub 2022 Jan 6. PMID:34992246.
   †These authors equally contributed to this work.

7. Fukushima T, Tanaka Y, Adachi K, Masuyama N, Tsuchiya A, Asada S, Ishiguro S, Mori H, Seki M, Yachie N, Goyama S, Kitamura T.
   CRISPR/Cas9-mediated base-editing enables a chain reaction through sequential repair of sgRNA scaffold mutations.
   Scientific Reports. 2021 Dec 13;11(1):23889. doi: 10.1038/s41598-021-02986-6. PMID: 34903756; PMCID: PMC8668876.

8. Yamamuro T, Nakamura S, Yamano Y, Endo T, Yanagawa K, Tokumura A, Matsumura T, Kobayashi K, Mori H, Enokidani Y, Yoshida G, Imoto H, Kawabata T, Hamasaki M, Kuma A, Kuribayashi S, Takezawa K, Okada Y, Ozawa M, Fukuhara S, Shinohara T, Ikawa M, Yoshimori T.
   Rubicon prevents autophagic degradation of GATA4 to promote Sertoli cell function.
   PLoS Genetics. 2021 Aug 5;17(8):e1009688. doi: 10.1371/journal.pgen.1009688. PMID: 34351902; PMCID: PMC8341604.

9. Sakata RC†, Ishiguro S†, Mori H†, Tanaka M, Tatsuno K, Ueda H, Yamamoto S, Seki M, Masuyama N, Nishida K, Nishimasu H, Arakawa K, Kondo A, Nureki O, Tomita M, Aburatani H, Yachie N.
   Base editors for simultaneous introduction of C-to-T and A-to-G mutations.
   Nature Biotechnology. 2020 Jul;38(7):865-869. doi: 10.1038/s41587-020-0509-0. Epub 2020 Jun 2. PMID: 32483365.
   †These authors equally contributed to this work.

10. Murai Y, Masuda T, Onuma Y, Evans-Yamamoto D, Takeuchi N, Mori H, Masuyama N, Ishiguro S, Yachie N, Arakawa K.
    Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment.
    Microbiology Resource Announcements. 2020 Apr 16;9(16):e00291-20. doi: 10.1128/MRA.00291-20. PMID: 32299884; PMCID: PMC7163022.

11. Masuyama N†, Mori H†, Yachie N.
    DNA barcodes evolve for high-resolution cell lineage tracing.
    Current Opinion Chemical Biology. 2019 Oct;52:63-71. doi: 10.1016/j.cbpa.2019.05.014. Epub 2019 Jun 15. PMID: 31212208.
    †These authors equally contributed to this work.

12. Ishiguro S, Mori H, Yachie N.
    DNA event recorders send past information of cells to the time of observation.
    Current Opinion Chemical Biology. 2019 Oct;52:54-62. doi:10.1016/j.cbpa.2019.05.009. Epub 2019 Jun 11. PMID: 31200335.

13. Evans-Yamamoto D, Takeuchi N, Masuda T, Murai Y, Onuma Y, Mori H, Masuyama N, Ishiguro S, Yachie N, Arakawa K.
    Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan.
    Microbiology Resource Announcements. 2019 Apr 18;8(16):e00326-19. doi: 10.1128/MRA.00326-19. PMID: 31000557; PMCID: PMC6473151.

14. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M, Yachie N.
    Fast and global detection of periodic sequence repeats in large genomic resources.
    Nucleic Acids Research. 2019 Jan 25;47(2):e8. doi: 10.1093/nar/gky890. PMID: 30304510; PMCID: PMC6344855.

15. Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O.
    Engineered CRISPR-Cas9 nuclease with expanded targeting space.
    Science. 2018 Sep 21;361(6408):1259-1262. doi: 10.1126/science.aas9129. Epub 2018 Aug 30. PMID: 30166441; PMCID: PMC6368452.

16. Yachie, N., Robotic Biology Consortium (Mori H was involved in the IT group), & Natsume, T. Robotic Biology Consortium, Natsume T.
    Robotic crowd biology with Maholo LabDroids.
    Nature Biotechnology. 2017 Apr 11;35(4):310-312. doi: 10.1038/nbt.3758. PMID: 28398329.

Review articles (in Japanese)

1. 坂田 莉奈 & 森 秀人 細胞プログラミング技法と治療応用③. 実験医学 37, 13, 2197-2202 (2019)

2. 坂田 莉奈 & 森 秀人 細胞プログラミング技法と治療応用②. 実験医学 37, 10, 1838-1846 (2019)

3. 坂田 莉奈 & 森 秀人 細胞プログラミング技法と治療応用①. 実験医学 37, 8, 1324-1333 (2019)

4. 森 秀人 & 谷内江 望 新規ゲノム編集ツールを探索する. 月刊細胞 51, 3, 114-118 (2019)

5. 森 秀人 DNAイベントレコーダーによって細胞の過去の状態を知る. 実験医学 37, 3 , 440-448 (2019)

6. 森 秀人 & 石黒 宗 ウェットなデータストレージメディアとしてのDNA. 実験医学 37, 1, 106-112 (2019)

7. 森 秀人. 谷内江 望（翻訳）Carvunis A-R & Ideker T. Siri of the cell. 〜生物学はiPhoneから何を学べるだろうか〜. 実験医学別冊 (2017)

Ph.D. thesis

1. Mori H., Computational tools to accelerate the development and application of genome editing technology. Keio University, 2023   

Talks

1. 森 秀人. 新規ゲノム編集システムの開発にむけた汎用的ソフトウェア群の開発. 2019年度 医学研セミナー(招待公演), 東京都医学総合研究所, 2020年2月

Poster presentations

1. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M &Yachie N. SPADE for exploring periodic sequence repeats as potential genome editing modules, Frontiers in Genome Engineering 2019, Kobe, Japan, November 2019

2. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M &Yachie N. SPADE for exploring periodic sequence repeats as potential genome editing modules, The 20th International Conference on Systems Biology, Okinawa, Japan, November 2019

3. Mori H, Masuyama N, Evans-Yamamoto D, Ishiguro S, Sakata R, Nishimatsu H, Tomita M, Miyaoka Y, Nureki O, Hiroyuki A and Yachie N. DIAMOND: fully automated software to analyze amplicon sequencing data. Keystone Symposia Conference on Genome Engineering: From Mechanisms to Therapies, Victoria, Canada, February 2019

4. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M & Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. RECOMB Comparative Genomics 2018, Quebec, Canada, October 2018

5. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M &Yachie N. Exploration of periodically patterned DNA elements in genomic and metagenomic sequences. 12th International Workshop on Advanced Genomics, Tokyo Japan, June 2017

Fellowships

1. JSPS Research Fellowship for Young Scientist (DC2) from Japan Society for the Promotion of Science (April 2020 – Sep 2022).