Updated on 2025/04/03

写真a

 
HAYAMIZU, Momoko
 
Affiliation
Faculty of Science and Engineering, School of Fundamental Science and Engineering
Job title
Associate Professor
Degree
M.D. ( 2017.03 総合研究大学院大学 )
Ph.D. ( 2010.03 東京大学 )
Homepage URL
https://www.youtube.com/c/hayamizu-lab
Profile

I went to medical school with the intention of becoming a researcher in basic medicine and worked as a clinician for several years after graduation. However, I ended up becoming an applied mathematician because I was keenly aware of the importance of methods for extracting information from data since my student days, and I wanted to contribute to medicine through theoretical research on methods for analysing biological data.

My research is therefore related to mathematical science, information science, statistical science and life science, but my specialisation is in discrete mathematics (combinatorics, graph theory, discrete geometry, discrete algorithms), which deals with problems related to graphs and networks. I believe that my strength and originality lie in formulating important biological problems into mathematical problems and creating new theorems and algorithms to solve them.

I am currently particularly interested in the mathematical and computational aspects of phylogenetic trees and networks and their applications. Studying them can help elucidate many important biological processes, such as cell differentiation and bacterial or viral evolution.

I am also active in education and outreach activities. For more information, please visit my laboratory's YouTube channel.

 

Research Experience

  • 2024.06
    -
    Now

    Waseda University   Department of Applied Mathematics, Faculty of Science and Engineering   Associate Professor

  • 2019.10
    -
    Now

    Japan Science and Technology Agency (JST)   PRESTO Researcher

  • 2022.04
    -
    2024.06

    Waseda University   Faculty of Science and Engineering   Associate Professor

  • 2020.04
    -
    2022.03

    Waseda University   Faculty of Science and Engineering   Assistant Professor

  • 2017.04
    -
    2020.03

    Department of Statistical Science, School of Multidisciplinary Sciences, The Graduate University for Advanced Studies   Assistant Professor

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Education Background

  • 2014.04
    -
    2017.03

    The Graduate University for Advanced Studies   School of Multidisciplinary Sciences   Department of Statistical Science  

  • 2006.04
    -
    2010.03

    The University of Tokyo   Faculty of Medicine  

  • 2004.04
    -
    2006.03

    The University of Tokyo   College of Arts and Sciences  

Committee Memberships

  • 2019.03
    -
    2020.02

    The Mathematical Society of Japan  Local Delegate

Professional Memberships

  • 　
    　
    　

    Society for Mathematical Biology

  • 　
    　
    　

    THE JAPAN SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS

  • 　
    　
    　

    Mathematical Society of Japan

Research Areas

  • Statistical science / Applied mathematics and statistics / Basic mathematics / Theory of informatics

Research Interests

  • computational biology

  • theoretical biology

  • discrete mathematics

Awards

  • 日本応用数理学会・年会優秀ポスター賞(2022年度)

    2022.09   日本応用数理学会   横断歩道における歩行者対向流の組合せ論的考察

    Winner： 村田 悠, 早水 桃子

  • The Young Scientists’ Prize of the Commendation for Science and Technology

    2022.04   The Minister of Education, Culture, Sports, Science and Technology, Japan   Research of discrete mathematical problems related to the data analysis of life sciences

    Winner： Momoko Hayamizu

  • The 10th WASEDA e-Teaching Award

    2022.03   Waseda University   Introduction to Discrete Mathematics

    Winner： Momoko Hayamizu

  • 2020 9th Waseda e-Teaching Award Grand Award

    2021.05   Waseda University  

    Winner： Momoko Hayamizu, Manabu Machida, Kenji Nakamura

  • Best presentation award at the 2019 Joint Meeting of JSIAM Activity Groups

    2019.06   The Japan Society for Industrial and Applied Mathematics (JSIAM)  

    　View Summary

    'A structure theorem for tree-based networks and its application to phylogenetic tree inference'

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Media Coverage

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Papers

  • Orientability of undirected phylogenetic networks to a desired class: Practical algorithms and application to tree-child orientation

    Tsuyoshi Urata, Manato Yokoyama, Momoko Hayamizu

    The Workshop on Algorithms in Bioinformatics (WABI 2024)    2024.07  [Refereed]  [International journal]

    Authorship：Last author, Corresponding author

    DOI

    Scopus

  • Bridging Between Deviation Indices for Non-Tree-Based Phylogenetic Networks

    Takatora Suzuki, Han Guo, Momoko Hayamizu

    IEEE/ACM Transactions on Computational Biology and Bioinformatics    2024

    DOI

    Scopus

  • Bridging between Deviation Indices for Non-Tree-Based Phylogenetic Networks (previous title: Rooted Almost-binary Phylogenetic Networks for which the Maximum Covering Subtree Problem is Solvable in Linear Time)

    Takatora Suzuki, Han Guo, Momoko Hayamizu

       2023.05  [International journal]

    Authorship：Last author, Corresponding author

    DOI DOI2

  • Orienting undirected phylogenetic networks to tree-child network

    Shunsuke Maeda, Yusuke Kaneko, Hideaki Muramatsu, Yukihiro Murakami, Momoko Hayamizu

    Preprint    2023.05  [International coauthorship]

    Authorship：Last author, Corresponding author

    DOI

  • Ranking top-k trees in tree-based phylogenetic networks

    Momoko Hayamizu, Kazuhisa Makino

    IEEE/ACM Transactions on Computational Biology and Bioinformatics    2022.12

    Authorship：Lead author, Corresponding author

    DOI

    Scopus

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Works

  • Treefit - The first software for quantitative trajectory inference

    Momoko Hayamizu, Kouhei Sutou, Ryohei Suzuki, Hiromi Ishii  Software 

    2020.02
    -
    Now

    　View Summary

    Treefit is a novel data analysis toolkit that helps you perform two types of quantitative analysis of single-cell RNA-seq data: 1) measuring the goodness-of-fit between your single-cell RNA-seq data and esimated tree trajectories; and 2) discovering novel cell types or detecting contaminating cell types by predicting the number of principal paths in the best-fit tree trajectory. Treefit can be used to analyze either row counts or normalized expression data.

    Treefit is implemented in both R and Python languages and can be used in conjunction with other popular software packages, such as Seurat and dynverse. User-friendly tutorials of Treefit are available on the website.

  • Introduction to Discrete Mathematics (YouTube - Public lecture series)

    Momoko Hayamizu  Educational material 

    2021.04
    -
    Now

Presentations

  • Combinatorics of evolutionary trees and networks

    Momoko Hayamizu  [Invited]

    The Mathematical Society of Japan Autumn Meeting 2022  (Hokkaido University)  The Mathematical Society of Japan

    Presentation date： 2022.09

    Event date：
    2022.09
    　
    　

  • Treefit: a method to measure the robustness of differentiation trajectories inferred from single-cell RNA-seq data

    Momoko Hayamizu  [Invited]

    The 55th Annual Meeting of the Japanese Society of Developmental Biologists Symposium 4：Novel insights into cellular plasticity in development, regeneration, and aging  (Kanazawa / Zoom)  Japanese Society of Developmental Biologists

    Presentation date： 2022.06

  • How to reconstruct a cell differentiation trajectory using scRNA-seq snapshot data

    Momoko Hayamizu  [Invited]

    The 1st International Symposium on Human InformatiX X-Dimensional Human Informatics and Biology  (Kyoto)  Advanced Telecommunications Research Institute International (ATR)

    Presentation date： 2020.02

  • Characterising fully labelled tree-like metric spaces without using the four-point condition

    Momoko Hayamizu  [Invited]

    mini-symposium Combinatorial Phylogenetics 1, SIAM Conference on Applied Algebraic Geometry (AG'15)  (KAIST, Daejeon (Korea))  SIAM

    Presentation date： 2015.08

  • An introduction to discrete mathematics of phylogenetic networks: from basic concepts to recent advances

    Momoko Hayamizu  [Invited]

    Math and Biology in the Age of Huge Date and Computation/The 130th Annual Meeting of the Japanese Association of Anatomists(JAA)・The 102nd Annual Meeting of the Physiological Society of Japan(PSJ)・The 98th Annual Meeting of the Japanese Pharmacological Society(JPS)（APPW2025） 

    Presentation date： 2025.03

    Event date：
    2025.03
    　
    　

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Research Projects

  • 離散数学と統計科学の融合による生命科学データ解析の技術革新

    JST (Japan Science and Technology Agency)  FOREST

    Project Year :

    2023.04
    -
    2030.03
     

    Momoko Hayamizu

  • 離散幾何学が拓く計算系統学の新展開

    科学技術振興機構 (JST)  戦略的基礎研究推進事業 さきがけ研究

    Project Year :

    2019.10
    -
    2023.03
     

    早水 桃子

  • Discrete geometrical modelling of biological processes and its medical applications

    Japan Science and Technology Agency (JST)  PRESTO

    Project Year :

    2016.10
    -
    2020.03
     

    Momoko Hayamizu

  • 細胞系譜を解明する新しい系統解析技術の創出

    早稲田大学  PI飛躍支援プログラム

    Project Year :

    2023.04
    -
    2026.03
     

    早水桃子

  • 上皮幹細胞可塑性を利用した新しい再生医療のための非侵襲的幹細胞同定法の開発

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

    Project Year :

    2021.10
    -
    2024.03
     

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Other

  • Visitor

    2019.04
    　
    　

    　View Summary

    Institute of Statistical Science, Academia Sinica (Hosted by Prof. Hsien-Kuei Hwang)

  • Visiting Fellow

    2017.03
    　
    　

    　View Summary

    School of Computing, Engineering and Mathematics at Western Sydney University (Hosted by Prof. Andrew Francis)

  • Involvement in other research projects

    2016.09
    　
    　

    　View Summary

    Member of Statistics Group, JST CREST Project 'Topological data analysis for new descriptors on soft matters' (Director: Yasuaki Hiraoka)

 

Syllabus

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Teaching Experience

  • 生命科学のための離散数学

    Waseda University  

    2021.09
    -
    Now
     

  • 離散数学入門

    Waseda University  

    2021.04
    -
    Now
     

  • Advanced Topic in Modern Mathematical Sciences 1, 2

    Waseda University  

    2020.04
    -
    Now
     

  • 数学B1（微分積分）生医・建築(1)

    Waseda University  

    2020.04
    -
    2021.03
     

  • Seminar on Applied Dsicrete Mathematics A, B, C, D

    Waseda University  

    2022.04
    -
    Now
     

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Social Activities

  • 教員の授業見学受入れ（対象科目：「離散数学入門」）

    Center for Higher Education Studies, Waseda University 

    2022.04
    -
    Now

  • フォントスイッチプロジェクトYouTube スライド添削動画シリーズ（全4回）

    株式会社モリサワ  フォントスイッチプロジェクト 

    2023.12
    -
    2024.03

  • YouTubeを気楽に始めよう／よくある10の質問と私の答え

    日本評論社  『数学セミナー』2024年3月号 通巻 749号  （数学を伝える） 

    2024.02
    -
    　

  • フォントとレイアウトでできる！ 研究発表ポスターデザイン改善術

    株式会社モリサワ  Zoomウェビナー 

    2023.12
    -
    　

  • 巻頭エッセイ「令和の研究者と博士課程」

    岩波書店  『科学』2024年1月号 

    2023.12
    -
    　

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Academic Activities

  • ICIAM 2023 Mini-symposium "Challenges and Recent Advances in Phylogenetics" (4 sessions)

    Competition, symposium, etc.

    ICIAM (International Council for Industrial and Applied Mathematics)   Waseda University (+Zoom)

    2023.08
    　
    　

    　View Summary

    Phylogenetic trees and networks are used to elucidate the evolutionary history of genes or species. Data proliferation due to recent technological advancements has led to the pursuit of more efficient algorithms and novel approaches. Advances in the area can lead to breakthroughs in various disciplines of biology and life sciences, including genetics, cell biology, zoology, botany, microbiology, epidemiology, drug discovery, and biodiversity conservation, to name a few. This mini-symposium will cover recent topics related to phylogenetic research, from both theoretical and practical viewpoints, with results from algebra, algorithms, bioinformatics, combinatorics, computational complexity, geometry, statistics, and software development.

  • バイオインフォマティクスセミナー

    Academic society, research group, etc.

    早水桃子  

    2023.05
    -
    　

  • ICIAM 2023

    Peer review

    ICIAM (International Council for Industrial and Applied Mathematics)  

    2023.02
    -
    2023.05

  • CAT(0) festival

    Academic society, research group, etc.

    Momoko Hayamizu   Waseda University

    2022.03
    -
    　

  • 第2回 JST数学領域 未解決問題ワークショップ（オーガナイザー・出題者）

    Academic society, research group, etc.

    2018.09
    　
    　

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Sub-affiliation

  • Faculty of Science and Engineering   Graduate School of Fundamental Science and Engineering

Research Institute

  • 2023
    -
    2024

    Center for Data Science   Concurrent Researcher

  • 2022
    -
    2024

    Waseda Research Institute for Science and Engineering   Concurrent Researcher