Basic Information

Email Address

• Email Address

  matsui.motomu.7zkyoto-u.ac.jp

Professional Memberships

• THE MOLECULAR BIOLOGY SOCIETY OF JAPAN
• JAPANESE SOCIETY FOR BIOINFORMATICS
• SOCIETY OF EVOLUTIONARY STUDIES, JAPAN
• 日本微生物生態学会

Academic Degree

• 27 Mar. 2009

  慶應義塾大学修士（政策・メディア）
• 23 Mar. 2014

  慶應義塾大学博士（学術）

Academic Resume (Undergraduate School/Majors)

• 慶應義塾大学, 環境情報学部, 卒業

Research History

• From Aug. 2024, To Present

  Kyoto University, Institute for Chemical Research, Assistant Professor
• From Apr. 2017, To Jul. 2024

  The University of Tokyo, Graduate School of Science, Research Associate
• From Apr. 2015, To Mar. 2017

  The University of Tokyo, Graduate School of Science, Postdoctral Fellow, Japan Society for the Promotion of Science (PD)
• From Apr. 2014, To Mar. 2015

  The University of Tokyo, Graduate School of Science, Postdoctral Fellow
• From Apr. 2009, To Mar. 2012

  Keio University, Graduate School of Media and Governance, Research Fellow, Japan Society for the Promotion of Science (DC1)

ID,URL

• J-Global ID

  201801005933091880

• External link

  https://sites.google.com/site/motomumatsui/

researchmap URL

• https://researchmap.jp/motomu_matsui

Research

Research Interests

• phylogenetics
• 微生物生態
• graph theory
• Graph Splitting method
• NeTaGFT
• 輪作圃場
• early evolution
• superfamily

Research Areas

• Informatics, Biological, health, and medical informatics, Bioinformatics
• Life sciences, Ecology and environmental science, 微生物生態学
• Life sciences, Evolutionary biology, phylogenetics

Papers

• Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management

  Susumu Morigasaki; Motomu Matsui; Iwao Ohtsu; Yuki Doi; Yusuke Kawano; Ryosuke Nakai; Wataru Iwasaki; Hisayoshi Hayashi; Naoki Takaya

  Scientific Reports, 30 Apr. 2024, Peer-reviewed, Lead author

  
• NeTaGFT: A similarity network‐based method for trait analysis

  Hirotaka Matsumoto; Motomu Matsui

  Methods in Ecology and Evolution, 23 Nov. 2023, Peer-reviewed

  
• Nondestructive microbial discrimination using single-cell Raman spectra and random forest machine learning algorithm

  Nanako Kanno; Shingo Kato; Moriya Ohkuma; Motomu Matsui; Wataru Iwasaki; Shinsuke Shigeto

  STAR Protocols, Dec. 2022, Peer-reviewed

  
• Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model

  Takao K. Suzuki; Motomu Matsui; Sira Sriswasdi; Wataru Iwasaki

  Methods in Molecular Biology, 2022, Peer-reviewed, Invited

  
• Frontier of Inferring Phylogenies

  Motomu Matsui

  JSBi Bioinformatics Review, Oct. 2021, Peer-reviewed, Invited, Lead author, Corresponding author

  
• Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes

  Nanako Kanno; Shingo Kato; Moriya Ohkuma; Motomu Matsui; Wataru Iwasaki; Shinsuke Shigeto

  iScience, Sep. 2021, Peer-reviewed

  
• Graph Splitting: A Graph-Based Approach for Superfamily-scale Phylogenetic Tree Reconstruction

  Motomu Matsui; Wataru Iwasaki

  Systematic Biology, Aug. 2019, Peer-reviewed, Lead author, Corresponding author

  
• Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago.

  Tazro Ohta; Takeshi Kawashima; Natsuko O Shinozaki; Akito Dobashi; Satoshi Hiraoka; Tatsuhiko Hoshino; Keiichi Kanno; Takafumi Kataoka; Shuichi Kawashima; Motomu Matsui; Wataru Nemoto; Suguru Nishijima; Natsuki Suganuma; Haruo Suzuki; Y-H Taguchi; Yoichi Takenaka; Yosuke Tanigawa; Momoka Tsuneyoshi; Kazutoshi Yoshitake; Yukuto Sato; Riu Yamashita; Kazuharu Arakawa; Wataru Iwasaki

  Journal of plant research, Jul. 2018, Peer-reviewed

  
• Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks

  Motomu Matsui; Masaru Tomita; Akio Kanai

  GENOME BIOLOGY AND EVOLUTION, 2013, Peer-reviewed, Lead author, Corresponding author

  
• Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

  Atsuko Shinhara; Motomu Matsui; Kiriko Hiraoka; Wataru Nomura; Reiko Hirano; Kenji Nakahigashi; Masaru Tomita; Hirotada Mori; Akio Kanai

  BMC GENOMICS, Aug. 2011, Peer-reviewed

  
• Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse

  Motomu Matsui; Nozomu Yachie; Yuki Okada; Rintaro Saito; Masaru Tomita

  FEBS LETTERS, Sep. 2007, Peer-reviewed, Lead author, Corresponding author

  
• SPLITS: A new program for predicting split and intron-containing tRNA genes at the genome level

  Junichi Sugahara; Nozomu Yachie; Yasuhiko Sekine; Akiko Soma; Motomu Matsui; Masaru Tomita; Akio Kanai

  In Silico Biology, 2006, Peer-reviewed

  
• A comprehensive software suite for the analysis of cDNAs

  Kazuharu Arakawa; Haruo Suzuki; Kosuke Fujishima; Kenji Fujimoto; Sho Ueda; Motomu Matsui; Masaru Tomita

  Genomics, Proteomics and Bioinformatics, 2005, Peer-reviewed

  

Misc.

• シン・近隣結合法:PANJEP法が問い直す系統解析の常識

  松井求; 岩崎渉

  日本進化学会大会プログラム・講演要旨集(Web), 2022

  
• Development and application of the novel phylogenetic method based on graph theory

  松井 求

  京都大学化学研究所スーパーコンピュータシステム研究成果報告書, 2017

  
• Cover image

  Motomu Matsui

  SGMJ news letter, May 2014, Invited

  
• Cover image

  Motomu Matsui

  Genome Biology and Evolution, Apr. 2013, Invited

  

Presentations

• Graph Splitting Method Resolves the Early Evolution of Protein Superfamilies

  Motomu Matsui

  IIBMP2018, 20 Sep. 2018

  
• Graph Splitting法でタンパク質スーパーファミリーの進化を俯瞰する

  松井求

  第20回日本進化学会, 23 Aug. 2018

  
• Graph Splitting Method: Novel Phylogenetic Approach Beyond the Twilight Zone

  Motomu Matsui

  JSBi2015, 29 Oct. 2015

  
• Graph Splitting法: トワイライトゾーンを越える新たな系統解析手法

  松井求

  第17回日本進化学会, 20 Aug. 2015

  
• バクテリアにおける転写制御ネットワークの包括的進化解析

  松井求

  第8回日本ゲノム微生物学会, 07 Mar. 2014

  
• Genome-wide Analysis of novel small Peptide in Escherichia coli

  Motomu Matsui

  CBI2006, 25 Jul. 2006

  

Awards

• 31 Oct. 2015

  研究奨励賞（日本バイオインフォマティクス学会）

External funds: Kakenhi

• 熱帯農地における生物的炭素隔離の実現に必要な機序解明と活用

  Grant-in-Aid for Scientific Research (B)

  Basic Section 41050:Environmental agriculture-related

  Tokyo University of Agriculture and Technology

  杉原 創

  From 01 Apr. 2024, To 31 Mar. 2028, Granted

  土壌炭素隔離;土壌微生物機能;生態系サービス;熱帯農業生態系

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-24K01889/
• 半乾燥熱帯畑作地における混作技術革新：根圏微生物機能と深層土水の活用

  Fund for the Promotion of Joint International Research (International Collaborative Research)

  Medium-sized Section 41:Agricultural economics and rural sociology, agricultural engineering, and related fields

  Tokyo University of Agriculture and Technology

  杉原 創

  From 08 Sep. 2023, To 31 Mar. 2027, Granted

  混作;窒素・リン・水循環;持続可能性;微生物群集;深層土

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23KK0122/
• Post-Koch Ecosystem revealed by Functional informatics

  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

  Complex systems

  The University of Tokyo

  Motomu Matsui

  From 28 Jun. 2019, To 31 Mar. 2024, Project Closed

  バイオインフォマティクス;微生物ダークマター;ポストコッホ生態系;データベース;機能インフォマティクス;ネットワーク解析;微生物生態;メタゲノム解析;ネットワーク;ポストコッホ生態;微生物生態学;窒素循環;微生物形態;微生物相互作用

  https://kaken.nii.ac.jp/grant/KAKENHI-PLANNED-19H05688/
• Post-Koch Ecology - The next-era microbial ecology

  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

  Complex systems

  University of Tsukuba

  高谷 直樹

  From 28 Jun. 2019, To 31 Mar. 2024, Granted

  微生物生態

  https://kaken.nii.ac.jp/grant/KAKENHI-ORGANIZER-19H05679/

Academic, Social Contribution

Committee Memberships

• From Apr. 2022, To Present

  director, Japanese Society for Bioinformatics
• From Apr. 2020, To Mar. 2022

  auditor, Japanese Society for Bioinformatics