Motomu MATSUI, Ph.D.
Assistant Professor
Institute for Chemical Research,
Kyoto University, Japan
E-mail: qm at kuicr.kyoto-u.ac.jp
Molecular Evolution; Phylogenetics, Genome evolution
Microbiome; Ecosystem, Trait-based ecology
RNA biology; non-coding RNA, post-transcriptional regulation
Japanese Archery; Ogasawara-ryu, 4th dan level
2024–present Assistant Professor; Institute for Chemical Research, Kyoto University, Japan
2017–2024 Research Associate; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
2015–2017 Postdoctral Fellow; Japan Society for the Promotion of Science (PD); Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
2014–2015 Postdoctral Fellow; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
2009–2011 Research Fellow; Japan Society for the Promotion of Science (DC1)
2009–2012 Part-time lecturer; Faculty of Environment and Information Studies, Keio University, Japan (Genetic Analysis Laboratory)
2014 Ph.D., Graduate School of Media and Governance, Keio University, Japan
2009 M.A. in Systems Biology, Graduate School of Media and Governance, Keio University, Japan
2007 B.S., Faculty of Environment and Information Studies, Keio University, Japan
The publication list in PubMed
16. Seiji Toki, Motomu Matsui, Kento Tominaga, Takao K. Suzuki, Takashi Tsuchimatsu, and Wataru Iwasaki
Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes
mSystems, 2026, 0:e00062-26
15. Hiroshi Mori, Takatomo Fujisawa, Koichi Higashi, Yasuhiro Tanizawa, Zenichi Nakagawa, Hiroyo Nishide, Masaki Fujiyoshi, Yasukazu Nakamura, Ikuo Uchiyama, Motomu Matsui, and Takuji Yamada
Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets
Microbiome, 2026
14. Masaki Fujiyoshi, Takao K Suzuki, Wataru Iwasaki, Chikara Furusawa, Motomu Matsui
Bac2Feature: an easy-to-use interface to predict prokaryotic traits from 16S rRNA gene sequences
Bioinformatics Advances, 2025, vbaf136
13. Susumu Morigasaki, Motomu Matsui, Iwao Ohtsu, Yuki Doi, Yusuke Kawano, Ryosuke Nakai, Wataru Iwasaki, Hisayoshi Hayashi, and Naoki Takaya
Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management
Scientific Reports, 2024, 14(1):9896
12. Hirotaka Matsumoto, Motomu Matsui
NeTaGFT: A similarity network-based method for trait analysis
Methods in Ecology and Evolution, 2023, 15:153–163
11. Nanako Kanno, Shingo Kato, Moriya Ohkuma, Motomu Matsui, Wataru Iwasaki, and Shinsuke Shigeto
Nondestructive microbial discrimination using single-cell Raman spectra and Random Forest machine learning algorithm
STAR Protocols, 2022, 3(4):101812
10. Takao K Suzuki, Motomu Matsui, Sira Sriswasdi, and Wataru Iwasaki
Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model
Methods in Molecular Biology, 2022, 2569:327–342
9. Motomu Matsui
Frontier of Inferring Phylogenies
JSBi Bioinformatics Review (in Japanese), 2021, 2(1):30-57
8. Nanako Kanno, Shingo Kato, Moriya Ohkuma, Motomu Matsui, Wataru Iwasaki, and Shinsuke Shigeto
Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes
iScience, 2021, 24(9):102975
7. Motomu Matsui, and Wataru Iwasaki
Graph Splitting: A Graph-Based Approach for Superfamily-scale Phylogenetic Tree Reconstruction
Systematic Biology, 2020, 69(2):265–279
PDF | Full Text | PubMed | Press release
6. 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 and Wataru Iwasaki
Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago
Journal of Plant Research, 2018, 131(4):709–717
5. Motomu Matsui, Masaru Tomita and Akio Kanai
Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks
Genome Biology Evolution, 2013, 5(2):267–282
Adopted as the cover art of Genome Biology and Evolution, 5(4), 2013.
4. Atsuko Shinhara, Motomu Matsui, Kiriko Hiraoka, Wataru Nomura, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori and Akio Kanai
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli
BMC Genomics, 2011, 12:428
Certified as Highly accessed in BMC Genomics, 12.
3. Motomu Matsui, Nozomu Yachie, Yuki Okada, Rintaro Saito and Masaru Tomita
Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse
FEBS Letter, 2007, 581:4184–4188
2. Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita and Akio Kanai
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level
In Silico Biology, 2006, 6:411–418
1. Kazuharu Arakawa, Haruo Suzuki, Kosuke Fujishima, Kenji Fujimoto, Shou Ueda, Motomu Matsui, and Masaru Tomita
A comprehensive software suite for the analysis of cDNAs
Genomics Proteomics Bioinformatics, 2005, 3:179–188
Graph Splitting Method
Bac2Feature
https://www.genome.jp/bac2feature/
OGT predictor
https://github.com/tsuchimatsu/OGT_prediction
Microbiome Datahub
https://mdatahub.org/
NeTaGFT
https://github.com/hmatsu1226/NeTaGFT
Escherichia coli sRNA Browser
Github