Work

I. Lecture note | 講義資料

Advanced Evolutional Systems (Population Genetics) 進化システム特論(集団遺伝学) @ Osaka Univ.

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Integrated Biological and Information Engineering 先端生物情報融合論 @ Osaka Univ.

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Introduction to Bioinformatic Engineering バイオ情報工学入門 @ Osaka Univ.

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II. Technical Papers | 査読済み原著論文, 査読済み総説論文, 査読中プレプリント

Saburo Tsuru's Google Scholar Citations

1. Hiroki Ono, Saburo Tsuru, and Chikara Furusawa, Carbon source diversity shapes bacterial interspecies interactions. bioRxiv (preprint), 2025. (role: corresponding author)

2. Naoki Konno, Keita Miyake, Satoshi Nishino, Kimiho Omae, Haruaki Yanagisawa, Saburo Tsuru, Yuki Nishimura, Masahide Kikkawa, Chikara Furusawa, and Wataru Iwasaki, Repeatability of protein structural evolution following convergent gene fusions. Nature Communications, 2025. Press Release

3. Saburo Tsuru and Chikara Furusawa, Congruence between noise and plasticity in protein expression. Scientific Reports, 2025, 15(24529): p. 1-13. (role: corresponding author)

4. Yuki Kanai, Atsushi Shibai, Naomi Yokoi, Saburo Tsuru and Chikara Furusawa, Laboratory evolution of the bacterial genome structure through insertion sequence activation. Nucleic Acids Research, 2025, 53(9): p. 1-17. (role: corresponding author) Press Release

5. Saburo Tsuru and Chikara Furusawa, Genetic properties underlying transcriptional variability across different perturbations. Nature Communications, 2025, 16(2421): p. 1-16. (role: corresponding author) Press Release

6. Saburo Tsuru, Naoki Hatanaka, and Chikara Furusawa, Promoters constrain evolution of expression levels of essential genes in Escherichia coli. Molecular Biology and Evolution, 2024, 41(9): p. 1-17. (role: corresponding author)

7. Yuki Kanai, Saburo Tsuru, and Chikara Furusawa, Insertion sequences: Simple mobile elements with rich ecological and evolutionary structures. Current Opinion in Systems Biology, 2023, 36(100481): p. 1-7.

8. Yuki Azuma, Saburo Tsuru, Masumi Habuchi, Risa Takami, Sotaro Takano, Kayo Yamamoto, and Kazufumi Hosoda, Synthetic symbiosis between a cyanobacterium and a ciliate toward novel chloroplast-like endosymbiosis. Scientific Reports, 2023, 13(6104): p. 1-9.

9. Sotaro Takano, Hiromi Takahashi, Yoshie Yama, Ryo Miyazaki, Chikara Furusawa, and Saburo Tsuru, Inference of transcriptome signatures of Escherichia coli in long-term stationary phase. Scientific Reports, 2023, 13(5647): p. 1-13. (role: corresponding author)

10. Atsushi Shibai, Hazuki Kotani, Natsue Sakata, Chikara Furusawa, and Saburo Tsuru, Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli. G3: Genes, Genomes, Genetics, 2022, 12(11): p. 1-11. (role: corresponding author)

11. Yuki Kanai, Saburo Tsuru, and Chikara Furusawa, Experimental demonstration of operon formation catalyzed by insertion sequence. Nucleic Acids Research, 2022, 50(3): p. 1673-86. (role: corresponding author) Press Release

12. Atsushi Shibai, Saburo Tsuru, and Tetsuya Yomo, Development of an automated UV irradiation device for microbial cell culture. SLAS Technology, 2018, 24 (3), 342-8. (role: corresponding author)

13. Takahiro Komori, Atsushi Shibai, Hiromi Saito, Yuya Akeno, Arnaud Germond, Takaaki Horinouchi, Chikara Furusawa, and Saburo Tsuru, Enhancement of K-strategy evolution in histidine utilization using a container with compartments. Genes to Cells, 2018, 23 (10): p. 893-903. (role: corresponding author)

14. Atsushi Shibai, Yusuke Takahashi, Yuka Ishizawa, Daisuke Motooka, Shota Nakamura, Bei-Wen Ying, and Saburo Tsuru, Mutation accumulation under UV radiation in Escherichia coli. Scientific Reports, 2017, 7(14531), 1-12. (role: corresponding author)

15. Sotaro Takano, Bogna J. Pawlowska, Ivana Gudelj, and Tetsuya Yomo, Saburo Tsuru, Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation. mBio, 2017, 8(1), 1-14. (role: corresponding author)

16. Rebecca Baumstark, Sonja Hänzelmann, Saburo Tsuru, Yolanda Schaerli, Mirko Francesconi, Francesco M. Mancuso, Robert Castelo, and Mark Isalan, The propagation of perturbations in rewired bacterial gene networks. Nature Communications, 2015, 6(10105): p. 1-11.

17. Saburo Tsuru, Yuka Ishizawa, Atsushi Shibai, Yusuke Takahashi, Daisuke Motooka, Shota Nakamura, and Tetsuya Yomo, Genomic confirmation of nutrient-dependent mutability of mutators in Escherichia coli. Genes to Cells, 2015, 20(12): p. 972-81.

18. Bei-Wen Ying, Tomoya Honda, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Yasuaki Kazuta, and Tetsuya Yomo, Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLOS ONE, 2015, 10(8): p. 1-19.

19. Toshihiko Kishimoto, Bei-Wen Ying, Saburo Tsuru, Leo Iijima,Shingo Suzuki, Tomomi Hashimoto, Ayana Oyake, Hisaka Kobayashi, Yuki Someya, Dai Narisawa, and Tetsuya Yomo, Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. PLOS Genetics, 2015, 11(7): p. 1-18. (role: co-first author)

20. Kazuya Nishimura, Saburo Tsuru, Hiroaki Suzuki, and Tetsuya Yomo, Stochasticity in gene expression in a cell-sized compartment. ACS Synthetic Biology, 2015, 4(5): p. 566-76.

21. Yoshie Murakami, Yuki Matsumoto, Saburo Tsuru, Bei-Wen Ying, and Tetsuya Yomo, Global coordination in adaptation to gene rewiring. Nucleic Acids Research, 2014, 42(2): p. 1304-16.

22. Yuka Ishizawa, Bei-Wen Ying, Saburo Tsuru, and Tetsuya Yomo, Nutrient-dependent growth defects and mutability of mutators in Escherichia coli. Genes to Cells, 2015, 20(1): p. 68-76.

23. Mari Yoshida, Saburo Tsuru, Naoko Hirata, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying, and Tetsuya Yomo, Directed evolution of cell size in Escherichia coli. BMC Evolutionary Biology, 2014, 14(257): p. 1-12.

24. Yuya Akeno, Bei-Wen Ying, Saburo Tsuru, and Tetsuya Yomo, A reduced genome decreases the host carrying capacity for foreign DNA. Microbial Cell Factories, 2014, 13(49): p. 1-9.

25. Bei-Wen Ying, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, and Tetsuya Yomo, Gene expression scaled by distance to the genome replication site. Molecular BioSystems, 2014, 10(3): p. 375-9.

26. Yuki Matsumoto, Yoshie Murakami, Saburo Tsuru, Bei-Wen Ying, and Tetsuya Yomo, Growth rate-coordinated transcriptome reorganization in bacteria. BMC Genomics, 2013, 14(808): p. 1-10.

27. Yuki Matsumoto, Yoichiro Ito, Saburo Tsuru, Bei-Wen Ying, and Tetsuya Yomo, Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation. Journal of Biomedicine and Biotechnology, 2011, 2011(489265): p. 1-10.

28. Yoshihiro Shimizu, Saburo Tsuru, Yoichiro Ito, Bei-Wen Ying, and Tetsuya Yomo, Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population. PLOS ONE, 2011, 6(9): p. 1-11. (role: co-first author)

29. Saburo Tsuru, Nao Yasuda, Yoshie Murakami, Junya Ushioda, Akiko Kashiwagi, Shingo Suzuki, Kotaro Mori, Bei-Wen Ying, and Tetsuya Yomo, Adaption by stochastic switching of a monostable genetic circuit in Escherichia coli. Molecular Systems Biology, 2011, 7(493): p. 1-10.

30. Saburo Tsuru, Junya Ichinose, Akiko Kashiwagi, Bei-Wen Ying, Kunihiko Kaneko, and Tetsuya Yomo, Noisy cell growth rate leads to fluctuating protein concentration in bacteria. Physical Biology, 2009, 6(3): p. 1-9.

31. Akiko Kashiwagi, Takahiro Sakurai, Saburo Tsuru, Bei-Wen Ying, Kotaro Mori, and Tetsuya Yomo, Construction of Escherichia coli gene expression level perturbation collection. Metabolic Engineering, 2009, 11(1): p. 56-63.

III. Technical Proceedings | 査読済み国際会議抄録

1. Atsushi Shibai, Daisuke Motooka, Shota Nakamura, and Saburo Tsuru, Reductive evolution towards primitive life: What will we see? The Fifteenth International Conference on the Synthesis and Simulation of Living Systems, 2016, p. 188-9, Cancun, Mexico.

2. Atsushi Shibai, Saburo Tsuru, Bei-Wen Ying, Daisuke Motooka, Kazuyoshi Gotoh, Shota Nakamura, and Tetsuya Yomo, Mutation Accumulation in Bacteria Exposed to UV Radiation. The Fourteenth International Conference on the Synthesis and Simulation of Living Systems, 2014, p. 757-8, Manhattan, New York, USA.

3. Saburo Tsuru, Akiko Kashiwagi, Bei-Wen Ying, and Tetsuya Yomo, Adaptive gene expression beyond operator-repressor molecular regulatory system. The Thirteenth International Symposium on Artificial Life and Robotics, 2008, OS6-7, 593-6, Beppu, Oita, Japan.

IV. General Public | 解説（日本語）

1. 津留三良, 古澤力, 進化に伴う突然変異の影響を受けやすい遺伝子. 現代化学, 2025, 7(652): p. 8-9.

2. 津留三良, 実験室で分子進化を再現する. 生物工学, 2022, 100 (11): p. 621.

3. Bei-Wen Ying，津留三良，四方哲也, 細胞の個性による運命の決定. 細胞工学, 2011, 30(10): p. 1078-83.

4. 津留三良，Bei-Wen Ying，四方哲也, 遺伝子発現ゆらぎの解析と応用. 実験医学, 2010, 28 (1): p. 7-11.

V. Software | ソフトウェア

GitHub