Experimental evolution is performed with model microbes both in test tube and in silico. Dynamics of adaptive evolution observed in the test tubes will be analyzed with multiple computational tools to explore the fundamental principles in living systems. 

1. Kashiwagi, A., Noumachi, W., Katsuno, M.,Alam, T. M., Urabe, I., Yomo, T., Plasticity of fitness and diversification process during an experimental molecular evolution, J. Mol. Evol, Vol 52, No.6, P502-509.

2. Yoichiro Ito, Hitoshi Toyota, Kunihiko Kaneko, Tetsuya Yomo, How selection affects phenotypic fluctuation, Mol. Syst. Biol, Vol 5, No.264, P1-7.

3. Toshihiko Kishimoto, Leo Iijima, Makoto Tatsumi, Naoaki Ono, Ayana Oyake, Tomomi Hashimoto Moe Matsuo Masato, Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution, PLoS Genetics, Vol 6, No.10, Pe1001164.

4. Akiko Kashiwagi, Tetsuya Yomo, Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Qβ and Escherichia coli, PLoS Genet, Vol 7, No.8,  Pe1002188. 

5. Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T,  Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages, PLOS ONE, Vol 10, No.8, Pe0135639, 10.1371/journal.pone.0135639. 

6.Kishimoto T, Ying BW, Tsuru S, Iijima L, Suzuki S, Hashimoto T, Oyake A, Kobayashi H Someya Y Narisawa D Yomo T, Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process, PLoS Genet , Vol 11, No.7, Pe1005392 , 10.1371/journal.pgen.10053 92.