Y Ozawa, T Hashizume, BW Ying (2025) A data-driven approach for cell culture medium optimization. Biochem Eng J 214: 109591
H Aida, BW Ying (2024) Data-driven discovery of the interplay between genetic and environmental factors in bacterial growth.Commun Biol 7: 1691
K Hitomi, Y Ishii, BW Ying (2024) Experimental evolution for the recovery of growth loss due to genome reduction. eLife 13: 93520
T Hashizume, BW Ying (2024) Challenges in developing cell culture media using machine learning. Biotechnol Adv 70: 108293
S Zhang, H Aida, BW Ying (2023) Employing Active Learning in Medium Optimization for Selective Bacterial Growth. Appl Microbiol 3: 1355–1369
H Aida, BW Ying (2023) Efforts to Minimise the Bacterial Genome as a Free-Living Growing System. Biology 12: 1170
T Hashizume, Y Ozawa, BW Ying (2023) Employing active learning in the optimization of culture medium for mammalian cells. npj Syst Biol Appl 9: 20
H Aida, K Uchida, M Nagai, T Hashizume, S Masuo, N Takaya, BW Ying (2023) Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites. Comput Struct Biotechnol J 21: 2654-2663
Y Matsui, M Nagai, BW Ying (2023) Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions. Front Microbiol 14: 1145673
Z Lao, Y Matsui, S Ijichi, BW Ying (2022) Global coordination of the mutation and growth rates across the genetic and nutritional variety in Escherichia coli. Front Microbiol 13: 990969
H Aida, T Hashizume, K Ashino, BW Ying (2022) Machine learning-assisted discovery of growth decision elements by relating bacterial population dynamics to environmental diversity. eLife 11: 76846
K Hitomi, J Weng, BW Ying (2022) Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies. Front Microbiol 13: 948657
H Lu, H Aida, M Kurokawa, F Chen, Y Xia, J Xu, K Li, BW Ying, T Yomo (2022) Primordial mimicry induces morphological change in Escherichia coli. Commun Biol 5: 24
M Kurokawa, I Nishimura, BW Ying (2022) Experimental evolution expands the breadth of adaptation to an environmental gradient correlated with genome reduction. Front Microbiol 13: 826894
H XUE, M Kurokawa, BW Ying (2021) Correlation between the spatial distribution and colony size was common for monogenetic bacteria in laboratory conditions. BMC Microbiol 21: 114
M Nagai, M Kurokawa, BW Ying (2020) The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli. DNA Res 3: 27
L Liu, M Kurokawa, M Nagai, S Seno, BW Ying (2020) Correlated chromosomal periodicities according to the growth rate and gene expression. Sci Rep 10: 1038
Y XIA, BW Ying, M Hanczyc, T Yomo (2020)Experimental challenges in the origin and post-origin of life. Journal of Syst Chem 8: 9-19
YY Cao, T Yomo, BW Ying (2020) Clustering of Bacterial Growth Dynamics in Response to Growth Media by Dynamic Time Warping. Microorganisms 8: 331
M Kurokawa, BW Ying (2020) Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli. Microorganisms 8: 3
K Ashino, K Sugano, T Amagasa, BW Ying (2019) Predicting the decision making chemicals used for bacterial growth. Sci Rep 9: 7251
BW Ying, K Yama (2018) Gene expression order attributed to genome reduction and the steady cellular state in Escherichia coli. Front Microbiol 9: 2255
K Tsuchiya, YY Cao, M Kurokawa, K Ashino, T Yomo, BW Ying (2018) A decay effect of the growth rate associated with genome reduction in Escherichia coli. BMC Microbiol 18: 101
M Kurokawa, BW Ying (2018) Growth data of the E. coli strains carrying the reduced genomes. figshare. Dataset.
A Shibai, Y Takahashi, Y Ishizawa, D Motooka, S Nakamura, BW Ying & S Tsuru (2017) Mutation accumulation under UV radiation in Escherichia coli. Sci Rep 7: 14531
M Kurokawa & BW Ying (2017) Precise, high-throughput analysis of bacterial growth. J Vis Exp 127: e56197.
I Nishimura, M Kurokawa, L Liu & BW Ying (2017) Coordinated changes in mutation and growth rates induced by genome reduction. mBio 8: e00676-17.
BW Ying, S Seno, H Matsuda & T Yomo (2017) A simple comparison of the extrinsic noise in gene expression between native and foreign regulations in Escherichia coli. Biochem Biophys Res Comm 486:852-857.
M Kurokawa, S Seno, H Matsuda & BW Ying (2016) Correlation between genome reduction and bacterial growth. DNA Res 23: 517-525.
BW Ying, K Yama, K Kitahara & T Yomo (2016) The Escherichia coli transcriptome linked to growth fitness. Genomics Data (2016) 7:1-3.
K Yama, Y Matsumoto, Y Murakami, S Seno, H Matsuda, K Gotoh, D Motooka, S Nakamura, BW Ying & T Yomo (2015) Functional specialization in regulation and quality control in thermal adaptive evolution. Genes Cells 20: 943-55.
BW Ying, Y Matsumoto, K Kitahara, S Suzuki, N Ono, C Furusawa, T Kishimoto & T Yomo (2015) Bacterial transcriptome reorganization in thermal adaptive evolution. BMC Genomics 16: 802.
BW Ying, T Honda, S Tsuru, S Seno, H Matsuda, Y Kazuta & T Yomo (2015) Evolutionary consequence of a trade-off between growth and maintenance along with ribosomal damages. PLOS ONE 10: 0135639.
T Kishimoto, BW Ying+, S Tsuru, L Iijima, S Suzuki, T Hashimoto, A Oyake, H Kobayashi, Y Someya, D Narisawa & T Yomo (2015) Molecular clock of neutral mutations in a fitness-increasing evolutionary process. PLOS Genet 11: 1005392. (+equal contribution)
Y Murakami, Y Matsumoto, S Tsuru, BW Ying & T Yomo (2015) Global coordination in adaptation to gene rewiring. Nucleic Acids Res 43: 1304-1316.
Y Ishizawa, BW Ying, S Tsuru & T Yomo (2015) Nutrient-dependent growth defects and mutability of mutators in Escherichia coli. Genes Cells 20: 68-76.
M Yoshida, S Tsuru, N Hirata, S Seno, H Matsuda, BW Ying & T Yomo (2014) Directed evolution of cell size in Escherichia coli. BMC Evol Biol 14: 257.
A Shibai, S Tsuru, BW Ying, D Motooka, K Gotoh, S Nakamura & T Yomo (2014) Mutation accumulation in bacteria exposed to UV radiation. Artificial Life 14, 757-758.
Y Akeno, BW Ying, S Tsuru & T Yomo (2014) A reduced genome decreases the host carrying capacity for foreign DNA. Microbial Cell Factories 13: 49.
BW Ying, S Tsuru, S Seno, H Matsuda & T Yomo (2014) Gene expression scaled by distance to the genome replication site. Mol Biosyst 10: 375-379.
Y Matsumoto, Y Murakami, S Tsuru, BW Ying & T Yomo (2013) Growth rate-coordinated transcriptome reorganization in bacteria. BMC Genomics 14: 808.
BW Ying, Y Akeno & T Yomo (2013) Construction of synthetic gene circuits in the Escherichia coli genome. Methods Mol Biol 1073:157-68.
BW Ying, S Seno, F Kaneko, H Matsuda & T Yomo (2013) Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome. BMC Genomics 14:25.
Y Matsumoto, Y Ito, S Tsuru, BW Ying & T Yomo (2011) Bacterial cells carrying synthetic dual-function operon survived starvation. J Biomed Biotechnol 2011: 489265.
Y Shimizu, S Tsuru, Y Ito, BW Ying & T Yomo (2011) Stochastic switching induced adaptation in a starved Escherichia coli population. PLOS ONE 6: 23953.
S Tsuru, N Yasuda, Y Murakami, J Ushioda, A Kashiwagi, S Suzuki, K Mori, BW Ying & T Yomo (2011) Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli. Mol Syst Biol 7: 493.
S Suzuki, N Ono, C Furusawa, BW Ying & T Yomo (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms. PLOS ONE 6: 19534.
T Kishimoto, L Iijima, M Tatsumi, N Ono, A Oyake, T Hashimoto, M Matsuo, M Okubo, S Suzuki, K Mori, A Kashiwagi, C Furusawa, BW Ying & T Yomo (2010) Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution. PLOS Genet 6: 1001164.
BW Ying, Y Ito, Y Shimizu & T Yomo (2010) Refined method for the genomic integration of complex synthetic circuits. J Biosci Bioeng 110: 529-536.
S Tsuru, J Ichinose, A Kashiwagi, BW Ying, K Kaneko & T Yomo (2009) Noisy cell growth rate leads to fluctuating protein concentration in bacteria. Phys Biol 6: 036015.
T Niwa, BW Ying, K Saito, WZ Jin, S Takada, T Ueda & H Taguchi (2009) Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proc Natl Acad Sci USA 106: 4201-4206.
A Kashiwagi, T Sakurai, S Tsuru, BW Ying, K Mori & T Yomo (2009) Construction of Escherchia coli gene expression level perturbation collection. Metab Eng 11: 56-63.
S Tsuru, A Kashiwagi, BW Ying & T Yomo (2008) Adaptive gene expression beyond operator-repressor molecular regulatory system. Proceedings of the 13th International Symposium on Artificial Life and Robotics pp. 593-596.
BW Ying, D Fourmy & S Yoshizawa (2007) Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA. RNA 13: 1-9.
H Ohashi, Y Shimizu, BW Ying & T. Ueda (2007) Efficient protein selection based on ribosome display system with purified components. Biochem Biophys Res Com 352: 270-276.
Y Shimizu, Y Kuruma, BW Ying, S Umekage & T Ueda (2006). Cell-free translation systems for protein engineering. FEBS J 273: 4133-4140.
BW Ying, H Taguchi & T Ueda (2006) Co-translational binding of GroEL to nascent polypeptides is followed by post-translational encapsulation by GroES to mediate protein folding. J Biol Chem 281: 21813-21819.
BW Ying, H Taguchi, M Kondo & T Ueda (2005) Co-translational involvement of the chaperonin GroEL in the folding of newly synthesized polypeptides. J Biol Chem 280: 12035-12040.
BW Ying, H Taguchi, H Ueda & T Ueda (2004) Chaperone-assisted folding of a single-chain antibody in a reconstituted translation system. Biochem Biophys Res Com 320: 1359-1364.
BW Ying, T Suzuki, Y Shimizu & T Ueda (2003) A novel screening system for self-mRNA targeting proteins. J Biochem 133: 485-491.
Book chapters
BW Ying & T Yomo (2016) Comparative analyses of bacterial transcriptome reorganisation in response to temperature increase. In Stress and Environmental Control of Gene Expression in Bacteria (ed. FJ de Bruijn), Wiley-VCH, Weinheim.
BW Ying & T Yomo (2012) Built-in synthetic gene circuits in Escherichia coli – methodology and applications. In Advances in Applied Biotechnology (ed. M Petre), p195-208, InTech, Rijeka.
BW Ying & T Ueda (2009) Protein generation using a reconstituted system. In Protein Engineering Handbook (eds. S Lutz & U Bornscheuer), p515-533, Wiley-VCH, Weinheim.
BW Ying, Y Shimizu & T Ueda (2007) The PURE system: a minimal cell-free translation system. In Cell-Free Expression (ed. W Kudlicki), p76-83, Landes Bioscience, Austin.
