C. Martínez, E. Cinquemani, H. de Jong, J.-L. Gouzé. Optimal protein production by a synthetic microbial consortium: Coexistence, distribution of labor, and syntrophy. Journal of Mathematical Biology. To appear
A. Pavlou, E. Cinquemani, J. Geiselmann, H. de Jong. Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity. Biophysical Journal, 121(21):4179-4188, 2022
A. Yabo, J.-B. Caillau, J.-L. Gouzé. Optimal allocation of bacterial resources in fed-batch reactors. Proceedings of the European Control Conference (ECC 2022), IEEE, 2022. Accepted for publication
D. Ropers, Y. Couté, L. Faure, S. Ferré, D. Labourdette, A. Shabani, L. Trouilh, P. Vasseur, G. Corre, M. Ferro, M.-A. Teste, J. Geiselmann, H. de Jong. A multi-omics study of bacterial growth arrest in a synthetic biology application. ACS Synthetic Biology, 10(11):2910-2926, 2021
N. Augier, A. Yabo (2021). Time-optimal control of piecewise affine bistable gene-regulatory networks (accepted for publication). International Journal of Robust and Nonlinear Control. To appear
N. Augier, A. Yabo (2021). Time-optimal control of piecewise affine bistable gene-regulatory networks: preliminary results. Proceedings of the 7th IFAC Conference on Analysis and Design of Hybrid Systems (ADHS 21), Brussels, Belgium. To appear
A. Yabo, J.B. Caillau, J.L. Gouzé, H. de Jong, F. Mairet (2021). Dynamical analysis and optimization of a generalized resource allocation model of microbial growth. SIAM Journal on Applied Dynamical Systems, 21(1):137-165, 2022
A. Yabo, J.B. Caillau, J.L. Gouzé (2021). Hierarchical MPC applied to bacterial resource allocation and metabolite synthesis. Proceedings of the 60th Conference on Decision and Control (CDC 2021), Texas, United States. To appear
F. Mairet, J.-L. Gouzé, H. de Jong. Optimal proteome allocation and the temperature dependence of microbial growth laws. npj Systems Biology and Applications, 7:14, 2021
M. Chaves, H. de Jong. Qualitative modeling, analysis and control of synthetic regulatory circuits. In: F. Menolascine (ed.), Design, Construction and Modelling of Synthetic Gene Circuits, Methods in Molecular Biology 2229, Humana Press, New York, 2021, 1-40
A. Yabo, J.-B. Caillau, J.-L. Gouzé. Optimal bacterial resource allocation: metabolite production in continuous bioreactors. Mathematical Biosciences and Engineering, 17(6):7074-7100, 2020
A. Yabo, J.-L. Gouzé. Optimizing bacterial resource allocation: metabolite production in continuous bioreactors. Proceedings IFAC World Congress 2020, 53(2):16753-16758, 2020
M. Mauri, J.-L. Gouzé, H. de Jong, E. Cinquemani. Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs. PLoS Computational Biology, 16(4):e1007795, 2019
E. Cinquemani, F. Mairet, I. Yegorov, H. de Jong, J.-L. Gouzé. Optimal control of bacterial growth for metabolite production: The role of timing and costs of control. Proceedings of the 17th European Control Conference (ECC 2019), Naples, Italy, 2019
I. Yegorov, F. Mairet, H. de Jong, J.-L. Gouzé. Optimal control of bacterial growth for the maximization of metabolite production. Journal of Mathematical Biology, 78(4):985–1032, 2019
A. Yabo, J.-B. Caillau, J.-L. Gouzé. Singular regimes for the maximization of metabolite production. Proceedings of the 58th IEEE Conference on Decision and Control (CDC 2019), Nice, France, 31-36, 2019
A. Yabo, Bacterial growth strategies as Optimal Control problems: maximizing metabolite production. 19th French-German-Swiss conference on Optimization, Nice, France.
