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BioPreDyn- Bench: Parameter estimation benchmark problems. Visit the web. Publication: Villaverde, A.F., Henriques, D., Smallbone, K. et al. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst Biol 9, 8 (2015).

Regularization in Parameter estimation: Examples related to Fitzhugh-Nagumo and Goodwin oscillator models. Publication: Gábor, A., Banga, J.R. Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst Biol 9, 74 (2015). (scripts)

L. monocytogenes L1A1 biofilm life cycle: 1D Reaction-diffusion model including glucose uptake and ageing. Publication: Balsa-Canto et al. Modeling Reveals the Role of Aging and Glucose Uptake Impairment in L1A1 Listeria monocytogenes Biofilm Life Cycle. Frontiers in Microbiology, 8:2118, 2017 (scripts)

Nonlinear Lotka-Volterra models: Microbial competitive behaviour in co-cultures using nonlinear Lotka-Volterra models. Publication: Eva Balsa-Canto, Javier Alonso-del-Real, Amparo Querol. Mixed growth curve data do not suffice to fully characterize the dynamics of mixed cultures. Proceedings of the National Academy of Sciences Jan 2020, 117 (2) 811-813; DOI: 10.1073/pnas.1916774117. (scripts)

Role of temperature in co-culture fermentations: Microbial competitive behaviour in co-cultures using Gilpin-Ayala model with saturable competition and temperature dependency. Publication: Balsa-Canto E, Alonso-Del-Real J, Querol A. Temperature Shapes Ecological Dynamics in Mixed Culture Fermentations Driven by Two Species of the Saccharomyces Genus. Front Bioeng Biotechnol. 2020 Aug 21;8:915. (scripts)

Dynamic genome-scale modeling of yeast fermentation: A multi-phase multi-objective genome-scale model of yeast batch fermentation. For this model, AMIGO2 calls COBRA toolbox. (scripts) Publication: Henriques, D., Minebois, R., Mendoza, S.N., Macías, L.G., Pérez-Torrado, R., Barrio, E., Teusink, B., Querol, A., Balsa-Canto, E. A multiphase multiobjective dynamic genome-scale model shows different redox balancing among yeast species of the Saccharomyces genus in fermentation (2021) mSystems, 6 (4), art. no. e00260-21. https://doi.org/10.1128/mSystems.00260-21

A model for nitrogen-limited yeast fermentation: A model of biomass growth including total protein, carbohydrates and mRNA used to predict nitrogen-limited yeast fermentations. (scripts) Publication: Henriques, D., Balsa-Canto, E. The Monod Model is insufficient to explain biomass growth in nitrogen-limited yeast fermentation (2021) App& Environ Microbiol, 87 (20), 1-22. https://journals.asm.org/doi/10.1128/AEM.01084-21

NEW: A continuous model to describe single-culture yeast fermentation: Publication: Modelling the physiological status of yeast during wine fermentation enables the prediction of secondary metabolism, AR Moimenta, D Henriques, R Minebois, A Querol, E Balsa‐Canto, (2023) Microbial Biotechnology 16 (4), 847-861 (scripts)

NEW: A continuous dynamic genome-scale model explains batch fermentation led by species of the Saccharomyces genus. bioRxiv, 2024 (scripts)

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