“…While these data are very beneficial, they are typically incomplete and noisy, which renders the inference of parameter values for complex dynamic models challenging. Fortunately, many biological systems have embedded linear mathematical features, which may be exploited, thereby improving fits and leading to better convergence of optimization algorithms. …”
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“…With the goal of shedding light on the functional integration of the yeast sphingolipid-ergosterol (SL-E) pathway, we constructed a dynamic model of the ergosterol pathway using the guidelines of Biochemical Systems Theory (BST) (Savageau., J. theor. …”
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“…The estimation of parameters in even moderately large biological systems is a significant challenge. This challenge is greatly exacerbated if the mathematical formats of appropriate process descriptions are unknown. …”
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“…As a case study, we illustrate dBST applied to the dynamics of the aryl hydrocarbon receptor (AhR), a signal transduction system that simultaneously involves time delays and stochasticity.…”
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“…As an aid that might facilitate our understanding of dopamine dynamics in the pathogenesis and treatment in PD, we have begun to merge currently available information and expert knowledge regarding presynaptic dopamine homeostasis into a computational model, following the guidelines of biochemical systems theory. …”
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“…The combination of traditional biology with mathematical and computational methods has had a profound effect on our current understanding of morphogenesis and led to significant insights and advancements in the field. …”
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“…Multivariate Autoregressive and Lotka-Volterra models are mathematically equivalent at the steady state, but the results of our comparison suggest that Lotka-Volterra models are generally superior in capturing the dynamics of networks with non-linear dynamics, whereas Multivariate Autoregressive models are better suited for analyses of networks of populations with process noise and close-to linear behavior. …”
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“…Using time dependent metabolic concentration data, we use a combination of mathematical modeling, reverse engineering, and optimization to infer dynamic changes in enzyme activities within the sphingolipid pathway. …”
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“…The regulatory roles of sphingolipids in diverse cell functions have been characterized extensively. However, the dynamics and interactions among the different sphingolipid species are difficult to assess, because de novo biosynthesis, metabolic inter-conversions, and the retrieval of sphingolipids from membranes form a complex, highly regulated pathway system. …”
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