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Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Constraint based methods, such as the Flux Balance Analysis, are widely used to model cellular growth processes without relying on extensive information on the regulatory features. The regulation is instead substituted by an optimization…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
Constraint-based metabolic modeling is the predominant framework for simulating cellular metabolism. The central assumption of these models is that metabolism operates at a steady state, meaning that the production and consumption rates of…
Constraint-based metabolic models can be used to investigate the intracellular physiology of microorganisms. These models couple genes to reactions, and typically seek to predict metabolite fluxes that optimize some biologically important…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…
An extensive rewiring of cell metabolism supports enhanced proliferation in cancer cells. We propose a systems level approach to describe this phenomenon based on Flux Balance Analysis (FBA). The approach does not explicit a cell biomass…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
We outline a modeling and optimization strategy for investigating dynamic metabolic engineering interventions. Our framework is particularly useful at the early stages of research and development, often constrained by limited knowledge and…
A metabolic model can be represented as bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
In this paper, a system architecture is proposed that approximately models the functionality of metabolic networks. The AND/OR graph model is used to represent the metabolic network and each processing element in the system emulates the…
Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…