Related papers: Model Validation and Selection in Metabolic Flux A…
Accurate quantification of intracellular metabolic fluxes is central to systems biology and biotechnology. Flux estimation relies on biochemical network models, with $^{13}$C metabolic flux analysis (MFA) being the state-of-the-art…
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…
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…
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…
Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of…
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…
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…
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…
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…
Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
For over two decades, Flux Balance Analysis (FBA) has been successfully used for predicting growth rates and intracellular reaction rates in microbiological metabolism. An aspect that is often omitted from this analysis, is segregation or…
Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
Background: The rational identification of essential genes is a cornerstone of drug discovery, yet standard computational methods like Flux Balance Analysis (FBA) often struggle to produce accurate predictions in complex, redundant…
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained…
Microorganisms have developed complex regulatory features controlling their reaction and internal adaptation to changing environments. When modeling these organisms we usually do not have full understanding of the regulation and rely on…