相关论文: A simple method to extend COBRApy dynamic FBA prot…
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,…
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 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…
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…
Many dynamic processes such as telecommunication and transport networks can be described through discrete time series of graphs. Modelling the dynamics of such time series enables prediction of graph structure at future time steps, which…
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…
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…
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…
A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of charge-consistent tight-binding DFT. A long-range correction is…
Resource Balance Analysis (RBA) is a framework for predicting steady-state cellular growth under resource constraints. However, classical RBA formulations are static and do not capture the dynamic regulation of biosynthetic resources or…
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…
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…
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…
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…
Resource Balance Analysis (RBA) is a computational method based on resource allocation, which performs accurate quantitative predictions of whole-cell states (i.e. growth rate, meta-bolic fluxes, abundances of molecular machines including…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
Motivation: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered…
13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction…
Carbon isotope labeling method is a standard metabolic engineering tool for flux quantification in living cells. To cope with the high dimensionality of isotope labeling systems, diverse algorithms have been developed to reduce the number…
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…