Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models
High-throughput data generation and genome-scale stoichiometric models have greatly
facilitated the comprehensive study of metabolic networks. The computation of all feasible …
facilitated the comprehensive study of metabolic networks. The computation of all feasible …
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks
The metabolism of organisms can be studied with comprehensive stoichiometric models of
their metabolic networks. Flux balance analysis (FBA) calculates optimal metabolic …
their metabolic networks. Flux balance analysis (FBA) calculates optimal metabolic …
From annotated genomes to metabolic flux models and kinetic parameter fitting
Significant advances in system-level modeling of cellular behavior can be achieved based
on constraints derived from genomic information and on optimality hypotheses. For steady …
on constraints derived from genomic information and on optimality hypotheses. For steady …
Identifying essential genes in Escherichia coli from a metabolic optimization principle
C Martelli, A De Martino, E Marinari… - Proceedings of the …, 2009 - National Acad Sciences
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 …
stoichiometry and the topology of the underlying biochemical network is a central issue in …
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models
JJ Hamilton, V Dwivedi, JL Reed - Biophysical journal, 2013 - cell.com
Constraint-based methods provide powerful computational techniques to allow
understanding and prediction of cellular behavior. These methods rely on physiochemical …
understanding and prediction of cellular behavior. These methods rely on physiochemical …
A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks
D De Martino, M Figliuzzi, A De Martino… - PLoS computational …, 2012 - journals.plos.org
The integration of various types of genomic data into predictive models of biological
networks is one of the main challenges currently faced by computational biology. Constraint …
networks is one of the main challenges currently faced by computational biology. Constraint …
NetRed, an algorithm to reduce genome-scale metabolic networks and facilitate the analysis of flux predictions
Flux balance analysis (FBA) of large, genome-scale stoichiometric models (GSMs) is a
powerful and popular method to predict cell-wide metabolic activity. FBA typically generates …
powerful and popular method to predict cell-wide metabolic activity. FBA typically generates …
Cellular determinants of metabolite concentration ranges
Cellular functions are shaped by reaction networks whose dynamics are determined by the
concentrations of underlying components. However, cellular mechanisms ensuring that a …
concentrations of underlying components. However, cellular mechanisms ensuring that a …
Estimating metabolic fluxes using a maximum network flexibility paradigm
Motivation Genome-scale metabolic networks can be modeled in a constraint-based
fashion. Reaction stoichiometry combined with flux capacity constraints determine the space …
fashion. Reaction stoichiometry combined with flux capacity constraints determine the space …
Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks
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 …
along which the Gibbs energy decreases, implying that viable steady-state flux patterns …