Probabilistic Thermodynamic Analysis of Metabolic Networks

Thermodynamic Constraints for Metabolic Networks

Probabilistic properties of nonextensive thermodynamic

Based on the Tsallis entropy, the nonextensive thermodynamic properties are studied as a qdeformation of classical statistical results using only probabilistic methods and straightforward calculations. It is shown that the constant in the Tsallis entropy depends on the deformation parameter and must be redefined to recover the usual thermodynamic relations. The notions of variance and covarianc...

Rule-based joint fuzzy and probabilistic networks

One of the important challenges in Graphical models is the problem of dealing with the uncertainties in the problem. Among graphical networks, fuzzy cognitive map is only capable of modeling fuzzy uncertainty and the Bayesian network is only capable of modeling probabilistic uncertainty. In many real issues, we are faced with both fuzzy and probabilistic uncertainties. In these cases, the propo...

Global probabilistic annotation of metabolic networks enables enzyme discovery

Annotation of organism-specific metabolic networks is one of the main challenges of systems biology. Importantly, owing to inherent uncertainty of computational annotations, predictions of biochemical function need to be treated probabilistically. We present a global probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlatio...

Stoichiometric analysis of metabolic networks

A major current challenge in systems biology is to clarify the relationship between structure, function and regulation in complex metabolic networks reconstructed from genomic data. However, dynamic mathematical modeling of large-scale networks meets difficulties as the necessary mechanistic detail and kinetic parameters are rarely available. In contrast, structure-oriented (stoichiometric / co...