Related papers: Computing knock out strategies in metabolic networ…
In our previous study, we showed that the branching process approximation is useful for estimating metabolic robustness, measured using the impact degree. By applying a theory of random family forests, we here extend the branching process…
Complex networks have been shown to be robust against random structural perturbations, but vulnerable against targeted attacks. Robustness analysis usually simulates the removal of individual or sets of nodes, followed by the assessment of…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
The complex interactions involved in regulation of a cell's function are captured by its interaction graph. More often than not, detailed knowledge about enhancing or suppressive regulatory influences and cooperative effects is lacking and…
Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far…
Despite the significant progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible. We introduce a novel approach to speed up the…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Metabolic networks have two properties that are generally regarded as unrelated: One, they have metabolic reactions whose single knockout is lethal for the organism, and two, they have correlated sets of reactions forming functional…
In this work we formalize a method to compute the degree of importance of biological agents that participates on the dynamics of a biological phenomenon build upon a complex network. We call this new procedure by theoretical knock-out (KO).…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…
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 systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular…
Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
Genetic and environmental perturbation experiments have been used to study microbes in a bid to gain insight into transcriptional regulation, adaptive evolution, and other cellular dynamics. These studies have potential in enabling rational…
Theoretical frameworks to estimate the tolerance of metabolic networks to various failures are important to evaluate the robustness of biological complex systems in systems biology. In this paper, we focus on a measure for robustness in…