Related papers: Metabolic graphs, LIFE method and the modeling of …
The metabolic process in a cell is modeled with the use of the Fourier transformation. The histograms of the invariant measures of chaotic attractors are constructed. In particular, a scenario of adaptation of the metabolic process under a…
The goal of this study is to develop a computational model of the progression of changes in mitochondrial phenotype resulting from infection with pathogenic mycobacteria. This ultimately will enable a large-scale virulence screen of mutant…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…
We study the urban-scale macroscopic traffic flow in city networks. Star graph is considered as traffic network. Star graphs with controlled traffic flow are transformed to various cell-transmission graphs by using the cell transmission…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Modeling and simulation approaches for infectious disease dynamics have proven to be essential tools for effective control of the spread of epidemics in the population. Among these approaches, it is obvious that compartmental mathematical…
his paper describes and analyzes the spatial spread of tuberculosis (TB) on complex metapopulation, that is, networks of populations connected by migratory flows whose configurations are described in terms of connectivity distribution of…
The emerging field of immunometabolism has underscored the central role of metabolic pathways in orchestrating immune cell function. Far from being passive background processes, metabolic activities actively regulate key immune responses.…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are…
This paper deals with the cellular biological network analysis of the tumor-growth model, consisting of multiple spaces and time scales. In this paper, we present a model in graph simulation using ABM for tumor growth. In particular, we…
We have modeled the metabolic process running in aerobic cells as open nonlinear dissipative systems. The map of metabolic paths and the general scheme of a dissipative system participating in the transformation of steroids are constructed.…
Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process 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…
This paper proposes a framework to ensure the existence of dynamical system trajectories in the state space of labeled, weighted, and attributed graphs. The evolution of such a system exhibits hybrid behavior: discrete jumps affecting the…
We propose a novel approach to the estimation of multiple Graphical Models to analyse temporal patterns of association among a set of metabolites over different groups of patients. Our motivating application is the Southall And Brent…
Recent progress has clarified many features of the global architecture of biological metabolic networks, which have highly organized and optimized tolerances and tradeoffs (HOT) for functional requirements of flexibility, efficiency,…