Related papers: Flux-dependent graphs for metabolic networks
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…
Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the network responds to external perturbations. We follow here a…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Metabolic fluxes are the rates of life-sustaining chemical reactions within a cell and metabolites are the components. Determining the changes in these fluxes is crucial to understanding diseases with metabolic causes and consequences.…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
System-level properties of metabolic networks may be the direct product of natural selection or arise as a by-product of selection on other properties. Here we study the effect of direct selective pressure for growth or viability in…
Biological transport networks are highly optimized structures that ensure power-efficient distribution of fluids across various domains, including animal vasculature and plant venation. Theoretically, these networks can be described as…
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…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
Migratory and tissue resident cells exhibit highly branched morphologies to perform their function and to adapt to the microenvironment. Immune cells, for example, display transient branched shapes while exploring the surrounding tissues.…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
This paper proposes a graph-based approach to representing spatio-temporal trajectory data that allows an effective visualization and characterization of city-wide traffic dynamics. With the advance of sensor, mobile, and Internet of Things…
Climate change is reshaping species interactions and movement across fragmented landscapes. Despite this, most mathematical models assume random diffusion, overlooking the influence of directed movement. Here, we develop a graph based…
Flows are essential to transport resources over large distances. As soon as diffusion becomes time-limiting, flows are needed. Flows are key for the function of multiple human organs, from the blood vasculature to the lungs, the digestive…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
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…
Networked dynamical systems, i.e., systems of dynamical units coupled via nontrivial interaction topologies, constitute models of broad classes of complex systems, ranging from gene regulatory and metabolic circuits in our cells to…