Related papers: Standardized network reconstruction of E. coli met…
It is known that the stationary distribution of the random walk process is dependent on the structure of the network. This could provide us a solution of the network reconstruction. However, the stationary distribution of the random walk…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
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…
Transport is an important function in many network systems and understanding its behavior on biological, social, and technological networks is crucial for a wide range of applications. However, it is a property that is not well-understood…
Many dynamical processes of complex systems can be understood as the dynamics of a group of nodes interacting on a given network structure. However, finding such interaction structure and node dynamics from time series of node behaviours is…
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the…
We propose a novel method of reconstructing the topology and interaction functions for a general oscillator network. An ensemble of initial phases and the corresponding instantaneous frequencies is constructed by repeating random…
We explore a novel method to generate and characterize complex networks by means of their embedding on hyperbolic surfaces. Evolution through local elementary moves allows the exploration of the ensemble of networks which share common…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
Recently, it has been claimed that some complex networks are self-similar under a convenient renormalization procedure. We present a general method to study renormalization flows in graphs. We find that the behavior of some variables under…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
The yeast galactose network has provided many insights into how eukaryotic gene circuits regulate metabolic function. However, there is currently no consensus model of the network that incorporates protein dilution due to cellular growth.…
Network reconstruction is a well-developed sub-field of network science, but it has only recently been applied to production networks, where nodes are firms and edges represent customer-supplier relationships. We review the literature that…
Research on generative models is a central project in the emerging field of network science, and it studies how statistical patterns found in real networks could be generated by formal rules. Output from these generative models is then the…
Network renormalization has traditionally relied on spatial adjacency-grouping nearby nodes together, but this approach fails to capture the dynamical correlations that govern system-wide behavior in scale-free networks. We present a…
We analyze a model that interpolates between scale-free and Erdos-Renyi networks. The model introduced generates a one-parameter family of networks and allows to analyze the role of structural heterogeneity. Analytical calculations are…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this…
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…