Related papers: Modular co-evolution of metabolic networks
Homophily, the tendency of individuals to connect with others who share similar attributes, is a defining feature of social networks. Understanding how groups interact, both within and across, is crucial for uncovering the dynamics of…
Links in a practical network may have different functions, which makes the original network a combination of some functional subnetworks. Here, by a model of coupled oscillators, we investigate how such functional subnetworks are evolved…
Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural…
Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…
The hyperbolic network models exhibit very fundamental and essential features, like small-worldness, scale-freeness, high-clustering coefficient, and community structure. In this paper, we comprehensively explore the presence of an…
In a recent paper, Bassett et al. (2011) have analyzed the static and dynamic organization of functional brain networks in humans. We here focus on the first claim made in this paper, which states that the static modular structure of such…
Many complex systems are organized in the form of a network embedded in space. Important examples include the physical Internet infrastucture, road networks, flight connections, brain functional networks and social networks. The effect of…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Methods for learning Bayesian network structure can discover dependency structure between observed variables, and have been shown to be useful in many applications. However, in domains that involve a large number of variables, the space of…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
Networks are important representations in computer science to communicate structural aspects of a given system of interacting components. The evolution of a network has several topological properties that can provide us information on the…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
Recent theoretical and experimental work in neuroscience has focused on the representational and dynamical character of neural manifolds --subspaces in neural activity space wherein many neurons coactivate. Importantly, neural populations…
We propose a growing network model that consists of two tunable mechanisms: growth by merging modules which are represented as complete graphs and a fitness-driven preferential attachment. Our model exhibits the three prominent statistical…
It is well-known that biological and social interaction networks have a varying degree of redundancy, though a consensus of the precise cause of this is so far lacking. In this paper, we introduce a topological redundancy measure for…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
The connectome, or the entire connectivity of a neural system represented by network, ranges various scales from synaptic connections between individual neurons to fibre tract connections between brain regions. Although the modularity they…