Related papers: Strong associations between microbe phenotypes and…
Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying…
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…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
We analyse growing networks ranging from collaboration graphs of scientists to the network of similarities defined among the various transcriptional profiles of living cells. For the explicit demonstration of the scale-free nature and…
The trophic levels of nodes in directed networks can reveal their functional properties. Moreover, the trophic coherence of a network, defined in terms of trophic levels, is related to properties such as cycle structure, stability and…
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…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Networked structure emerged from a wide range of fields such as biological systems, World Wide Web and technological infrastructure. A deeply insight into the topological complexity of these networks has been gained. Some works start to pay…
Topological properties of "scale-free" networks are investigated by determining their spectral dimensions $d_S$, which reflect a diffusion process in the corresponding graphs. Data bases for citation networks and metabolic networks together…
Many complex networks demonstrate a phenomenon of striking degree correlations, i.e., a node tends to link to other nodes with similar (or dissimilar) degrees. From the perspective of degree correlations, this paper attempts to characterize…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the…
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the…
We present a network model in which words over a specific alphabet, called {\it structures}, are associated to each node and undirected edges are added depending on some distance between different structures. It is shown that this model can…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
Multilayer networks represent systems in which there are several topological levels each one representing one kind of interaction or interdependency between the systems' elements. These networks have attracted a lot of attention recently…
Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model…
Network architecture design is very important for the optimization of industrial networks. The type of network architecture can be divided into small-scale network and large-scale network according to its scale. Graph theory is an efficient…
Background: Networks in different domains are characterized by similar global characteristics while differing in local structures. To further extend this concept, we investigated network regularities on a fine scale in order to examine the…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…