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Many real-world networks are so large that we must simplify their structure before we can extract useful information about the systems they represent. As the tools for doing these simplifications proliferate within the network literature,…
Ecological networks describe the interactions between different species, informing us of how they rely on one another for food, pollination and survival. If a species in an ecosystem is under threat of extinction, it can affect other…
Recently, some studies started to unveil the wealthy of interactions that occur between groups of nodes when looking at the small scale of interactions taking place in complex networks. Such findings claim for a new systematic methodology…
Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to…
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic, prognostic and treatment choice to individual…
Complex systems are often driven by higher-order interactions among multiple units, naturally represented as hypergraphs. Understanding dependency structures within these hypergraphs is crucial for understanding and predicting the behavior…
A significant problem in analysis of complex network is to reveal community structure, in which network nodes are tightly connected in the same communities, between which there are sparse connections. Previous algorithms for community…
Community detection is an important research topic in complex networks. We present the employment of a genetic algorithm to detect communities in complex networks which is based on optimizing network modularity. It does not need any prior…
Stochasticity and spatial heterogeneity are of great interest recently in studying the spread of an infectious disease. The presented method solves an inverse problem to discover the effectively decisive topology of a heterogeneous network…
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly…
In a complex network, different groups of nodes may have existed for different amounts of time. To detect the evolutionary history of a network is of great importance. We present a general method based on spectral analysis to address this…
The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose…
Large-scale human social network structure is typically inferred from digital trace samples of online social media platforms or mobile communication data. Instead, here we investigate the social network structure of a complete population,…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Uncovering structural properties of ecological networks is a crucial starting point of studying the system's stability in response to various types of perturbations. We analyze pollination and seed disposal networks, which are…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Algorithms to find communities in networks rely just on structural information and search for cohesive subsets of nodes. On the other hand, most scholars implicitly or explicitly assume that structural communities represent groups of nodes…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
Community structure is of paramount importance for the understanding of complex networks. Consequently, there is a tremendous effort in order to develop efficient community detection algorithms. Unfortunately, the issue of a fair assessment…