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Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
Network growth processes can be understood as generative models of the structure and history of complex networks. This point of view naturally leads to the problem of network archaeology: reconstructing all the past states of a network from…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
The interactions among human beings represent the backbone of our societies. How people interact, establish new connections, and allocate their activities among these links can reveal a lot of our social organization. Despite focused…
Recent years have seen tremendous growth of many online social networks such as Facebook, LinkedIn and MySpace. People connect to each other through these networks forming large social communities providing researchers rich datasets to…
The study of human interactions is of central importance for understanding the behavior of individuals, groups and societies. Here, we observe the formation and evolution of networks by monitoring the addition of all new links and we…
Recent years have seen tremendous growth of many online social networks such as Facebook, LinkedIn and MySpace. People connect to each other through these networks forming large social communities providing researchers rich datasets to…
There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How various preferential linking mechanisms produce networks with different features? In this paper we…
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…
Owing to the influence of real-world networks both in science and society, numerous mathematical models have been developed to understand the structure and evolution of these systems, particularly in a temporal context. Recent advancements…
Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows…
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…
Online social networks represent a main source of communication and information exchange in today's life. They facilitate exquisitely news sharing, knowledge elicitation, and forming groups of same interests. Researchers in the last two…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Studying the topology of so-called {\em real networks}, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
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…