Related papers: Reconstructing the evolution history of networked …
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
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…
The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…
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…
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…
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…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
For decades, complex networks, such as social networks, biological networks, chemical networks, technological networks, have been used to study the evolution and dynamics of different kinds of complex systems. These complex systems can be…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
In spite of its relevance to the origin of complex networks, the interplay between form and function and its role during network formation remains largely unexplored. While recent studies introduce dynamics by considering rewiring processes…
Networks are widely used in the biological, physical, and social sciences as a concise mathematical representation of the topology of systems of interacting components. Understanding the structure of these networks is one of the outstanding…
The past decade has seen tremendous growth in the field of Complex Social Networks. Several network generation models have been extensively studied to develop an understanding of how real world networks evolve over time. Two important…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
The quest to understand structure-function relationships in networks across scientific disciplines has intensified. However, the optimal network architecture remains elusive, particularly for complex information processing. Therefore, we…
We study aggregation as a mechanism for the creation of complex networks. In this evolution process vertices merge together, which increases the number of highly connected hubs. We study a range of complex network architectures produced by…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
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…
This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real…
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…