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Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
Effects of changes in functional composition of soil communities on nutrient cycling are still not well understood. Models simulating community dynamics overcome the technical challenges of conducting species removal experiments in the…
The structure of complex networks has been of interest in many scientific and engineering disciplines over the decades. A number of studies in the field have been focused on finding the common properties among different kinds of networks…
Here we introduce a model in which individuals differ in the rate at which they seek new interactions with others, making rational decisions modeled as general symmetric two-player games. Once a link between two individuals has formed, the…
The demand for Internet based services has exploded over the last decade. Many organizations use the Internet and particularly the World Wide Web as their primary medium for communication and business. This phenomenal growth has…
We present an individual based model of evolutionary ecology. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and…
Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…
We study the evolution of networks when the creation and decay of links are based on the position of nodes in the network measured by their centrality. We show that the same network dynamics arises under various centrality measures, and…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
Observations of the evolution of species groups in nature, such as well recognized Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with such radiations. The Penna model is one such…
We construct a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species posses genetic information, which is inherited according to the rules of the Penna model of genetic evolution.…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most…
This paper presents an evolution model of weighted networks in which the structural growth and weight dynamics are driven by human behavior, i.e. passenger route choice behavior. Transportation networks grow due to people's increasing…
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…
In order to understand the role of space in ecological communities where each species produces a certain type of resource and has varying abilities to exploit the resources produced by its own species and by the other species, we carry out…
Food webs can be regarded as energy transporting networks in which the weight of each edge denotes the energy flux between two species. By investigating 21 empirical weighted food webs as energy flow networks, we found several ubiquitous…
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…
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…