Related papers: Structural distance and evolutionary relationship …
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
This paper presents methods to compare networks where relationships between pairs of nodes in a given network are defined. We define such network distance by searching for the optimal method to embed one network into another network, prove…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this…
Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from differ- ent domains may vary quite significantly. Since there is an interplay be- tween network architecture…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…
Inspired by the structure of technological networks, we discuss network evolution mechanisms which give rise to topological properties found in real spatial networks. Thus, the peculiar structure of transport and distribution networks is…
Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species. The architecture of these webs seems to pervade some of their robust and fragile behaviour. Recent work indicates that there is…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…
The paper deals with the problem of reconstructing the topological structure of a network of dynamical systems. A distance function is defined in order to evaluate the "closeness" of two processes and a few useful mathematical properties…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
We introduce a method that can be used to evolve the topology of a network in a way that preserves both the network's spectral as well as local structure. This method is quite versatile in the sense that it can be used to evolve a network's…
Whether comparing networks to each other or to random expectation, measuring dissimilarity is essential to understanding the complex phenomena under study. However, determining the structural dissimilarity between networks is an ill-defined…