Related papers: How the global structure of protein interaction ne…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food…
We derive a general statistical model of interactions, starting from probabilistic principles and elementary requirements. Prevailing interaction models in biomedical researches diverge both mathematically and practically. In particular,…
The complexity of interactions between networks and territories has been widely acknowledged empirically, in particular through the existence of circular causal relations in their co-development, that can be understood as a co-evolution.…
We propose a natural model of evolving weighted networks in which new links are not necessarily connected to new nodes. The model allows a newly added link to connect directly two nodes already present in the network. This is plausible in…
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…
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…
Genetic interactions have been widely used to define functional relationships between proteins and pathways. In this study, we demonstrated that yeast synthetic lethal genetic interactions can be explained by the genetic interactions…
All types of networks arise as intricate combinations of dyadic building blocks formed by pairs of vertices. In directed networks, the dyadic patterns are entirely determined by reciprocity, i.e. the tendency to form, or to avoid, mutual…
Many important real-world networks manifest "small-world" properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is "preferential attachment", where nodes…
Many social, technological and biological interactions involve network relationships whose outcome intimately depends on the structure of the network and on the strengths of the connections. Yet, although much information is now available…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Random graphs are more and more used for modeling real world networks such as evolutionary networks of proteins. For this purpose we look at two different models and analyze how properties like connectedness and degree distributions are…
We present a general model for the growth of weighted networks in which the structural growth is coupled with the edges' weight dynamical evolution. The model is based on a simple weight-driven dynamics and a weights' reinforcement…
(Bi)multi-partite interaction patterns are commonly observed in real world systems which have inhibitory and excitatory couplings. We hypothesize these structural interaction pattern to be stable and naturally arising in the course of…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Many social and biological networks consist of communities - groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting…