Related papers: Lethality and centrality in protein networks
Scale-free and non-computable characteristics of natural networks are found to result from the least-time dispersal of energy. To consider a network as a thermodynamic system is motivated since ultimately everything that exists can be…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Scale-free networks are ubiquitous in social, biological and technological networked systems. Dynamic Scale-free networks and their synchronizations are important to understand and predict the behavior of social, biological and…
We investigate the higher-order connectivity of scale-free networks using algebraic topology. We model scale-free networks as preferential attachment graphs, and we study the algebraic-topological properties of their clique complexes. We…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
Different weighted scale-free networks show weights-topology correlations indicated by the non linear scaling of the node strength with node connectivity. In this paper we show that networks with and without weight-topology correlations can…
Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…
Components in many real-world complex systems depend on each other for the resources required for survival, and may die of a shortage. These patterns of dependencies often take the form of a complex network whose structure potentially…
Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental…
Self-avoiding random walks were performed on protein residue networks. Compared with protein residue networks with randomized links, the probability of a walk being successful is lower and the length of successful walks shorter in…
Self-similar networks with scale-free degree distribution have recently attracted much attention, since these apparently incompatible properties were reconciled in a paper by Song et al. by an appropriate box-counting method that enters the…
Many complex systems can be represented as networks composed by distinct layers, interacting and depending on each others. For example, in biology, a good description of the full protein-protein interactome requires, for some organisms, up…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
The local minima (inherent structures) of a system and their associated transition links give rise to a network. Here we consider the topological and distance properties of such a network in the context of spin glasses. We use steepest…
The structure of social contact networks strongly influences the dynamics of epidemic diseases. In particular the scale-free structure of real-world social networks allows unlikely diseases with low infection rates to spread and become…
There are many networks in real life which exist as form of Scale-free networks such as World Wide Web, protein-protein interaction network, semantic networks, airline networks, interbank payment networks, etc. If we want to analyze these…
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 this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Real-world networks tend to be scale free, having heavy-tailed degree distributions with more hubs than predicted by classical random graph generation methods. Preferential attachment and growth are the most commonly accepted mechanisms…