Related papers: Some protein interaction data do not exhibit power…
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…
Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
The degree distributions of many real world networks follow power-laws whose exponents tend to fall between two and three. Within the framework of the Barabasi-Albert model (BA model), we explain this empirical observation by a simple fact.…
We bring rigor to the vibrant activity of detecting power laws in empirical degree distributions in real-world networks. We first provide a rigorous definition of power-law distributions, equivalent to the definition of regularly varying…
We study a modified version of a model previously proposed by Jackson and Wolinsky to account for communicating information and allocating goods in socioeconomic networks. In the model, the utility function of each node is given by a…
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…
The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…
The concept of scale-free networks has been widely applied across natural and physical sciences. Many claims are made about the properties of these networks, even though the concept of scale-free is often vaguely defined. We present tools…
The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
In this paper, we address the logarithmic corrections to the leading power laws that govern thermodynamic quantities as a second-order phase transition point is approached. For phase transitions of spin systems on d-dimensional lattices,…
Hierarchical networks actually have many applications in the real world. Firstly, we propose a new class of hierarchical networks with scale-free and fractal structure, which are the networks with triangles compared to traditional…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
There is increasing evidence that dense networks occur in on-line social networks, recommendation networks and in the brain. In addition to being dense, these networks are often also scale-free, i.e. their degree distributions follow…
Many real networks share three generic properties: they are scale-free, display a small-world effect, and show a power-law strength-degree correlation. In this paper, we propose a type of deterministically growing networks called Sierpinski…
The concept of network efficiency, recently proposed to characterize the properties of small-world networks, is here used to study the effects of errors and attacks on scale-free networks. Two different kinds of scale-free networks, i.e.…
In their recent work "Scale-free networks are rare", Broido and Clauset address the problem of the analysis of degree distributions in networks to classify them as scale-free at different strengths of "scale-freeness." Over the last two…
In this paper, we present a simple model of scale-free networks that incorporates both preferential & random attachment and anti-preferential & random deletion at each time step. We derive the degree distribution analytically and show that…
We formulate a general model for the growth of scale-free networks under filtering information conditions--that is, when the nodes can process information about only a subset of the existing nodes in the network. We find that the…