Related papers: Node similarity within subgraphs of protein intera…
Complex networks can be understood as graphs whose connectivity deviates from those of regular or near-regular graphs, which are understood as being `simple'. While a great deal of the attention so far dedicated to complex networks has been…
The similarity between protein sequences is a directly and easly computed quantity from which to deduce information about their evolutionary distance and to detect homologous proteins. The SIMAP database -- Similarity Matrix of Proteins --…
Understanding of how protein interaction networks (PIN) of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce a hybrid network model composed…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
A standard approach to reduce the complexity of very large networks is to group together sets of nodes into clusters according to some criterion which reflects certain structural properties of the network. Beyond the well-known modularity…
Over the years, quantifying the similarity of nodes has been a hot topic in complex networks, yet little has been known about the distributions of node-similarity. In this paper, we consider a typical measure of node-similarity called the…
Bibliographic coupling (BC) and co-citation (CC) are the two most common citation-based coupling measures of similarity between scientific items. One can interpret these measures as second-neighbor relations distinguished by the direction…
Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of…
As a fundamental problem in many different fields, link prediction aims to estimate the likelihood of an existing link between two nodes based on the observed information. Since this problem is related to many applications ranging from…
Finding graph indices which are unbiased to network size and density is of high importance both within a given field and across fields for enhancing comparability of modern network science studies. The degree variance is an important metric…
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…
Comparative graph and network analysis play an important role in both systems biology and pattern recognition, but existing surveys on the topic have historically ignored or underserved one or the other of these fields. We present an…
The study of the topological structure of complex networks has fascinated researchers for several decades, and today we have a fairly good understanding of the types and reoccurring characteristics of many different complex networks.…
The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world…
Networks represent relationships between entities in many complex systems, spanning from online social interactions to biological cell development and brain connectivity. In many cases, relationships between entities are unambiguously…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
The use of graph centrality measures applied to biological networks, such as protein interaction networks, underpins much research into identifying key players within biological processes. This approach however is restricted to dyadic…
In this paper, we propose a network whose nodes are labeled by the composite numbers and two nodes are connected by an undirected link if they are relatively prime to each other. As the size of the network increases, the network will be…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…