相关论文: Node similarity within subgraphs of protein intera…

Graph theory is a branch of mathematics in which pair-wise relations between objects are studied. My PhD thesis, supervised by David R. Wood, introduces and investigates a new family of graphs, called link graphs, that generalises the…

Link prediction requires predicting which new links are likely to appear in a graph. Being able to predict unseen links with good accuracy has important applications in several domains such as social media, security, transportation, and…

In principle, the rules of links formation of a network model can be considered as a kind of link prediction algorithm. By revisiting the preferential attachment mechanism for generating a scale-free network, here we propose a class of…

Motivation: Protein-protein interactions (PPIs) are usually modelled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They…

Link prediction is the problem of inferring whether potential edges between pairs of vertices in a graph will be present or absent in the near future. To perform this task it is usual to use information provided by a number of available and…

Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…

Understanding functional associations among genes discovered in sequencing projects is a key issue in post-genomic biology. However, reliable interpretation of the protein interaction data has been difficult. In this work, we show that if…

Networks are often characterized by node heterogeneity for which nodes exhibit different degrees of interaction and link homophily for which nodes sharing common features tend to associate with each other. In this paper, we propose a new…

In this paper, we compared cancerous and normal cell according to their protein-protein interaction network. Cancer is one of the complicated diseases and experimental investigations have been showed that protein interactions have an…

This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…

Social networks involve both positive and negative relationships, which can be captured in signed graphs. The {\em edge sign prediction problem} aims to predict whether an interaction between a pair of nodes will be positive or negative. We…

We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…

Nestedness characterizes the linkage pattern of networked systems, indicating the likelihood that a node is linked to the nodes linked to the nodes with larger degrees than it. Networks of mutualistic relationship between distinct groups of…

Nowadays there is a multitude of measures designed to capture different aspects of network structure. To be able to say if the structure of certain network is expected or not, one needs a reference model (null model). One frequently used…

Relations between discrete quantities such as people, genes, or streets can be described by networks, which consist of nodes that are connected by edges. Network analysis aims to identify important nodes in a network and to uncover…

Nestedness is a common property of communication, finance, trade, and ecological networks. In networks with high levels of nestedness, the link positions of low-degree nodes (those with few links) form nested subsets of the link positions…

Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…

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…

Recently, graphs have been widely used to represent many different kinds of real world data or observations such as social networks, protein-protein networks, road networks, and so on. In many cases, each node in a graph is associated with…

In this paper we present the first mathematical analysis of the protein interaction network found in the yeast, S. cerevisiae. We show that, (a) the identified protein network display a characteristic scale-free topology that demonstrate…