Related papers: CFinder: Locating cliques and overlapping modules …

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…

The identification of essential proteins can help in understanding the minimum requirements for cell survival and development. Network-based centrality approaches are commonly used to identify essential proteins from protein-protein…

Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer…

Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…

Many networks in real-life typically contain parts in which some nodes are more highly connected to each other than the other nodes of the network. The collection of such nodes are usually called clusters, communities, cohesive groups or…

We present a novel method for detecting communities in bipartite networks. Based on an extension of the $k$-clique community detection algorithm, we demonstrate how modular structure in bipartite networks presents itself as overlapping…

Many complex networks display a mesoscopic structure with groups of nodes sharing many links with the other nodes in their group and comparatively few with nodes of different groups. This feature is known as community structure and encodes…

Community structure is a typical property of many real-world networks, and has become a key to understand the dynamics of the networked systems. In these networks most nodes apparently lie in a community while there often exists a few nodes…

Much effort has gone into understanding the modular nature of complex networks. Communities, also known as clusters or modules, are typically considered to be densely interconnected groups of nodes that are only sparsely connected to other…

Community detection in social graphs has attracted researchers' interest for a long time. With the widespread of social networks on the Internet it has recently become an important research domain. Most contributions focus upon the…

Overlapping communities are key characteristics of the structure and function analysis of complex networks. Shared or overlapping nodes within overlapping communities can form either subcommunities or act as intersections between larger…

Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…

Recent researches have discovered that rich interactions among entities in nature and society bring about complex networks with community structures. Although the investigation of the community structures has promoted the development of…

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…

Role discovery is the task of dividing the set of nodes on a graph into classes of structurally similar roles. Modern strategies for role discovery typically rely on graph embedding techniques, which are capable of recognising complex local…

Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user…

Matrices are two-dimensional data structures allowing one to conceptually organize information. For example, adjacency matrices are useful to store the links of a network; correlation matrices are simple ways to arrange gene co-expression…

Complex networks possess a rich, multi-scale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one…

Community detection, which focuses on clustering nodes or detecting communities in (mostly) a single network, is a problem of considerable practical interest and has received a great deal of attention in the research community. While being…

Identification of communities in complex networks has become an effective means to analysis of complex systems. It has broad applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of…