相关论文: The Function of Communities in Protein Interaction…

It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…

Community structure is one of the most important features of complex networks. Modularity-based methods for community detection typically rely on heuristic algorithms to optimize a specific community quality function. Such methods are…

Many real-world complex networks exhibit a community structure, in which the modules correspond to actual functional units. Identifying these communities is a key challenge for scientists. A common approach is to search for the network…

Most community detection algorithms from the literature work as optimization tools that minimize a given \textit{fitness function}, while assuming that each node belongs to a single community. Since there is no hard concept of what a…

The most widely used techniques for community detection in networks, including methods based on modularity, statistical inference, and information theoretic arguments, all work by optimizing objective functions that measure the quality of…

Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional…

Modularity maximization has been one of the most widely used approaches in the last decade for discovering community structure in networks of practical interest in biology, computing, social science, statistical mechanics, and more.…

The goal of community detection algorithms is to identify densely-connected units within large networks. An implicit assumption is that all the constituent nodes belong equally to their associated community. However, some nodes are more…

Research data sets are growing to unprecedented sizes and network modeling is commonly used to extract complex relationships in diverse domains, such as genetic interactions involved in disease, logistics, and social communities. As the…

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…

Many networks in nature, society and technology are characterized by a mesoscopic level of organization, with groups of nodes forming tightly connected units, called communities or modules, that are only weakly linked to each other.…

As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…

Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…

Characterizing large-scale organization in networks, including multilayer networks, is one of the most prominent topics in network science and is important for many applications. One type of mesoscale feature is community structure, in…

Many important cellular functions are implemented by protein complexes that act as sophisticated molecular machines of varying size and temporal stability. Here we demonstrate quantitatively that protein complexes in the yeast,…

Community detection is a well established method for studying the meso scale structure of social networks. Applying a community detection algorithm results in a division of a network into communities that is often used to inspect and reason…

Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…

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…

We focus on the detection of communities in multi-scale networks, namely networks made of different levels of organization and in which modules exist at different scales. It is first shown that methods based on modularity are not…