相关论文: Characterizing the structure of protein-protein in…

Network models have been widely used to study diverse systems and analyze their dynamic behaviors. Given the structural variability of networks, an intriguing question arises: Can we infer the type of system represented by a network based…

It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…

Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…

A network is a typical expressive form of representing complex systems in terms of vertices and links, in which the pattern of interactions amongst components of the network is intricate. The network can be static that does not change over…

Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…

Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…

We review the main tools which allow for the statistical characterization of weighted networks. We then present two case studies, the airline connection network and the scientific collaboration network, which are representative of critical…

Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…

We show that the protein-protein interaction networks can be surprisingly well described by a very simple evolution model of duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the…

The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…

Protein-protein interactions can be properly modeled as scale-free complex networks, while the lethality of proteins has been correlated with the node degrees, therefore defining a lethality-centrality rule. In this work we revisit this…

In the study of networked systems such as biological, technological, and social networks the available data are often uncertain. Rather than knowing the structure of a network exactly, we know the connections between nodes only with a…

Many animals live in societies where individuals frequently interact socially with each other. The social structures of these systems can be studied in depth by means of network analysis. A large number of studies on animal social networks…

Graphs are a powerful data structure to represent relational data and are widely used to describe complex real-world data structures. Probabilistic Graphical Models (PGMs) have been well-developed in the past years to mathematically model…

Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…

Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein functions and biological processes. Some curated datasets contain…

Data describing the three-dimensional structure of physical networks is increasingly available, leading to a surge of interest in network science to explore the relationship between the shape and connectivity of physical networks. We…

Signed networks provide a principled framework for representing systems in which interactions are not merely present or absent but qualitatively distinct: friendly or antagonistic, supportive or conflicting, excitatory or inhibitory. This…