相关论文: A simple physical model for scaling in protein-pro…

Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…

The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer…

Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…

The Saccharomyces cerevisiae protein-protein interaction map, as well as many natural and man-made networks, shares the scale-free topology. The preferential attachment model was suggested as a generic network evolution model that yields…

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…

Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…

Co-evolution exhibited by a network system, involving the intricate interplay between the dynamics of the network itself and the subsystems connected by it, is a key concept for understanding the self-organized, flexible nature of…

We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only…

The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…

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…

Most social, technological and biological networks are embedded in a finite dimensional space, and the distance between two nodes influences the likelihood that they link to each other. Indeed, in social systems, the chance that two…

Diverse implicit structures of fluids are discovered lately, providing opportunities to study the physics of fluids applying network analysis. Although considerable works devote to identifying informative network structures of fluids, we…

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…

The structure of real-world networks is usually difficult to characterize owing to the variation of topological scales, the nondyadic complex interactions, and the fluctuations in the network. We aim to address these problems by introducing…

Graphical models are useful tools for describing structured high-dimensional probability distributions. Development of efficient algorithms for learning graphical models with least amount of data remains an active research topic.…

Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…

The hidden variable formalism (based on the assumption of some intrinsic node parameters) turned out to be a remarkably efficient and powerful approach in describing and analyzing the topology of complex networks. Owing to one of its most…

Modeling human dynamics responsible for the formation and evolution of the so-called social networks - structures comprised of individuals or organizations and indicating connectivities existing in a community - is a topic recently…

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…

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…