相关论文: Structure and evolution of protein interaction net…

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…

There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How various preferential linking mechanisms produce networks with different features? In this paper we…

Network theory-based approaches provide valuable insights into the variations in global structural connectivity between differing dynamical states of proteins. Our objective is to review network-based analyses to elucidate such variations,…

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for…

The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…

Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…

Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…

Link prediction is an important network science problem in many domains such as social networks, chem/bio-informatics, etc. Most of these networks are dynamic in nature with patterns evolving over time. In such cases, it is necessary to…

Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…

The problem of predicting links in large networks is an important task in a variety of practical applications, including social sciences, biology and computer security. In this paper, statistical techniques for link prediction based on the…

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…

Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…

Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…

Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…

The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…

This study examines long-term trends and shifting behavior in the collaboration network of mathematics literature, using a subset of data from Mathematical Reviews spanning 1985-2009. Rather than modeling the network cumulatively, this…

The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…

Here we introduce a model in which individuals differ in the rate at which they seek new interactions with others, making rational decisions modeled as general symmetric two-player games. Once a link between two individuals has formed, the…

Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this…

Complex networks often exhibit co-evolutionary dynamics, meaning that the network topology and the state of nodes or links are coupled, affecting each other in overlapping time scales. We focus on the co-evolutionary dynamics of online…