Related papers: Strong associations between microbe phenotypes and…

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…

The topology of any complex system is key to understanding its structure and function. Fundamentally, algebraic topology guarantees that any system represented by a network can be understood through its closed paths. The length of each path…

Networks are ubiquitous structure that describes complex relationships between different entities in the real world. As a critical component of prediction task over nodes in networks, learning the feature representation of nodes has become…

High-throughput methods for yielding the set of connections in a neural system, the connectome, are now being developed. This tutorial describes ways to analyze the topological and spatial organization of the connectome at the macroscopic…

Complex network theory aims to model and analyze complex systems that consist of multiple and interdependent components. Among all studies on complex networks, topological structure analysis is of the most fundamental importance, as it…

Many real life networks present an average path length logarithmic with the number of nodes and a degree distribution which follows a power law. Often these networks have also a modular and self-similar structure and, in some cases -…

The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…

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…

The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world…

Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…

Designing strong and robust bio-inspired structures requires an understanding of how function arises from the architecture and geometry of materials found in nature. We draw from trabecular bone, a lightweight bone tissue that exhibits a…

Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…

Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…

Evolutionary mechanism in a self-organized system cause some functional changes that force to adapt new conformation of the interaction pattern between the components of that system. Measuring the structural differences one can retrace the…

We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…

A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…

The past few years has witnessed the great success of recommender systems, which can significantly help users find relevant and interesting items for them in the information era. However, a vast class of researches in this area mainly focus…

Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess…

Let a collection of networks represent interactions within several (social or ecological) systems. We pursue two objectives: identifying similarities in the topological structures that are held in common between the networks and clustering…

Interactions between units in phyical, biological, technological, and social systems usually give rise to intrincate networks with non-trivial structure, which critically affects the dynamics and properties of the system. The focus of most…