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This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
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 design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the…
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into…
Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and…
The human body consists of microbiomes associated with the development and prevention of several diseases. These microbial organisms form several complex interactions that are informative to the scientific community for explaining disease…
Community structure is one of the key properties of complex networks and plays a crucial role in their topology and function. While an impressive amount of work has been done on the issue of community detection, very little attention has…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
While the majority of approaches to the characterization of complex networks has relied on measurements considering only the immediate neighborhood of each network node, valuable information about the network topological properties can be…
We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and,…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds.…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
We investigate the application of mesoscopic response functions (MRFs) to characterize a large set of networks of fungi and slime moulds grown under a wide variety of different experimental treatments, including inter-species competition…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Understanding how different networks relate to each other is key for obtaining a greater insight into complex systems. Here, we introduce an intuitive yet powerful framework to characterise the relationship between two networks comprising…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…