Related papers: Biological Networks
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Biological networks are customarily described as structurally robust. This means that they often function extremely well under large forms of perturbations affecting both the concentrations and the kinetic parameters. In order to explain…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
Networks are pervasive in the real world. Nature, society, economy, and technology are supported by ostensibly different networks that in fact share an amazing number of interesting structural properties. Network thinking exploded in the…
Motivation: Since susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and…
This chapter discusses the interplay between structure and dynamics in complex networks. Given a particular network with an endowed dynamics, our goal is to find partitions aligned with the dynamical process acting on top of the network. We…
It is a fundamental challenge to understand how the function of a network is related to its structural organization. Adaptive dynamical networks represent a broad class of systems that can change their connectivity over time depending on…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of…
The topological analysis of biological networks has been a prolific topic in network science during the last decade. A persistent problem with this approach is the inherent uncertainty and noisy nature of the data. One of the cases in which…
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…
Biological networks have two modes. The first mode is static: a network is a passage on which something flows. The second mode is dynamic: a network is a pattern constructed by gluing functions of entities constituting the network. In this…
Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great…
Complex systems are very often organized under the form of networks where nodes and edges are embedded in space. Transportation and mobility networks, Internet, mobile phone networks, power grids, social and contact networks, neural…