Related papers: Biological Networks
Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Community structure is one of the most relevant features encountered in numerous real-world applications of networked systems. Despite the tremendous effort of scientists working on this subject over the past few decades to characterize,…
It is well-known that biological and social interaction networks have a varying degree of redundancy, though a consensus of the precise cause of this is so far lacking. In this paper, we introduce a topological redundancy measure for…
Processes on networks consist of two interdependent parts: the network topology, consisting of the links between nodes, and the dynamics, specified by some governing equations. This work considers the prediction of the future dynamics on an…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
We look at the internal structure of neural networks which is usually treated as a black box. The easiest and the most comprehensible thing to do is to look at a binary classification and try to understand the approach a neural network…
A major achievement in the study of complex networks is the observation that diverse systems, from sub-cellular biology to social networks, exhibit universal topological characteristics. Yet this universality does not naturally translate to…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…
These are exciting times for quantum physics as new quantum technologies are expected to soon transform computing at an unprecedented level. Simultaneously network science is flourishing proving an ideal mathematical and computational…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
We use mathematical methods from the theory of tailored random graphs to study systematically the effects of sampling on topological features of large biological signalling networks. Our aim in doing so is to increase our quantitative…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
Despite their widespread utility across domains, basic network models face fundamental limitations when applied to complex biological systems, particularly in neuroscience. This paper critically examines these limitations and explores…
A survey is made of several aspects of the dynamics of networks, with special emphasis on unsupervised learning processes, non-Gaussian data analysis and pattern recognition in networks with complex nodes.
The network density matrix formalism allows for describing the dynamics of information on top of complex structures and it has been successfully used to analyze from system's robustness to perturbations to coarse graining multilayer…
Network theory provides tools which are particularly appropriate for assessing the complex interdependencies that characterise our modern connected world. This article presents an introduction to network theory, in a way that doesn't…
The brain is a complex organ characterized by heterogeneous patterns of structural connections supporting unparalleled feats of cognition and a wide range of behaviors. New noninvasive imaging techniques now allow these patterns to be…