Related papers: Evolution of complex modular biological networks
Routing information through networks is a universal phenomenon in both natural and manmade complex systems. When each node has full knowledge of the global network connectivity, finding short communication paths is merely a matter of…
Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural…
Complex networks from such different fields as biology, technology or sociology share similar organization principles. The possibility of a unique growth mechanism promises to uncover universal origins of collective behaviour. In…
Topology and weights are closely related in weighted complex networks and this is reflected in their modular structure. We present a simple network model where the weights are generated dynamically and they shape the developing topology. By…
To understand the structure of a large-scale biological, social, or technological network, it can be helpful to decompose the network into smaller subunits or modules. In this article, we develop an information-theoretic foundation for the…
Dynamics in biological networks are in general robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems which are robust against phenotypic perturbations…
A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices and relations between them are directed and signed…
How self-organized networks develop, mature and degenerate is a key question for sociotechnical, cyberphysical and biological systems with potential applications from tackling violent extremism through to neurological diseases. So far, it…
The learned weights of a neural network are often considered devoid of scrutable internal structure. To discern structure in these weights, we introduce a measurable notion of modularity for multi-layer perceptrons (MLPs), and investigate…
In spite of its relevance to the origin of complex networks, the interplay between form and function and its role during network formation remains largely unexplored. While recent studies introduce dynamics by considering rewiring processes…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here, we describe first the protein structure networks of molecular chaperones, then characterize chaperone containing…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
The observed architecture of ecological and socio-economic networks differs significantly from that of random networks. From a network science standpoint, non-random structural patterns observed in real networks call for an explanation of…
Investigating relation between various structural patterns found in real-world networks and stability of underlying systems is crucial to understand importance and evolutionary origin of such patterns. We evolve multiplex networks,…
Many complex networks depend upon biological entities for their preservation. Such entities, from human cognition to evolution, must first encode and then replicate those networks under marked resource constraints. Networks that survive are…
Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…