Related papers: A statistical method for revealing form-function r…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Functional networks of complex systems are obtained from the analysis of the temporal activity of their components, and are often used to infer their unknown underlying connectivity. We obtain the equations relating topology and function in…
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…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
It has become increasingly popular to study the brain as a network due to the realization that functionality cannot be explained exclusively by independent activation of specialized regions. Instead, across a large spectrum of behaviors,…
Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…
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,…
Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…
Characterizing motif (i.e., locally connected subgraph patterns) statistics is important for understanding complex networks such as online social networks and communication networks. Previous work made the strong assumption that the graph…
Complex networks have acquired a great popularity in recent years, since the graph representation of many natural, social and technological systems is often very helpful to characterize and model their phenomenology. Additionally, the…
Money flow models are essential tools to understand different economical phenomena, like saving propensities and wealth distributions. In spite of their importance, most of them are based on synthetic transaction networks with simple…
Finding the common structural brain connectivity network for a given population is an open problem, crucial for current neuro-science. Recent evidence suggests there's a tightly connected network shared between humans. Obtaining this…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
Software systems emerge from mere keystrokes to form intricate functional networks connecting many collaborating modules, objects, classes, methods, and subroutines. Building on recent advances in the study of complex networks, I have…
Endowing brain anatomy, dynamics, and function with a network structure is becoming standard in neuroscience. In its simplest form, a network is a collection of units and relationships between them. The pattern of relations among the units…
Over the last two decades, network theory has shown to be a fruitful paradigm in understanding the organization and functioning of real-world complex systems. One technique helpful to this endeavor is identifying functionally influential…