Related papers: A dynamic logic method for determining behaviors o…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
In evolving complex systems such as air traffic and social organizations, collective effects emerge from their many components' dynamic interactions. While the dynamic interactions can be represented by temporal networks with nodes and…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…
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…
Understanding biological network dynamics is a fundamental issue in various scientific and engineering fields. Network theory is capable of revealing the relationship between elements and their propagation; however, for complex collective…
A computer model is described which is used to assess the dynamical complexity of a class of networks of spiking neurons with small-world properties. Networks are constructed by forming an initially segregated set of highly intra-connected…
Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…
Historically studies of behaviour on networks have focused on the behaviour of individuals (node-based) or on the aggregate behaviour of the entire network. We propose a new method to decompose a temporal network into macroscale components…
We formulate general rules for a coarse-graining of the dynamics, which we term `symbolic dynamics', of feedback networks with monotone interactions, such as most biological modules. Networks which are more complex than simple cyclic…
We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g. the activities of cell-cycle proteins during the mitotic cell-cycle progression. Using the framework of deterministic…
Large-scale online campaigns, malicious or otherwise, require a significant degree of coordination among participants, which sparked interest in the study of coordinated online behavior. State-of-the-art methods for detecting coordinated…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
Dynamic processes of interacting units on a network are out of equilibrium in general. In the case of a directed tree, the dynamic cavity method provides an efficient tool that characterises the dynamic trajectory of the process for the…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
Complex networks are used to depict topological features of complex systems. The structure of a network characterizes the interactions among elements of the system, and facilitates the study of many dynamical processes taking place on it.…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…