Related papers: Combinatorial Algorithms for Control of Biological…
This review explains in a self-contained way the properties of random Boolean networks and their attractors, with a special focus on critical networks. Using small example networks, analytical calculations, phenomenological arguments, and…
We introduce a new threshold model of social networks, in which the nodes influenced by their neighbours can adopt one out of several alternatives. We characterize social networks for which adoption of a product by the whole network is…
We consider the problem of selecting a minimum size subset of nodes in a network, that allows to activate all the nodes of the network. We present a fast and simple algorithm that, in real-life networks, produces solutions that outperform…
Estimating the influence that individual nodes have on one another in a Boolean network is essential to predict and control the system's dynamical behavior, for example, detecting key therapeutic targets to control pathways in models of…
Boolean networks is a well-established formalism for modelling biological systems. A vital challenge for analysing a Boolean network is to identify all the attractors. This becomes more challenging for large asynchronous Boolean networks,…
It has recently been shown that the minimum energy solution of the control problem for a linear system produces a control trajectory that is nonlocal. An issue then arises when the dynamics represents a linearization of the underlying…
From gene regulatory networks to mutualistic networks, controlling a single node in the network topology can transform these complex dynamical systems from undesirable states to desirable ones. Corresponding methods have been well-studied…
The study of control mechanisms of biological systems allows for interesting applications in bioengineering and medicine, for instance in cell reprogramming or drug target identification. A control strategy often consists of a set of…
Boolean networks are powerful frameworks for capturing the logic of gene-regulatory circuits, yet their combinatorial explosion hampers exhaustive analyses. Here, we present a systematic reduction of a 31-node Boolean model that describes…
A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain…
Minimal input/output selection is investigated in this paper for each subsystem of a networked system. Some novel sufficient conditions are derived respectively for the controllability and observability of a networked system, as well as…
We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…
This paper considers the problem of minimal control inputs to affect the system states such that the resulting system is structurally controllable. This problem and the dual problem of minimal observability are claimed to have no…
This paper details a method for optimising the size of Boolean automata networks in order to compute their attractors under the parallel update schedule. This method relies on the formalism of modules introduced recently that allows for…
The control and sensing of large-scale systems results in combinatorial problems not only for sensor and actuator placement but also for scheduling or observability/controllability. Such combinatorial constraints in system design and…
Boolean networks have been used successfully in modeling biological networks and provide a good framework for theoretical analysis. However, the analysis of large networks is not trivial. In order to simplify the analysis of such networks,…
A Boolean network (BN) is a discrete dynamical system defined by a Boolean function that maps to the domain itself. A trap space of a BN is a generalization of a fixed point, which is defined as the sub-hypercubes closed by the function of…
This work aims at optimizing injection networks, which consist in adding a set of long-range links (called bypass links) in mobile multi-hop ad hoc networks so as to improve connectivity and overcome network partitioning. To this end, we…
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…