Related papers: Combinatorial Algorithms for Control of Biological…
We study the problem of computing a minimal subset of nodes of a given asynchronous Boolean network that need to be controlled to drive its dynamics from an initial steady state (or attractor) to a target steady state. Due to the phenomenon…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
Given a Boolean network BN and a subset A of attractors of BN, we study the problem of identifying a minimal subset C of vertices of BN, such that the dynamics of BN can reach from a state s in any attractor As in A to any attractor At in A…
Using a graph-theoretic approach, we derive a new sufficient condition for observability of a Boolean control network (BCN). Based on this condition, we describe two algorithms: the first selects a set of nodes so that observing this set…
The minimum number of inputs needed to control a network is frequently used to quantify its controllability. Control of linear dynamics through a minimum set of inputs, however, often has prohibitively large energy requirements and there is…
Boolean networks are dynamical models of disease development in which the activation levels of genes are represented by binary variables. Given a Boolean network, controls represent mutations or medical treatments that fix the activation…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…
Previous work in Boolean dynamical networks has suggested that the number of components that must be controlled to select an existing attractor is typically set by the number of attractors admitted by the dynamics, with no dependence on the…
We present and discuss the results of an experimental analysis in the design of Boolean networks by means of genetic algorithms. A population of networks is evolved with the aim of finding a network such that the attractor it reaches is of…
We study the target control problem of asynchronous Boolean networks, to identify a set of nodes, the perturbation of which can drive the dynamics of the network from any initial state to the desired steady state (or attractor). We are…
Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
Understanding control mechanisms in biological systems plays a crucial role in important applications, for instance in cell reprogramming. Boolean modeling allows the identification of possible efficient strategies, helping to reduce the…
We study the target control of asynchronous Boolean networks, to identify efficacious interventions that can drive the dynamics of a given Boolean network from any initial state to the desired target attractor. Based on the application…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
This paper addresses the problem of finding cycles in the state transition graphs of synchronous Boolean networks. Synchronous Boolean networks are a class of deterministic finite state machines which are used for the modeling of gene…
This paper studies the problem of selecting a minimum-size set of input nodes to guarantee stability of a networked system in the presence of uncertainties and time delays. Current approaches to input selection in networked dynamical…
Boolean networks model finite discrete dynamical systems with complex behaviours. The state of each component is determined by a Boolean function of the state of (a subset of) the components of the network. This paper addresses the…