Related papers: Sequential Control of Boolean Networks with Tempor…
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…
Boolean networks are conventionally used to represent and simulate gene regulatory networks. In the analysis of the dynamic of a Boolean network, the attractors are the objects of a special attention. In this work, we propose a novel…
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…
The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables,…
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…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
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…
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…
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…
Cellular reprogramming can be used for both the prevention and cure of different diseases. However, the efficiency of discovering reprogramming strategies with classical wet-lab experiments is hindered by lengthy time commitments and high…
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…
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…
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…
A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…
Controllability, one of the fundamental concepts in control theory, consists in guiding a system from an initial state to a desired one within a limited (and possibly minimum) time interval. When the objective is limited to a specific…
In spite of the recent interest and advances in linear controllability of complex networks, controlling nonlinear network dynamics remains to be an outstanding problem. We develop an experimentally feasible control framework for nonlinear…
In this paper, we address the formal characterization of targets triggering cellular trans-differentiation in the scope of Boolean networks with asynchronous dynamics. Given two fixed points of a Boolean network, we are interested in all…
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of…
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…
Identification of attractors, that is, stable states and sustained oscillations, is an important step in the analysis of Boolean models and exploration of potential variants. We describe an approach to the search for asynchronous cyclic…