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Molecular Network Control Through Boolean Canalization [PDF]

EURASIP Journal on Bioinformatics and Systems Biology, 2015
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 network ...
Dimitrova, Elena S., Murrugarra, David
core   +6 more sources

Modular Control of Boolean Network Models. [PDF]

Bull Math Biol
Abstract The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational models need to encode these. Applications often focus on model-based control, such as in biomedicine
Murrugarra D, Veliz-Cuba A, Dimitrova E, Kadelka C, Wheeler M, Laubenbacher R.   +5 more
europepmc   +5 more sources

Control in Boolean Networks With Model Checking

Frontiers in Applied Mathematics and Statistics, 2022
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 usually high and
Laura Cifuentes-Fontanals, Laura Cifuentes-Fontanals, Elisa Tonello, Heike Siebert   +3 more
doaj   +4 more sources

Sampled-data stabilization of delayed Boolean control networks with state inequality constraints [PDF]

Scientific Reports
This paper studies the set stabilization of delayed Boolean control networks (DBCNs) with state inequality constraints via time-variant nonuniform sampled-data control. State inequality constraints are introduced into DBCNs.
Xiangshan Kong, Enguo Gu, Xinyun Liu, Yalu Li, Guanpeng Wang   +4 more
doaj   +2 more sources

Node and edge control strategy identification via trap spaces in Boolean networks [PDF]

BMC Bioinformatics
Background 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.
Laura Cifuentes-Fontanals, Elisa Tonello, Heike Siebert   +2 more
doaj   +2 more sources

Global stabilization of Boolean networks with applications to biomolecular network control [PDF]

Scientific Reports
Boolean networks (BNs) are vital modeling tools in systems biology for biomolecular regulatory networks. After a transient phase, BNs converge to attractors that represent distinct cell types or conditions.
Mohammad Reza Rafimanzelat
doaj   +2 more sources

Target Control of Asynchronous Boolean Networks [PDF]

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023
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 time, the control can be realised with three types of perturbations, including instantaneous, temporary and permanent ...
Cui Su, Jun Pang
openaire   +3 more sources

Parallel One-Step Control of Parametrised Boolean Networks

Mathematics, 2021
Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of Boolean functions.
Luboš Brim, Samuel Pastva, David Šafránek, Eva Šmijáková   +3 more
doaj   +1 more source

Optimal Control of Boolean Control Networks [PDF]

IEEE Transactions on Automatic Control, 2014
In this paper, we address the optimal control problem for Boolean control networks (BCNs). We first consider the problem of finding the input sequences that minimize a given cost function over a finite time horizon. The problem solution is obtained by means of a recursive algorithm that represents the analogue for BCNs of the difference Riccati ...
FORNASINI, ETTORE, VALCHER, MARIA ELENA
openaire   +1 more source

Influence maximization in Boolean networks

Nature Communications, 2022
Boolean networks modelling various biological processes are characterized by nonlinear reversible dynamics that makes their control challenging. The authors introduce extended concepts of influence and control, typically considered in the study of ...
Thomas Parmer, Luis M. Rocha, Filippo Radicchi   +2 more
doaj   +1 more source