scholarly journals Edgetic perturbations to eliminate fixed-point attractors in Boolean regulatory networks

2019 ◽  
Vol 29 (2) ◽  
pp. 023130 ◽  
Author(s):  
Colin Campbell ◽  
Réka Albert
Keyword(s):  
Fixed Point ◽  
Regulatory Networks ◽  
Boolean Regulatory Networks

scholarly journals Semi-automatic model revision of Boolean regulatory networks: confronting time-series observations with (a)synchronous dynamics

2020 ◽  
Author(s):  
Filipe Gouveia ◽  
Inês Lynce ◽  
Pedro T. Monteiro
Keyword(s):  
Time Series ◽  
Regulatory Networks ◽  
Computational Models ◽  
Optimal Solutions ◽  
Biological Models ◽  
Logical Models ◽  
Manual Task ◽  
Cellular Processes ◽  
Biological Regulatory Networks ◽  
Boolean Regulatory Networks

AbstractMotivationComplex cellular processes can be represented by biological regulatory networks. Computational models of such networks have successfully allowed the reprodution of known behaviour and to have a better understanding of the associated cellular processes. However, the construction of these models is still mainly a manual task, and therefore prone to error. Additionally, as new data is acquired, existing models must be revised. Here, we propose a model revision approach of Boolean logical models capable of repairing inconsistent models confronted with time-series observations. Moreover, we account for both synchronous and asynchronous dynamics.ResultsThe proposed tool is tested on five well known biological models. Different time-series observations are generated, consistent with these models. Then, the models are corrupted with different random changes. The proposed tool is able to repair the majority of the corrupted models, considering the generated time-series observations. Moreover, all the optimal solutions to repair the models are produced.Contact{[email protected],[email protected]}

scholarly journals Detecting controlling nodes of boolean regulatory networks

2011 ◽  
Vol 2011 (1) ◽  
Author(s):  
Steffen Schober ◽  
David Kracht ◽  
Reinhard Heckel ◽  
Martin Bossert
Keyword(s):  
Regulatory Networks ◽  
Boolean Regulatory Networks

scholarly journals Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids

2018 ◽  
Vol 335 ◽  
pp. 113-130 ◽  
Author(s):  
Pedro L. Varela ◽  
Inês Lynce ◽  
Vasco Manquinho ◽  
Claudine Chaouiya ◽  
Pedro T. Monteiro
Keyword(s):  
Regulatory Networks ◽  
Stable States ◽  
Hexagonal Grids ◽  
Boolean Regulatory Networks
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