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Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
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…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
In the field of Business Process Management formal models for the control flow of business processes have been designed since more than 15 years. Which methods are best suited to verify the bulk of these models? The first step is to select…
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…
Probabilistic Boolean networks (PBNs) is an important mathematical framework widely used for modelling and analysing biological systems. PBNs are suited for modelling large biological systems, which more and more often arise in systems…
We have considered a Boolean control network where the state evolution equations depend on past states, controls and first derivatives of a function with respect to controls. Total approach has been the efficient use of matrix semi tensor…
This paper focuses on proposing a general control framework for large-scale Boolean networks (\texttt{BNs}). Only by the network structure, the concept of structural controllability for \texttt{BNs} is formalized. A necessary and sufficient…
Boolean circuits abstract away from physical details to focus on the logical structure and computational behaviour of digital components. Although such circuits have been studied for many decades, compositionality has been widely ignored or…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
Canalization is a key organizing principle in complex systems, particularly in gene regulatory networks. It describes how certain input variables exert dominant control over a function's output, thereby imposing hierarchical structure and…
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…
Controlling a dynamical system is the ability of changing its configuration arbitrarily through a suitable choice of inputs. It is a very well studied concept in control theory, with wide ranging applications in medicine, biology, social…
In the applications of Boolean networks to modeling biological systems, an important computational problem is the detection of the fixed points of these networks. This is an NP-complete problem in general. There have been various attempts…
The mutations of a complex systemic disease like cancer can be modeled as stuck-at faults in the Boolean system paradigm. For a class of multiple faults, the fault identification is exceptionally significant under the incomplete access of…
The emergence of Context-aware systems in the domains of autonomic, monitoring, and safety-critical applications asks for the definition of methods to formally assess their correctness and dependability properties. Many of these properties…
It is an increasingly important problem to study conditions on the structure of a network that guarantee a given behavior for its underlying dynamical system. In this paper we report that a Boolean network may fall within the chaotic…
This paper studies the mathematical properties of collectively canalizing Boolean functions, a class of functions that has arisen from applications in systems biology. Boolean networks are an increasingly popular modeling framework for…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…