Related papers: Molecular Network Control Through Boolean Canaliza…

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…

Boolean networks are special types of finite state time-discrete dynamical systems. A Boolean network can be described by a function from an n-dimensional vector space over the field of two elements to itself. A fundamental problem in…

Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable…

Controlling a complex network is of great importance in many applications. The network can be controlled by inputting external control signals through some selected nodes, which are called input nodes. Previous works found that the majority…

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…

Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…

Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may,…

Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…

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…

Control of complex processes is a major goal of network analyses. Most approaches to control nonlinearly coupled systems require the network topology and/or network dynamics. Unfortunately, neither the full set of participating nodes nor…

Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a…

Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on…

Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…

The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…

Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Here we develop a novel network control…

The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…

Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…

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…

Controlling a complex network towards a desired state is of great importance in many applications. A network can be controlled by inputting suitable external signals into some selected nodes, which are called driver nodes. Previous works…

Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be…