Related papers: Boolean nested canalizing functions: a comprehensi…
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 canalizing properties of biological functions have been mainly studied in the context of Boolean modelling of gene regulatory networks. An important mathematical consequence of canalization is a low average sensitivity, which ensures in…
The concept of a nested canalizing Boolean function has been studied over the course of the last decade in the context of understanding the regulatory logic of molecular interaction networks, such as gene regulatory networks. Such functions…
Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The…
We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
Nested canalizing Boolean (NCF) functions play an important role in biological motivated regulative networks and in signal processing, in particular describing stack filters. It has been conjectured that NCFs have a stabilizing effect on…
Identifying features of molecular regulatory networks is an important problem in systems biology. It has been shown that the combinatorial logic of such networks can be captured in many cases by special functions called nested canalyzing 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…
This paper focuses on the study of certain classes of Boolean functions that have appeared in several different contexts. Nested canalyzing functions have been studied recently in the context of Boolean network models of gene regulatory…
Boolean networks are used to model biological networks such as gene regulatory networks. Often Boolean networks show very chaotic behaviour which is sensitive to any small perturbations. In order to reduce the chaotic behaviour and to…
We prove that nested canalizing functions are the minimum-sensitivity Boolean functions for any activity ratio and we determine the functional form of this boundary which has a nontrivial fractal structure. We further observe that the…
Boolean networks are used to model biological networks such as gene regulatory networks. Often Boolean networks show very chaotic behavior which is sensitive to any small perturbations.In order to reduce the chaotic behavior and to attain…
Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of…
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…
In this paper, we obtain complete characterization for nested canalyzing functions (NCFs) by obtaining its unique algebraic normal form (polynomial form). We introduce a new concept, LAYER NUMBER for NCF. Based on this, we obtain explicit…
Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…
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…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
We obtain the phase diagram of random Boolean networks with nested canalizing functions. Using the annealed approximation, we obtain the evolution of the number $b_t$ of nodes with value one, and the network sensitivity $\lambda$, and we…