The number and probability of canalizing functions

We study critical random Boolean networks with two inputs per node that contain only canalyzing functions. We present a phenomenological theory that explains how a frozen core of nodes that are frozen on all attractors arises. This theory leads to an intuitive understanding of the system's dynamics as it demonstrates the analogy between standard random Boolean networks and networks with canalyzing functions only. It reproduces correctly the scaling of the number of nonfrozen ...

In this work we consider random Boolean networks that provide a general model for genetic regulatory networks. We extend the analysis of James Lynch who was able to proof Kauffman's conjecture that in the ordered phase of random networks, the number of ineffective and freezing gates is large, where as in the disordered phase their number is small. Lynch proved the conjecture only for networks with connectivity two and non-uniform probabilities for the Boolean functions. We sh...

This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate Boolean functions with probability distributions that govern the activation frequency of each Boolean function. Owing to the stochasticity, the uniform state feedback controller, independent of switching signal, might be out of work, and in this...

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 that constrain network dynamics. This paper contributes to the identification of patterns in the mechanisms that govern network dynamics. The control of nodes in gene regulatory, signaling, and metabolic networks is governed by a variety of b...

Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of criticality uses automata network connectivity and node bias (to be on or off) as tuning parameters. This parsimony in the number of parameters needed sometimes leads to uncertain predictions about the dynamical regime of both random and s...

Many researchers have studied symmetry properties of various Boolean functions. A class of Boolean functions, called nested canalyzing functions (NCFs), has been used to model certain biological phenomena. We identify some interesting relationships between NCFs, symmetric Boolean functions and a generalization of symmetric Boolean functions, which we call $r$-symmetric functions (where $r$ is the symmetry level). Using a normalized representation for NCFs, we develop a charac...

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 majority of the gene regulatory functions found in known biological networks (submitted to the Cell Collective database) lie on the line of minimum sensitivity which paradoxically remains largely in the unstable regime. Our results provide a qua...

The dynamic stability of the Boolean networks representing a model for the gene transcriptional regulation (Kauffman model) is studied by calculating analytically and numerically the Hamming distance between two evolving configurations. This turns out to behave in a universal way close to the phase boundary only for in-degree distributions with a finite second moment. In-degree distributions of the form $P_d(k)\sim k^{-\gamma}$ with $2<\gamma<3$, thus having a diverging secon...

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 uncorrelated random network structure. Real gene networks typically have nontrivial topology significantly different from the random network paradigm. In order to address such situations, we present a general method for determining the sta...

Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and interpretation of those systems. Defining rules that determine how the output activity of biological entities is regulated by their respective inputs has proven to be challenging, due to increasingly larger models and the presence of noise in data, all...