相关论文: Canalization reduces the nonlinearity of regulatio…

Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…

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 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…

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…

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are…

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…

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…

Canalization is a classic concept in Developmental Biology that is thought to be an important feature of evolving systems. In a Boolean network it is a form of network robustness in which a subset of the input signals control the behavior…

The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…

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…

Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…

Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…

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…

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…

The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…

Canalization of genetic regulatory networks has been argued to be favored by evolutionary processes due to the stability that it can confer to phenotype expression. We explore whether a significant amount of canalization and partial…

The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…

The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…

Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…

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…