相关论文: Dynamics of Unperturbed and Noisy Generalized Bool…

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,…

There is an obvious need for improving the performance and accuracy of a Bayesian network as new data is observed. Because of errors in model construction and changes in the dynamics of the domains, we cannot afford to ignore the…

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…

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…

Since their introduction, Boolean networks have been traditionally studied in view of their rich dynamical behavior under different update protocols and for their qualitative analogy with cell regulatory networks. More recently, tools…

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…

This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…

Many familial diseases are caused by genetic accidents, which affect both the genome and its epigenetic environment, expressed as an interaction graph between the genes as that involved in one familial disease we shall study, the hereditary…

We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…

We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…

We study the nature of fitness landscapes of 'quenched' Kauffman's Boolean model with a scale-free network. We have numerically calculated the rugged fitness landscapes, the distributions, its tails, and the correlation between the fitness…

We systematically study and compare damage spreading for random Boolean and threshold networks under small external perturbations (damage), a problem which is relevant to many biological networks. We identify a new characteristic…

There are three main aims of this paper. 1- I explain reasons why I await life to lie significantly deeper in chaos than Kauffman approach does, however still in boundary area near `the edge of chaos and order'. The role of negative…

Boolean networks are a valuable class of discrete dynamical systems models, but they remain fundamentally limited by their inability to capture multi-way interactions in their components. To remedy this limitation, we propose a model of…

Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This…

We consider two mathematical dynamical models of gene regulatory networks (GRNs) and obtain results on robust synchronization on these dynamical models based on the existing theoretical results in the coupled cell network formalism. We also…

There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…

The description of gene interactions that constantly occur in the cellular environment is an extremely challenging task due to an immense number of degrees of freedom and incomplete knowledge about microscopic details. Hence, a…

In this work we investigate time varying networks with complex dynamics at the nodes. We consider two scenarios of network change in an interval of time: first, we have the case where each link can change with probability pt, i.e. the…

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…