相关论文: Coherent organization in gene regulation: a study …

One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…

In this paper we introduce a neural network model of self-organization. This model uses a variation of Hebb rule for updating its synaptic weights, and surely converges to the equilibrium status. The key point of the convergence is the…

Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…

The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems…

Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…

Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…

The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…

Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…

The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…

We study the evolution of heterogeneous networks of oscillators subject to a state-dependent interconnection rule. We find that heterogeneity in the node dynamics is key in organizing the architecture of the functional emerging networks. We…

We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…

We study the emergence of coherence in complex networks of mutually coupled non-identical elements. We uncover the precise dependence of the dynamical coherence on the network connectivity, on the isolated dynamics of the elements and the…

Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…

Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…

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…

Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…

Many natural, complex systems are remarkably stable thanks to an absence of feedback acting on their elements. When described as networks, these exhibit few or no cycles, and associated matrices have small leading eigenvalues. It has been…

Network coherence generally refers to the emergence of simple aggregated dynamical behaviours, despite heterogeneity in the dynamics of the subsystems that constitute the network. In this paper, we develop a general frequency domain…

The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…