Related papers: Robustness, Stability and Efficiency of Phage lamb…
The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this robustness property is a challenging task,…
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including cell-fate decision in developmental processes as well as genesis and progression of cancers. While various attempts have…
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…
Complex gene regulatory networks often display emergent simple behavior. Sometimes this simplicity can be traced to a nearly equivalent energy landscape, but not always. Here, we show how a topological theory for stochastic and biochemical…
In spite of the recent interest and advances in linear controllability of complex networks, controlling nonlinear network dynamics remains to be an outstanding problem. We develop an experimentally feasible control framework for nonlinear…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
Control of the living cell functions with remarkable reliability despite the stochastic nature of the underlying molecular networks -- a property presumably optimized by biological evolution. We here ask to what extent the property of a…
In a "structured system" of equations, each equation depends on a specified subset of the variables. In this article, we explore properties common to "almost every" system with a fixed structure and how the properties can be read from the…
In this paper, we address the problem of dynamic network embedding, that is, representing the nodes of a dynamic network as evolving vectors within a low-dimensional space. While the field of static network embedding is wide and…
A self-regulatory genetic circuit, where a protein acts as a positive regulator of its own production, is known to be a simplest form of biological network with a positive feedback loop. Although at least three components, DNA, RNA, and the…
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…
Understanding which system structure can sustain stable dynamics is a fundamental step in the design and analysis of large scale dynamical systems. Towards this goal, we investigate here the structural stability of systems with a random…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
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…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
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.…
The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are…
The problem of reliability of the dynamics in biological regulatory networks is studied in the framework of a generalized Boolean network model with continuous timing and noise. Using well-known artificial genetic networks such as the…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…