Related papers: Stabilizing Gene Regulatory Networks Through Feedf…
Regulatory dynamics in biology is often described by continuous rate equations for continuously varying chemical concentrations. Binary discretization of state space and time leads to Boolean dynamics. In the latter, the dynamics has been…
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…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
Gene expression in response to stimuli is regulated by transcription factors (TFs) through feedback loop motifs, aimed at maintaining the desired TF concentration despite uncertainties and perturbations. In this work, we consider a…
Motivation: Recent studies of genomic-scale regulatory networks suggested that a feed-forward loop (FFL) circuitry is a key component of many such networks. This led to a study of the functional properties of different FFL types, where the…
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…
We compare asynchronous vs. synchronous update of discrete dynamical networks and find that a simple time delay in the nodes may induce a reproducible deterministic dynamics even in the case of asynchronous update in random order. In…
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…
Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single…
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…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…
MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to…
Stability is a fundamental property of dynamical systems, yet to this date it has had little bearing on the practice of recurrent neural networks. In this work, we conduct a thorough investigation of stable recurrent models. Theoretically,…
Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…
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…
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a…