Related papers: Boolean versus continuous dynamics on simple two-g…
In this paper we use a continuous model to describe the development of a single cell lineage following the committal of stem cells. Three separate controls are implemented in the model, namely the proliferative control of stem cells, the…
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation…
Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold…
Random boolean cellular automata are investigated, where each gate has two randomly chosen inputs and is randomly assigned a boolean function of its inputs. The effect of non-uniform distributions on the choice of the boolean functions is…
Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model of…
Gene Regulatory Networks(GRNs) with feedback are essential components of many cellular processes and may exhibit oscillatory behavior. Analyzing such systems becomes increasingly complex as the number of components increases. Since gene…
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…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the…
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…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
Motivation: In systems biology, modelling strategies aim to decode how molecular components interact to generate dynamical behaviour. Boolean modelling is more and more used, but the description of the dynamics from two-levels components…
This paper studies the mathematical properties of collectively canalizing Boolean functions, a class of functions that has arisen from applications in systems biology. Boolean networks are an increasingly popular modeling framework for…
Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…
Complex coherent dynamics is present in a wide variety of neural systems. A typical example is the voltage transitions between up and down states observed in cortical areas in the brain. In this work, we study this phenomenon via a…
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…
Modelling genetic phenomena affecting biological traits is important for the development of agriculture as it allows breeders to predict the potential of breeding for certain traits. One such phenomenon is heterosis or hybrid vigor:…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…