Related papers: Single-cell stochastic gene expression kinetics wi…
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene,…
Gene regulatory circuits must contend with intrinsic noise that arises due to finite numbers of proteins. While some circuits act to reduce this noise, others appear to exploit it. A striking example is the competence circuit in Bacillus…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node…
Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising…
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a…
This paper compares the auto-repressed gene to a simple one (a gene without auto-regulation) in terms of response time and output noise under the assumption of fixed metabolic cost. The analysis shows that, in the case of non-vanishing leak…
Bifurcation analysis has many applications in different scientific fields, such as electronics, biology, ecology, and economics. In population biology, deterministic methods of bifurcation are commonly used. In contrast, stochastic…
Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities…
Multiple cellular processes are triggered when the concentration of a regulatory protein reaches a critical threshold. Previous analyses have characterized timing statistics for single-gene systems. However, many biological timers are based…
Gene expression (GE) is an inherently random or stochastic or noisy process. The randomness in different steps of GE, e.g., transcription, translation, degradation, etc., leading to cell-to-cell variations in mRNA and protein levels. This…
We study by mean-field analysis and stochastic simulations chemical models for genetic toggle switches formed from pairs of genes that mutually repress each other. In order to determine the stability of the genetic switches, we make a…
Understanding how stochastic gene expression is regulated in biological systems using snapshots of single-cell transcripts requires state-of-the-art methods of computational analysis and statistical inference. A Bayesian approach to…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
We show that \emph{stochastic bursting} is observed in a ring of unidirectional delay-coupled noisy excitable systems, thanks to the combinational action of time-delayed coupling and noise. Under the approximation of timescale separation,…
Cells sense their surrounding by employing intracellular signaling pathways that transmit hormonal signals from the cell membrane to the nucleus. TGF-$\beta$/SMAD signaling encodes various cell fates, controls tissue homeostasis and is…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…