Related papers: Timing and dynamics of single cell gene expression…

We investigate the consequences of periodic, on-off glucose infusion on the glucose-insulin regulatory system on the basis of a system-level mathematical model with two explicit time delays. Studying the effects of such infusion protocols…

Gene expression time delays, modelling the complex biological processes of gene transcription and translation, have been shown to play an important role in cellular dynamics. Time delays, motivated by the gene expression process, can also…

Time delays, modelling the process of intracellular gene expression, have been shown to have important impacts on the dynamics of pattern formation in reaction-diffusion systems. In particular, past work has shown that such time delays can…

Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…

Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…

How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…

In many biological systems, chemical reactions or changes in a physical state are assumed to occur instantaneously. For describing the dynamics of those systems, Markov models that require exponentially distributed inter-event times have…

We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…

The lactose uptake-pathway of E. coli is a paradigmatic example of multistability in gene-regulatory circuits. In the induced state of the lac-pathway, the genes comprising the lac-operon are transcribed, leading to the production of…

We examine quantitatively the transition process from emitting to not-emitting states of fluorescent molecules with a machine learning technique. In a fluorescently labeled DNA, the fluorescence occurs continuously under irradiation, but it…

How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…

Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be…

Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…

We introduce a general methodology of update rules accounting for arbitrary interevent time distributions in simulations of interacting agents. In particular we consider update rules that depend on the state of the agent, so that the update…

Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…

Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…

Genetically engineered bacteria to increase the tumbling frequency of the run-and-tumble motion for the higher local bacterial density form visible stripe pattern composed of successive high and low density regions on an agar plate. We…

In Escherichia coli the response to DNA damage shows strong cell-to-cell-heterogenity. This results in a random delay in cell division and asymmetrical binary fission of single cells, which can compromise the size homeostasis of the…

Time delay is ubiquitous in many experimental and real-world situations. It is often unclear whether time delay plays a significant role in observed phenomena, and if it does, how long the time lag really is. This would be invaluable…