Related papers: Stochastic Simulation of Gene Expression in a Sing…
In this work, we develop a stochastic model of gene gain and loss with the aim of inferring when (if at all) in evolutionary history and association between two genes arises. The data we consider is a species tree along with information on…
We show how to construct a reduced description of interacting genes in noisy, small regulatory networks using coupled binary "spin" variables. Treating both the protein number and gene expression state variables stochastically and on equal…
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…
Cancer invasion and metastasis depend on angiogenesis. The cellular processes (growth, migration, and apoptosis) that occur during angiogenesis are tightly regulated by signaling molecules. Thus, understanding how cells synthesize multiple…
The effects of intrinsic noise on stochastic delay systems is studied within an expansion in the inverse system size. We show that the stochastic nature of the underlying dynamics may induce oscillatory behaviour in parameter ranges where…
Recent experimental advances in biology allow researchers to obtain gene expression profiles at single-cell resolution over hundreds, or even thousands of cells at once. These single-cell measurements provide snapshots of the states of the…
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…
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…
We examine immunostaining experimental data for the formation of the strip 2 of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An estimate of the factor converting immunofluorescence intensity units into molecular…
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…
In a stochastic process, noise often modifies the picture offered by the mean field dynamics. In particular, when there is an absorbing state, the noise erases a stable fixed point of the mean field equation from the stationary…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
The problem of controlling the mean and the variance of a species of interest in a simple gene expression is addressed. It is shown that the protein mean level can be globally and robustly tracked to any desired value using a simple PI…
Systems biology approaches combining theoretical modeling with experiments have been singularly successful in uncovering novel features of cellular phenomena. One such feature is that of binary gene expression in which the expression level…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
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,…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
The genetic repressilator circuit consists of three transcription factors, or repressors, which negatively regulate each other in a cyclic manner. This circuit was synthetically constructed on plasmids in {\it Escherichia coli} and was…
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is…