Reconstructing an epigenetic landscape using a genetic pulling approach.

Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway.

Reducing the extinction risk of stochastic populations via nondemographic noise.

We consider nondemographic noise in the form of uncertainty in the reaction step size and reveal a dramatic effect this noise may have on the stability of self-regulating populations. Employing the reaction scheme mA→kA but allowing, e.g.

Publisher's Note: Effect of reaction-step-size noise on the switching dynamics of stochastic populations [Phys. Rev. E 93, 052117 (2016)].

This corrects the article DOI: 10.1103/PhysRevE.93.

Effect of reaction-step-size noise on the switching dynamics of stochastic populations.

In genetic circuits, when the messenger RNA lifetime is short compared to the cell cycle, proteins are produced in geometrically distributed bursts, which greatly affects the cellular switching dynamics between different metastable phenotypic states. Motivated by this scenario, we study a general problem of switching or escape in stochastic populations, where influx of particles occurs in groups or bursts, sampled from an arbitrary distribution. The fact that the step size of the influx reaction is a priori unknown and, in general, may fluctuate in time with a given correlation time and statistics, introduces an additional nondemographic reaction-step-size noise into the system.

Dynamics of simple gene-network motifs subject to extrinsic fluctuations.

Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the biomolecular interaction networks. Most previous work has been focused on the intrinsic noise (IN) of these networks.