Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct;80(4 Pt 1):041921. Epub 2009 Oct 20.

Spectral solutions to stochastic models of gene expression with bursts and regulation.

Author information

  • 1Department of Physics, Columbia University, New York, New York 10027, USA. ajm2121@columbia.edu

Abstract

Signal-processing molecules inside cells are often present at low copy number, which necessitates probabilistic models to account for intrinsic noise. Probability distributions have traditionally been found using simulation-based approaches which then require estimating the distributions from many samples. Here we present in detail an alternative method for directly calculating a probability distribution by expanding in the natural eigenfunctions of the governing equation, which is linear. We apply the resulting spectral method to three general models of stochastic gene expression: a single gene with multiple expression states (often used as a model of bursting in the limit of two states), a gene regulatory cascade, and a combined model of bursting and regulation. In all cases we find either analytic results or numerical prescriptions that greatly outperform simulations in efficiency and accuracy. In the last case, we show that bimodal response in the limit of slow switching is not only possible but optimal in terms of information transmission.

PMID:
19905356
[PubMed - indexed for MEDLINE]
PMCID:
PMC3115574
Free PMC Article

Images from this publication.See all images (5)Free text

FIG. 1
FIG. 2
FIG. 3
FIG. 4
FIG. 5
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for PubMed Central
    Loading ...
    Write to the Help Desk