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Computation of steady-state probability distributions in stochastic models of cellular networks.

Publication ,  Journal Article
Hallen, M; Li, B; Tanouchi, Y; Tan, C; West, M; You, L
Published in: PLoS computational biology
October 2011

Cellular processes are "noisy". In each cell, concentrations of molecules are subject to random fluctuations due to the small numbers of these molecules and to environmental perturbations. While noise varies with time, it is often measured at steady state, for example by flow cytometry. When interrogating aspects of a cellular network by such steady-state measurements of network components, a key need is to develop efficient methods to simulate and compute these distributions. We describe innovations in stochastic modeling coupled with approaches to this computational challenge: first, an approach to modeling intrinsic noise via solution of the chemical master equation, and second, a convolution technique to account for contributions of extrinsic noise. We show how these techniques can be combined in a streamlined procedure for evaluation of different sources of variability in a biochemical network. Evaluation and illustrations are given in analysis of two well-characterized synthetic gene circuits, as well as a signaling network underlying the mammalian cell cycle entry.

Duke Scholars

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Published In

PLoS computational biology

DOI

EISSN

1553-7358

ISSN

1553-734X

Publication Date

October 2011

Volume

7

Issue

10

Start / End Page

e1002209

Related Subject Headings

  • Stochastic Processes
  • Probability
  • Models, Biological
  • Bioinformatics
  • 08 Information and Computing Sciences
  • 06 Biological Sciences
  • 01 Mathematical Sciences
 

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Hallen, M., Li, B., Tanouchi, Y., Tan, C., West, M., & You, L. (2011). Computation of steady-state probability distributions in stochastic models of cellular networks. PLoS Computational Biology, 7(10), e1002209. https://doi.org/10.1371/journal.pcbi.1002209
Hallen, Mark, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, and Lingchong You. “Computation of steady-state probability distributions in stochastic models of cellular networks.PLoS Computational Biology 7, no. 10 (October 2011): e1002209. https://doi.org/10.1371/journal.pcbi.1002209.
Hallen M, Li B, Tanouchi Y, Tan C, West M, You L. Computation of steady-state probability distributions in stochastic models of cellular networks. PLoS computational biology. 2011 Oct;7(10):e1002209.
Hallen, Mark, et al. “Computation of steady-state probability distributions in stochastic models of cellular networks.PLoS Computational Biology, vol. 7, no. 10, Oct. 2011, p. e1002209. Epmc, doi:10.1371/journal.pcbi.1002209.
Hallen M, Li B, Tanouchi Y, Tan C, West M, You L. Computation of steady-state probability distributions in stochastic models of cellular networks. PLoS computational biology. 2011 Oct;7(10):e1002209.

Published In

PLoS computational biology

DOI

EISSN

1553-7358

ISSN

1553-734X

Publication Date

October 2011

Volume

7

Issue

10

Start / End Page

e1002209

Related Subject Headings

  • Stochastic Processes
  • Probability
  • Models, Biological
  • Bioinformatics
  • 08 Information and Computing Sciences
  • 06 Biological Sciences
  • 01 Mathematical Sciences