» Articles » PMID: 19139763

Stochastic Modelling for Quantitative Description of Heterogeneous Biological Systems

Overview
Journal Nat Rev Genet
Specialty Genetics
Date 2009 Jan 14
PMID 19139763
Citations 185
Authors
Affiliations
Soon will be listed here.
Abstract

Two related developments are currently changing traditional approaches to computational systems biology modelling. First, stochastic models are being used increasingly in preference to deterministic models to describe biochemical network dynamics at the single-cell level. Second, sophisticated statistical methods and algorithms are being used to fit both deterministic and stochastic models to time course and other experimental data. Both frameworks are needed to adequately describe observed noise, variability and heterogeneity of biological systems over a range of scales of biological organization.

Citing Articles

Bayesian classification of OXPHOS deficient skeletal myofibres.

Childs J, Gomes T, Vincent A, Golightly A, Lawless C PLoS Comput Biol. 2025; 21(2):e1012770.

PMID: 39970187 PMC: 11838899. DOI: 10.1371/journal.pcbi.1012770.


Data-driven model discovery and model selection for noisy biological systems.

Wu X, McDermott M, MacLean A PLoS Comput Biol. 2025; 21(1):e1012762.

PMID: 39836686 PMC: 11753677. DOI: 10.1371/journal.pcbi.1012762.


Preexisting cell state rather than stochastic noise confers high or low infection susceptibility of human lung epithelial cells to adenovirus.

Petkidis A, Suomalainen M, Andriasyan V, Singh A, Greber U mSphere. 2024; 9(10):e0045424.

PMID: 39315811 PMC: 11542551. DOI: 10.1128/msphere.00454-24.


Computational Synthetic Biology Enabled through JAX: A Showcase.

Gallup O, Sechkar K, Towers S, Steel H ACS Synth Biol. 2024; 13(9):3046-3050.

PMID: 39230510 PMC: 11421211. DOI: 10.1021/acssynbio.4c00307.


Transcriptional bursting: from fundamentals to novel insights.

Hebenstreit D, Karmakar P Biochem Soc Trans. 2024; 52(4):1695-1702.

PMID: 39119657 PMC: 11668302. DOI: 10.1042/BST20231286.


References
1.
Orlando D, Lin C, Bernard A, Iversen E, Hartemink A, Haase S . A probabilistic model for cell cycle distributions in synchrony experiments. Cell Cycle. 2007; 6(4):478-88. DOI: 10.4161/cc.6.4.3859. View

2.
Li H, Cao Y, Petzold L, Gillespie D . Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol Prog. 2007; 24(1):56-61. PMC: 2664303. DOI: 10.1021/bp070255h. View

3.
Bar-Even A, Paulsson J, Maheshri N, Carmi M, OShea E, Pilpel Y . Noise in protein expression scales with natural protein abundance. Nat Genet. 2006; 38(6):636-43. DOI: 10.1038/ng1807. View

4.
Shahrezaei V, Ollivier J, Swain P . Colored extrinsic fluctuations and stochastic gene expression. Mol Syst Biol. 2008; 4:196. PMC: 2424296. DOI: 10.1038/msb.2008.31. View

5.
Raser J, OShea E . Noise in gene expression: origins, consequences, and control. Science. 2005; 309(5743):2010-3. PMC: 1360161. DOI: 10.1126/science.1105891. View