Literature DB >> 21979825

Multiscale stochastic modelling of gene expression.

Pavol Bokes1, John R King, Andrew T A Wood, Matthew Loose.   

Abstract

Stochastic phenomena in gene regulatory networks can be modelled by the chemical master equation for gene products such as mRNA and proteins. If some of these elements are present in significantly higher amounts than the rest, or if some of the reactions between these elements are substantially faster than others, it is often possible to reduce the master equation to a simpler problem using asymptotic methods. We present examples of such a procedure and analyse the relationship between the reduced models and the original.

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Year:  2011        PMID: 21979825     DOI: 10.1007/s00285-011-0468-7

Source DB:  PubMed          Journal:  J Math Biol        ISSN: 0303-6812            Impact factor:   2.259


  39 in total

1.  Regulation of noise in the expression of a single gene.

Authors:  Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

Review 2.  Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression.

Authors:  D A Hume
Journal:  Blood       Date:  2000-10-01       Impact factor: 22.113

3.  Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks.

Authors:  J Paulsson; M Ehrenberg
Journal:  Phys Rev Lett       Date:  2000-06-05       Impact factor: 9.161

4.  Modeling stochasticity in gene regulation: characterization in the terms of the underlying distribution function.

Authors:  Pawel Paszek
Journal:  Bull Math Biol       Date:  2007-03-15       Impact factor: 1.758

5.  Two classes of quasi-steady-state model reductions for stochastic kinetics.

Authors:  Ethan A Mastny; Eric L Haseltine; James B Rawlings
Journal:  J Chem Phys       Date:  2007-09-07       Impact factor: 3.488

6.  The finite state projection algorithm for the solution of the chemical master equation.

Authors:  Brian Munsky; Mustafa Khammash
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

7.  Stochastic protein expression in individual cells at the single molecule level.

Authors:  Long Cai; Nir Friedman; X Sunney Xie
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

8.  A model for the statistical fluctuations of protein numbers in a microbial population.

Authors:  O G Berg
Journal:  J Theor Biol       Date:  1978-04-20       Impact factor: 2.691

9.  The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation.

Authors:  M A Shea; G K Ackers
Journal:  J Mol Biol       Date:  1985-01-20       Impact factor: 5.469

Review 10.  Single-molecule approaches to stochastic gene expression.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Annu Rev Biophys       Date:  2009       Impact factor: 12.981

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  12 in total

1.  A geometric analysis of fast-slow models for stochastic gene expression.

Authors:  Nikola Popović; Carsten Marr; Peter S Swain
Journal:  J Math Biol       Date:  2015-04-02       Impact factor: 2.259

2.  A stochastic analysis of autoregulation of gene expression.

Authors:  Renaud Dessalles; Vincent Fromion; Philippe Robert
Journal:  J Math Biol       Date:  2017-03-13       Impact factor: 2.259

3.  Assigning probabilities to qualitative dynamics of gene regulatory networks.

Authors:  Liliana Ironi; Ettore Lanzarone
Journal:  J Math Biol       Date:  2014-02-20       Impact factor: 2.259

4.  Gene expression noise is affected differentially by feedback in burst frequency and burst size.

Authors:  Pavol Bokes; Abhyudai Singh
Journal:  J Math Biol       Date:  2016-09-24       Impact factor: 2.259

5.  Path integral approach to generating functions for multistep post-transcription and post-translation processes and arbitrary initial conditions.

Authors:  Jaroslav Albert
Journal:  J Math Biol       Date:  2019-09-05       Impact factor: 2.259

6.  Analytical Expressions and Physics for Single-Cell mRNA Distributions of the lac Operon of E. coli.

Authors:  Krishna Choudhary; Atul Narang
Journal:  Biophys J       Date:  2019-07-03       Impact factor: 4.033

7.  Protein copy number distributions for a self-regulating gene in the presence of decoy binding sites.

Authors:  Pavol Bokes; Abhyudai Singh
Journal:  PLoS One       Date:  2015-03-26       Impact factor: 3.240

8.  Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models.

Authors:  Niraj Kumar; Abhyudai Singh; Rahul V Kulkarni
Journal:  PLoS Comput Biol       Date:  2015-10-16       Impact factor: 4.475

9.  Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay.

Authors:  Qianqian Wu; Tianhai Tian
Journal:  Sci Rep       Date:  2016-08-24       Impact factor: 4.379

10.  Limits of noise for autoregulated gene expression.

Authors:  Peter Czuppon; Peter Pfaffelhuber
Journal:  J Math Biol       Date:  2018-05-24       Impact factor: 2.259

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