Literature DB >> 16670776

Noise in a Small Genetic Circuit that Undergoes Bifurcation.

Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart Kauffman.   

Abstract

Based on the consideration of Boolean dynamics, it has been hypothesized that cell types may correspond to alternative attractors of a gene regulatory network. Recent stochastic Boolean network analysis, however, raised the important question concerning the stability of such attractors. In this paper a detailed numerical analysis is performed within the framework of Langevin dynamics. While the present results confirm that the noise is indeed an important dynamical element, the cell type as represented by attractors can still be a viable hypothesis. It is found that the stability of an attractor depends on the strength of noise related to the distance of the system to the bifurcation point and it can be exponentially stable depending on biological parameters.

Year:  2005        PMID: 16670776      PMCID: PMC1456069          DOI: 10.1002/cplx.20099

Source DB:  PubMed          Journal:  Complexity        ISSN: 1076-2787            Impact factor:   2.833


  7 in total

1.  Classification of biological networks by their qualitative dynamics.

Authors:  L Glass
Journal:  J Theor Biol       Date:  1975-10       Impact factor: 2.691

2.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

3.  Structure and function of the feed-forward loop network motif.

Authors:  S Mangan; U Alon
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-06       Impact factor: 11.205

4.  Robustness, stability and efficiency of phage lambda genetic switch: dynamical structure analysis.

Authors:  X-M Zhu; L Yin; L Hood; P Ao
Journal:  J Bioinform Comput Biol       Date:  2004-12       Impact factor: 1.122

5.  Metabolic stability and epigenesis in randomly constructed genetic nets.

Authors:  S A Kauffman
Journal:  J Theor Biol       Date:  1969-03       Impact factor: 2.691

6.  A mathematical framework for describing and analysing gene regulatory networks.

Authors:  T Mestl; E Plahte; S W Omholt
Journal:  J Theor Biol       Date:  1995-09-21       Impact factor: 2.691

7.  Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.

Authors:  Radu Dobrin; Qasim K Beg; Albert-László Barabási; Zoltán N Oltvai
Journal:  BMC Bioinformatics       Date:  2004-01-30       Impact factor: 3.169

  7 in total
  6 in total

1.  An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium.

Authors:  Marc Bailly-Bechet; Arndt Benecke; Wolf Dietrich Hardt; Valentina Lanza; Alexander Sturm; Riccardo Zecchina
Journal:  J Math Biol       Date:  2010-11-24       Impact factor: 2.259

2.  Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution.

Authors:  Ping Ao; David Galas; Leroy Hood; Xiaomei Zhu
Journal:  Med Hypotheses       Date:  2007-09-04       Impact factor: 1.538

3.  Global view of bionetwork dynamics: adaptive landscape.

Authors:  Ping Ao
Journal:  J Genet Genomics       Date:  2009-02       Impact factor: 4.275

4.  Modeling stochasticity and variability in gene regulatory networks.

Authors:  David Murrugarra; Alan Veliz-Cuba; Boris Aguilar; Seda Arat; Reinhard Laubenbacher
Journal:  EURASIP J Bioinform Syst Biol       Date:  2012-06-06

5.  Attraction basins as gauges of robustness against boundary conditions in biological complex systems.

Authors:  Jacques Demongeot; Eric Goles; Michel Morvan; Mathilde Noual; Sylvain Sené
Journal:  PLoS One       Date:  2010-08-05       Impact factor: 3.240

6.  Modeling Basins of Attraction for Breast Cancer Using Hopfield Networks.

Authors:  Alessandra Jordano Conforte; Leon Alves; Flávio Codeço Coelho; Nicolas Carels; Fabrício Alves Barbosa da Silva
Journal:  Front Genet       Date:  2020-04-07       Impact factor: 4.599

  6 in total

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