Literature DB >> 19658525

Boolean modeling of collective effects in complex networks.

Johannes Norrell1, Joshua E S Socolar.   

Abstract

Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may, however, introduce dynamical possibilities that are not accessible to the original system. We show that large random networks of variables coupled through continuous transfer functions often fail to exhibit the complex dynamics of corresponding Boolean models in the disordered (chaotic) regime, even when each individual function appears to be a good candidate for Boolean idealization. A suitably modified Boolean theory explains the behavior of systems in which information does not propagate faithfully down certain chains of nodes. Model networks incorporating calculated or directly measured transfer functions reported in the literature on transcriptional regulation of genes are described by the modified theory.

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Year:  2009        PMID: 19658525      PMCID: PMC2718684          DOI: 10.1103/PhysRevE.79.061908

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  18 in total

1.  A synthetic oscillatory network of transcriptional regulators.

Authors:  M B Elowitz; S Leibler
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  On schemes of combinatorial transcription logic.

Authors:  Nicolas E Buchler; Ulrich Gerland; Terence Hwa
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-17       Impact factor: 11.205

3.  Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

Authors:  Sara Hooshangi; Stephan Thiberge; Ron Weiss
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-28       Impact factor: 11.205

4.  Canalizing Kauffman networks: nonergodicity and its effect on their critical behavior.

Authors:  André Auto Moreira; Luís A Nunes Amaral
Journal:  Phys Rev Lett       Date:  2005-06-03       Impact factor: 9.161

5.  Iterated maps for annealed Boolean networks.

Authors:  Juha Kesseli; Pauli Rämö; Olli Yli-Harja
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-10-05

6.  The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model.

Authors:  Maria Davidich; Stefan Bornholdt
Journal:  J Theor Biol       Date:  2008-07-23       Impact factor: 2.691

7.  Molecular titration and ultrasensitivity in regulatory networks.

Authors:  Nicolas E Buchler; Matthieu Louis
Journal:  J Mol Biol       Date:  2008-10-10       Impact factor: 5.469

Review 8.  Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs.

Authors:  J E Ferrell
Journal:  Trends Biochem Sci       Date:  1996-12       Impact factor: 13.807

9.  Quantification of information transfer via cellular signal transduction pathways.

Authors:  B N Kholodenko; J B Hoek; H V Westerhoff; G C Brown
Journal:  FEBS Lett       Date:  1997-09-08       Impact factor: 4.124

10.  Detailed map of a cis-regulatory input function.

Authors:  Y Setty; A E Mayo; M G Surette; U Alon
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-12       Impact factor: 11.205

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  2 in total

1.  Boolean versus continuous dynamics in modules with two feedback loops.

Authors:  Eva Ackermann; Eva Marie Weiel; Torsten Pfaff; Barbara Drossel
Journal:  Eur Phys J E Soft Matter       Date:  2012-10-26       Impact factor: 1.890

2.  Encoding the β-Arrestin Trafficking Fate of Ghrelin Receptor GHSR1a: C-Tail-Independent Molecular Determinants in GPCRs.

Authors:  Krisztian Toth; Karim Nagi; Lauren M Slosky; Lauren Rochelle; Caroline Ray; Suneet Kaur; Sudha K Shenoy; Marc G Caron; Larry S Barak
Journal:  ACS Pharmacol Transl Sci       Date:  2019-06-03
  2 in total

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