Characterizing short-term stability for Boolean networks over any distribution of transfer functions

Seshadhri, C.; Smith, Andrew M.; Vorobeychik, Yevgeniy; Mayo, Jackson R.; Armstrong, Robert C.

doi:10.1103/PhysRevE.94.012301

Title: Characterizing short-term stability for Boolean networks over any distribution of transfer functions

Abstract

Here we present a characterization of short-term stability of random Boolean networks under arbitrary distributions of transfer functions. Given any distribution of transfer functions for a random Boolean network, we present a formula that decides whether short-term chaos (damage spreading) will happen. We provide a formal proof for this formula, and empirically show that its predictions are accurate. Previous work only works for special cases of balanced families. Finally, it has been observed that these characterizations fail for unbalanced families, yet such families are widespread in real biological networks.

Authors:

Seshadhri, C. ^[1]; Smith, Andrew M. ^[2]; Vorobeychik, Yevgeniy ^[3]; Mayo, Jackson R. ^[2]; Armstrong, Robert C. ^[2]

Univ. of California, Santa Cruz, CA (United States)
Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Vanderbilt Univ., Nashville, TN (United States)

Publication Date:: Tue Jul 05 00:00:00 EDT 2016

Research Org.:: Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Sponsoring Org.:: USDOE National Nuclear Security Administration (NNSA)

OSTI Identifier:: 1338403

Alternate Identifier(s):: OSTI ID: 1260301

Report Number(s):: SAND2016-12902J
Journal ID: ISSN 2470-0045; PLEEE8; 650102; TRN: US1701803

Grant/Contract Number:: AC04-94AL85000

Resource Type:: Accepted Manuscript

Journal Name:: Physical Review E

Additional Journal Information:: Journal Volume: 94; Journal Issue: 1; Journal ID: ISSN 2470-0045

Publisher:: American Physical Society (APS)

Country of Publication:: United States

Language:: English

Subject:: 97 MATHEMATICS AND COMPUTING

Citation Formats


                    Seshadhri, C., Smith, Andrew M., Vorobeychik, Yevgeniy, Mayo, Jackson R., and Armstrong, Robert C. Characterizing short-term stability for Boolean networks over any distribution of transfer functions.  United States: N. p., 2016. 
Web.  doi:10.1103/PhysRevE.94.012301.

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                    Seshadhri, C., Smith, Andrew M., Vorobeychik, Yevgeniy, Mayo, Jackson R., & Armstrong, Robert C. Characterizing short-term stability for Boolean networks over any distribution of transfer functions.  United States.  https://doi.org/10.1103/PhysRevE.94.012301

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                    Seshadhri, C., Smith, Andrew M., Vorobeychik, Yevgeniy, Mayo, Jackson R., and Armstrong, Robert C. Tue .  
"Characterizing short-term stability for Boolean networks over any distribution of transfer functions".  United States.  https://doi.org/10.1103/PhysRevE.94.012301.  https://www.osti.gov/servlets/purl/1338403.

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@article{osti_1338403,

  title        = {Characterizing short-term stability for Boolean networks over any distribution of transfer functions},

  author       = {Seshadhri, C. and Smith, Andrew M. and Vorobeychik, Yevgeniy and Mayo, Jackson R. and Armstrong, Robert C.},

  abstractNote = {Here we present a characterization of short-term stability of random Boolean networks under arbitrary distributions of transfer functions. Given any distribution of transfer functions for a random Boolean network, we present a formula that decides whether short-term chaos (damage spreading) will happen. We provide a formal proof for this formula, and empirically show that its predictions are accurate. Previous work only works for special cases of balanced families. Finally, it has been observed that these characterizations fail for unbalanced families, yet such families are widespread in real biological networks.},

  doi          = {10.1103/PhysRevE.94.012301},

  journal      = {Physical Review E},

  number       = 1,

  volume       = 94,

  place        = {United States},

  year         = {Tue Jul 05 00:00:00 EDT 2016},

  month        = {Tue Jul 05 00:00:00 EDT 2016}

}

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https://doi.org/10.1103/PhysRevE.94.012301

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Works referenced in this record:

Metabolic stability and epigenesis in randomly constructed genetic nets
journal, March 1969

Kauffman, S. A.
Journal of Theoretical Biology, Vol. 22, Issue 3
DOI: 10.1016/0022-5193(69)90015-0

The yeast cell-cycle network is robustly designed
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Li, F.; Long, T.; Lu, Y.
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DOI: 10.1073/pnas.0305937101

Random Boolean network models and the yeast transcriptional network
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Kauffman, S.; Peterson, C.; Samuelsson, B.
Proceedings of the National Academy of Sciences, Vol. 100, Issue 25
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Threshold Models of Collective Behavior
journal, May 1978

Granovetter, Mark
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Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast
journal, February 2008

Davidich, Maria I.; Bornholdt, Stefan
PLoS ONE, Vol. 3, Issue 2
DOI: 10.1371/journal.pone.0001672

Dynamics of Boolean Networks: An Exact Solution
journal, May 2011

Mozeika, Alexander; Saad, David
Physical Review Letters, Vol. 106, Issue 21
DOI: 10.1103/PhysRevLett.106.214101

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Title: Characterizing short-term stability for Boolean networks over any distribution of transfer functions

Abstract

Citation Formats

Metabolic stability and epigenesis in randomly constructed genetic nets journal, March 1969

The yeast cell-cycle network is robustly designed journal, March 2004

Random Boolean network models and the yeast transcriptional network journal, December 2003

Threshold Models of Collective Behavior journal, May 1978

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast journal, February 2008

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journal, March 2004

Random Boolean network models and the yeast transcriptional network
journal, December 2003

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journal, May 1978

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journal, February 2008

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journal, May 2011