Literature DB >> 24045959

Robustness, canalyzing functions and systems design.

Johannes Rauh1, Nihat Ay.   

Abstract

We study a notion of knockout robustness of a stochastic map (Markov kernel) that describes a system of several input random variables and one output random variable. Robustness requires that the behaviour of the system does not change if one or several of the input variables are knocked out. Gibbs potentials are used to give a mechanistic description of the behaviour of the system after knockouts. Robustness imposes structural constraints on these potentials. We show that robust systems can be described in terms of suitable interaction families of Gibbs potentials, which allows us to address the problem of systems design. Robustness is also characterized by conditional independence constraints on the joint distribution of input and output. The set of all probability distributions corresponding to robust systems can be decomposed into a finite union of components, and we find parametrizations of the components.

Mesh:

Year:  2013        PMID: 24045959     DOI: 10.1007/s12064-013-0186-3

Source DB:  PubMed          Journal:  Theory Biosci        ISSN: 1431-7613            Impact factor:   1.919


  10 in total

1.  Quasi-independence, homology and the unity of type: a topological theory of characters.

Authors:  Günter P Wagner; Peter F Stadler
Journal:  J Theor Biol       Date:  2003-02-21       Impact factor: 2.691

Review 2.  Perspective: Evolution and detection of genetic robustness.

Authors:  J Arjan G M de Visser; Joachim Hermisson; Günter P Wagner; Lauren Ancel Meyers; Homayoun Bagheri-Chaichian; Jeffrey L Blanchard; Lin Chao; James M Cheverud; Santiago F Elena; Walter Fontana; Greg Gibson; Thomas F Hansen; David Krakauer; Richard C Lewontin; Charles Ofria; Sean H Rice; George von Dassow; Andreas Wagner; Michael C Whitlock
Journal:  Evolution       Date:  2003-09       Impact factor: 3.694

3.  Random Boolean network models and the yeast transcriptional network.

Authors:  Stuart Kauffman; Carsten Peterson; Björn Samuelsson; Carl Troein
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-01       Impact factor: 11.205

4.  Genetic networks with canalyzing Boolean rules are always stable.

Authors:  Stuart Kauffman; Carsten Peterson; Björn Samuelsson; Carl Troein
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-30       Impact factor: 11.205

5.  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

6.  Geometric robustness theory and biological networks.

Authors:  Nihat Ay; David C Krakauer
Journal:  Theory Biosci       Date:  2006-08-02       Impact factor: 1.919

7.  Nested Canalyzing, Unate Cascade, and Polynomial Functions.

Authors:  Abdul Salam Jarrah; Blessilda Raposa; Reinhard Laubenbacher
Journal:  Physica D       Date:  2007-09-15       Impact factor: 2.300

8.  From sequences to shapes and back: a case study in RNA secondary structures.

Authors:  P Schuster; W Fontana; P F Stadler; I L Hofacker
Journal:  Proc Biol Sci       Date:  1994-03-22       Impact factor: 5.349

9.  Robustness of Boolean dynamics under knockouts.

Authors:  Gunnar Boldhaus; Nils Bertschinger; Johannes Rauh; Eckehard Olbrich; Konstantin Klemm
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-08-18

10.  Boolean network simulations for life scientists.

Authors:  István Albert; Juilee Thakar; Song Li; Ranran Zhang; Réka Albert
Journal:  Source Code Biol Med       Date:  2008-11-14
  10 in total
  2 in total

1.  The Identity of Information: How Deterministic Dependencies Constrain Information Synergy and Redundancy.

Authors:  Daniel Chicharro; Giuseppe Pica; Stefano Panzeri
Journal:  Entropy (Basel)       Date:  2018-03-05       Impact factor: 2.524

Review 2.  Ingredients for robustness.

Authors:  Nihat Ay
Journal:  Theory Biosci       Date:  2020-12-02       Impact factor: 1.919

  2 in total

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