Reduction of Boolean network models

Journal of Theoretical Biology
Alan Veliz-Cuba

Abstract

Boolean networks have been successfully used in modelling gene regulatory networks. However, for large networks, analysis by simulation becomes unfeasible. In this paper we propose a reduction method for Boolean networks that decreases the size of the network, while preserving important dynamical properties and topological features. As a result, the reduced network can be used to infer properties about the original network and to gain a better understanding of the role of network topology on the dynamics. In particular, we use the reduction method to study steady states of Boolean networks and apply our results to models of Th-lymphocyte differentiation and the lac operon.

References

Mar 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fangting LiChao Tang
May 8, 2010·Bioinformatics·Alan Veliz-CubaReinhard Laubenbacher
Sep 28, 2010·Journal of Theoretical Biology·Gilles DidierClaudine Chaouiya
May 14, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alan Veliz-Cuba, Brandilyn Stigler
Jul 22, 2011·BMC Bioinformatics·Franziska HinkelmannReinhard Laubenbacher

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Citations

Oct 20, 2012·Bulletin of Mathematical Biology·Therese LorenzAlexander Bockmayr
Nov 13, 2012·Methods : a Companion to Methods in Enzymology·Assieh Saadatpour, Réka Albert
Oct 2, 2014·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Réka Albert, Juilee Thakar
Oct 7, 2015·Frontiers in Bioengineering and Biotechnology·Hannes Klarner, Heike Siebert
Apr 8, 2015·PLoS Computational Biology·Jorge G T Zañudo, Réka Albert
Sep 25, 2016·BMC Systems Biology·David MurrugarraReinhard Laubenbacher
Apr 9, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Mohammadmahdi R Yousefi, Edward R Dougherty
Dec 6, 2017·PLoS Computational Biology·Patrick MeyerKarin Scharffetter-Kochanek
Jun 27, 2014·BMC Bioinformatics·Alan Veliz-CubaReinhard Laubenbacher
Sep 27, 2012·Physical Biology·Rui-Sheng WangRéka Albert
Apr 11, 2018·The Journal of Pharmacology and Experimental Therapeutics·Vidya Ramakrishnan, Donald E Mager
Jul 15, 2015·The Journal of Pharmacology and Experimental Therapeutics·Vaishali L ChudasamaDonald E Mager
Jan 8, 2018·Journal of Pharmacokinetics and Pharmacodynamics·Peter BloomingdaleDonald E Mager
Jul 16, 2016·Bulletin of Mathematical Biology·Mihaela T Matache, Valentin Matache
Apr 1, 2018·Chaos·Mohammad Reza Rafimanzelat, Fariba Bahrami
Jun 9, 2018·BMC Systems Biology·Brian C RossJames C Costello
Jan 1, 2013·SIAM Journal on Applied Dynamical Systems·Assieh SaadatpourTimothy C Reluga
Nov 3, 2020·Bioinformatics·Julio AracenaLilian Salinas

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