Literature DB >> 15234201

Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic.

Gilles Bernot1, Jean-Paul Comet, Adrien Richard, Janine Guespin.   

Abstract

Based on the discrete definition of biological regulatory networks developed by René Thomas, we provide a computer science formal approach to treat temporal properties of biological regulatory networks, expressed in computational tree logic. It is then possible to build all the models satisfying a set of given temporal properties. Our approach is illustrated with the mucus production in Pseudomonas aeruginosa. This application of formal methods from computer science to biological regulatory networks should open the way to many other fruitful applications.

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Year:  2004        PMID： 15234201     DOI： 10.1016/j.jtbi.2004.04.003

Source DB:  PubMed          Journal:  J Theor Biol        ISSN： 0022-5193            Impact factor:   2.691


  35 in total

Review 1.  Topology-based abstraction of complex biological systems: application to the Golgi apparatus.

Authors:  Mathieu Poudret; Agnès Arnould; Jean-Paul Comet; Pascale Le Gall; Philippe Meseure; François Képès
Journal:  Theory Biosci       Date:  2008-05-06       Impact factor: 1.919

2.  On the impact of the distance between two genes on their interaction curve.

Authors:  Siamak Taati; Enrico Formenti; Jean-Paul Comet; Gilles Bernot
Journal:  J Math Biol       Date:  2011-02-15       Impact factor: 2.259

Review 3.  Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.

Authors:  Madalena Chaves; Hidde de Jong
Journal:  Methods Mol Biol       Date:  2021

4.  Faithful modeling of transient expression and its application to elucidating negative feedback regulation.

Authors:  Amir Rubinstein; Vyacheslav Gurevich; Zohar Kasulin-Boneh; Lilach Pnueli; Yona Kassir; Ron Y Pinter
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-30       Impact factor: 11.205

5.  Learning delayed influences of biological systems.

Authors:  Tony Ribeiro; Morgan Magnin; Katsumi Inoue; Chiaki Sakama
Journal:  Front Bioeng Biotechnol       Date:  2015-01-16

6.  Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.

Authors:  Sabine Pérès; Liza Felicori; Stéphanie Rialle; Elodie Jobard; Franck Molina
Journal:  Bioinformatics       Date:  2010-05-06       Impact factor: 6.937

7.  Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.

Authors:  Gregory Batt; Michel Page; Irene Cantone; Gregor Goessler; Pedro Monteiro; Hidde de Jong
Journal:  Bioinformatics       Date:  2010-09-15       Impact factor: 6.937

8.  STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification.

Authors:  Szymon Stoma; Alexandre Donzé; François Bertaux; Oded Maler; Gregory Batt
Journal:  PLoS Comput Biol       Date:  2013-05-09       Impact factor: 4.475

9.  A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking.

Authors:  Ovidiu Pârvu; David Gilbert
Journal:  PLoS One       Date:  2016-05-17       Impact factor: 3.240

10.  A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.

Authors:  Pedro T Monteiro; Estelle Dumas; Bruno Besson; Radu Mateescu; Michel Page; Ana T Freitas; Hidde de Jong
Journal:  BMC Bioinformatics       Date:  2009-12-30       Impact factor: 3.169
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