Journal ArticleDOI
Boolean formalization of genetic control circuits
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This paper is an attempt to formalize in Boolean terms genetic situations, from simple concepts like recessitivity and cis-dominance, to models describing complex control circuits, to describe in compact and unambiguous way, systems which become more and more difficult to describe as their complexity is being unravelled.About:
This article is published in Journal of Theoretical Biology.The article was published on 1973-12-01. It has received 986 citations till now. The article focuses on the topics: Expression (mathematics) & Binary function.read more
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Qualitative networks: a symbolic approach to analyze biological signaling networks
TL;DR: An approach for constructing computational models of biological systems that extends the framework of Boolean networks and uses formal verification methods for the analysis of the model is introduced, which can scale to multicellular models of complex pathways, and is therefore a useful tool for theAnalysis of complex biological systems.
Journal ArticleDOI
Polynomial algebra of discrete models in systems biology
TL;DR: A unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets can be provided, which allows the use of a variety of mathematical tools from computer algebra for their analysis.
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Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis
Matthieu Vignes,Jimmy Vandel,David Allouche,Nidal Ramadan-Alban,Christine Cierco-Ayrolles,Thomas Schiex,Brigitte Mangin,Simon de Givry +7 more
TL;DR: A simple yet very powerful meta-analysis is proposed, which combines a wide panel of methods ranging from Bayesian networks to penalised linear regressions to analyse gene regulatory networks from different genetical genomics data sets and was ranked first among the teams participating in Challenge 3A.
Posted Content
SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Claudine Chaouiya,Duncan Berenguier,Sarah M. Keating,Aurélien Naldi,Martijn P. van Iersel,Nicolas Rodriguez,Nicolas Rodriguez,Andreas Dräger,Andreas Dräger,Finja Büchel,Thomas Cokelaer,Bryan Kowal,Benjamin Wicks,Emanuel Gonçalves,Julien Dorier,Michel Page,Michel Page,Pedro T. Monteiro,Pedro T. Monteiro,Axel von Kamp,Ioannis Xenarios,Hidde de Jong,Michael Hucka,Steffen Klamt,Denis Thieffry,Nicolas Le Novère,Nicolas Le Novère,Julio Saez-Rodriguez,Tomáš Helikar +28 more
TL;DR: The collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models.
Journal ArticleDOI
Matrix formalism to describe functional states of transcriptional regulatory systems.
TL;DR: This study illustrates how the matrix representation of a TRS coupled with its environment (R*) allows for a sampling of all possible expression states of a given network, and furthermore, how the fundamental subspaces of the matrix provide a way to study key TRS features and may assist in experimental design.
References
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Journal ArticleDOI
Genetic regulatory mechanisms in the synthesis of proteins.
François Jacob,Jacques Monod +1 more
TL;DR: The synthesis of enzymes in bacteria follows a double genetic control, which appears to operate directly at the level of the synthesis by the gene of a shortlived intermediate, or messenger, which becomes associated with the ribosomes where protein synthesis takes place.
Journal ArticleDOI
Metabolic stability and epigenesis in randomly constructed genetic nets
TL;DR: The hypothesis that contemporary organisms are also randomly constructed molecular automata is examined by modeling the gene as a binary (on-off) device and studying the behavior of large, randomly constructed nets of these binary “genes”.
Journal ArticleDOI
INHIBITION BY GLUCOSE OF THE INDUCED SYNTHESIS OF THE β-GALACTOSIDE-ENZYME SYSTEM OF ESCHERICHIA COLI. ANALYSIS OF MAINTENANCE
Melvin Cohn,Kengo Horibata +1 more
TL;DR: The Novick-Weiner effect and the one to be analyzed here prove to be aspects of the same situation and a heterogeneity with respect to the induced synthesis of ,B-galactosidase simulating genetic differences could be provoked within a growing population of otherwise identical cells.
Journal ArticleDOI
ANALYSIS OF THE DIFFERENTIATION AND OF THE HETEROGENEITY WITHIN A POPULATION OF ESCHERICHIA COLI UNDERGOING INDUCED β-GALACTOSIDASE SYNTHESIS
Melvin Cohn,Kengo Horibata +1 more
TL;DR: The kinetics of induction of the galactozymase of certain yeasts and the permease-3-galactosidase system of Escherichia coli can, under certain conditions, be described as autocatalytic.
Journal ArticleDOI
Functional analysis of chemical systems in vivo using a logical circuit equivalent. II. The idea of a molecular automaton
TL;DR: The theory presented by the author in his previous paper in this journal, which concerned the use of logical circuits or symbolic logic, is revised and extended and the idea of a molecular automaton is introduced.
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Metabolic stability and epigenesis in randomly constructed genetic nets
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