Boolean formalization of genetic control circuits

Thomas, René

doi:10.1016/0022-5193(73)90247-6

Cited by 772 publications

(450 citation statements)

References 7 publications

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“…The theory of biological regulatory networks [1,3,4,65] was born in parallel to the theory of neural networks [66,67]. It is now an extensive research topic which aims at interpreting the "omic" data from bio-array devices.…”

Section: Appendix B Biological Regulation Network Modelingmentioning

confidence: 99%

“Immunetworks”, intersecting circuits and dynamics

Demongeot

Elena

Noual

et al. 2011

Journal of Theoretical Biology

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This paper proposes a study of biological regulatory networks based on a multi-level strategy. Given a network, the first structural level of this strategy consists in analysing the architecture of the network interactions in order to describe it. The second dynamical level consists in relating the patterns found in the architecture to the possible dynamical behaviours of the network. It is known that circuits are the patterns that play the most important part in the dynamics of a network in the sense that they are responsible for the diversity of its asymptotic behaviours. Here, we pursue further this idea and argue that beyond the influence of underlying circuits, intersections of circuits also impact significantly on the dynamics of a network and thus need to be payed special attention to. For some genetic regulation networks involved in the control of the immune system ("immunetworks"), we show that the small number of attractors can be explained by the presence, in the underlying structures of these networks, of intersecting circuits that "inter-lock".

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Section: Appendix B Biological Regulation Network Modelingmentioning

confidence: 99%

“Immunetworks”, intersecting circuits and dynamics

Demongeot

Elena

Noual

et al. 2011

Journal of Theoretical Biology

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“…A few years prior, Umbarger, Pardee and others had observed early versions of negative feedback circuits with the phenomenon of enzymatic feedback inhibition [9,10]. The Monod and Jacob teleonomic arguments were subsequently formalized by Thomas and others in terms of theoretical requirements for positive and negative feedback circuits using Boolean modeling [11].…”

Section: Systems Biologymentioning

confidence: 99%

A unifying view of 21st century systems biology

Vidal

2009

FEBS Letters

119

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The idea that multi‐scale dynamic complex systems formed by interacting macromolecules and metabolites, cells, organs and organisms underlie some of the most fundamental aspects of life was proposed by a few visionaries half a century ago. We are witnessing a powerful resurgence of this idea made possible by the availability of nearly complete genome sequences, ever improving gene annotations and interactome network maps, the development of sophisticated informatic and imaging tools, and importantly, the use of engineering and physics concepts such as control and graph theory. Alongside four other fundamental “great ideas” as suggested by Sir Paul Nurse, namely, the gene, the cell, the role of chemistry in biological processes, and evolution by natural selection, systems‐level understanding of “What is Life” may materialize as one of the major ideas of biology.

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“…Boolean models of gene regulatory networks-Boolean networks [25] are a frequent alternative to using reactions and species to describe GRNs. In the Boolean framework, each gene can have two states: 'on' or 'off'.…”

Section: Modeling Gene Regulatory Networkmentioning

confidence: 99%

Mathematical modeling and synthetic biology

Chandran

Copeland

Sleight

et al. 2008

Drug Discovery Today: Disease Models

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Synthetic biology is an engineering discipline that builds on our mechanistic understanding of molecular biology to program microbes to carry out new functions. Such predictable manipulation of a cell requires modeling and experimental techniques to work together. The modeling component of synthetic biology allows one to design biological circuits and analyze its expected behavior. The experimental component merges models with real systems by providing quantitative data and sets of available biological 'parts' that can be used to construct circuits. Sufficient progress has been made in the combined use of modeling and experimental methods, which reinforces the idea of being able to use engineered microbes as a technological platform.

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Boolean formalization of genetic control circuits

Cited by 772 publications

References 7 publications

“Immunetworks”, intersecting circuits and dynamics

“Immunetworks”, intersecting circuits and dynamics

A unifying view of 21st century systems biology

Mathematical modeling and synthetic biology

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