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Modeling and simulation of genetic regulatory systems: A literature review (2002)

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by Hidde De Jong
Venue:JOURNAL OF COMPUTATIONAL BIOLOGY
Citations:737 - 15 self
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BibTeX

@ARTICLE{Jong02modelingand,
    author = {Hidde De Jong},
    title = {Modeling and simulation of genetic regulatory systems: A literature review},
    journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
    year = {2002},
    volume = {9},
    pages = {67--103}
}

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Abstract

In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rule-based formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.

Keyphrases

genetic regulatory system    genetic regulatory network    literature review    computer tool    actual regulatory system    small molecule    formal method    intuitive understanding    mathematical modeling    rule-based formalism    negative feedback loop    qualitative differential equation    partial differential equation    gene expression    molecular level    computational biology    many component    stochastic equation    boolean network    bayesian network    mathematical biology    key word   

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