Modeling and Simulation of Genetic Regulatory Systems: A Literature Review

By Hidde de Jong. J. Comput. Biol., 2002

2,826 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/aee9709704f84defcf97d622b490eb662593d026

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Citations in the corpus

A class of piecewise linear differential equations arising in biological models (2002, methodology): “It was often used to define continuous homologues of the PL system (Glass and Pasternack 1978a, b, de Jong 2002).”
Feedback Systems: An Introduction for Scientists and Engineers (2008, positive): “A simple model of the transcriptional regulation process is through the use of a Hill function [54, 147].”
A tutorial on the positive realization problem (2004, background): “A huge number of evidences are just before our eyes: Any variable representing any possible type of resource measured by a quantity such as time [14], [35], money and goods [20], [21], buffer size and queues [31], data packets flowing in a network [24], human, animal and plant populations [22], [25]”
Dynamic modeling of genetic networks using genetic algorithm and S-system (2003, methodology): “Many gene regulation models have been proposed; they are listed in the recent reviews (D'haeseleer et al., 2000; Jong, 2002).”
Aqueous Humor Dynamics: A Review (2010, background): “Current pharmacological therapies for lowering the intraocular pressure in glaucoma include increasing aqueous humor outflow and suppression of aqueous humor production.”
Logic-Based Models for the Analysis of Cell Signaling Networks (2010, background): “We focus on logic-basedmodels of biochemical signaling networks and refer the reader to the literature for amore in-depth explanation of theoretical considerations (34), applications of logic-based models to gene regulatory networks (11), andmodels of intercellular communication (35, 36).”
Stability of Genetic Networks With SUM Regulatory Logic: Lur'e System and LMI Approach (2006, background): “Basically, there are two types of genetic network models, i.e., the Boolean model (or discrete model) and the differential equation model (or continuous model) [1], [2], [4], [ 22 ]–[24].”
Mathematical Analysis of Chemical Reaction Systems (2018, background): “Mathematical models that use mass-action kinetics (or kinetics derived from the law of mass-action, such as Michaelis-Menten kinetics or Hill kinetics) are ubiquitous in chemistry and biology [1, 16, 28, 30, 36, 40, 45, 47, 67, 69].”
Inferring cellular networks – a review (2007, methodology): “Further reading There are a number of other reviews and method comparisons available: some focus on applications and biological interpretations [126-128], and some concentrate on methodology [129-137].”
Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. (2004, background): “One can refer to de Jong (2002) to have an overview of different approaches for genetic networks (notice that the following additional references of Demongeot et al. (1995, 2000, 2003) are relevant too).”
An Introduction for Scientists and Engineers SECOND EDITION (2021, neutral): “[dJ02] H.”
Colloquium: Criticality and dynamical scaling in living systems (2017, background): “See De Jong (2002) for a review.”
Qualitative simulation of genetic regulatory networks using piecewise-linear models (2004, background): “The use of formal methods to study regulatory networks is currently subject to two major constraints (de Jong, 2002).”
Petri net modelling of biological networks (2007, background): “While the study of the sole topology of the network provides some knowledge on the involved biological components, the dynamical modelling aims at understanding the dynamical properties of the system (see [1] for a review on the modelling of regulatory networks and [2] for a recent survey of computa”