ArticleBiophysical journal2004
A nonlinear discrete dynamical model for transcriptional regulation: construction and properties.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 52 citations in OpenAlex.
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data.BMC systems biology · 2014Article
- Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster.PLoS computational biology · 2013Article
- Thermodynamic state ensemble models of cis-regulation.PLoS computational biology · 2012Article
- Information theory and the ethylene genetic network.Plant signaling & behavior · 2011Review
- miRNA regulatory circuits in ES cells differentiation: a chemical kinetics modeling approach.PloS one · 2011Article
- A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Optimal in silico target gene deletion through nonlinear programming for genetic engineering.PloS one · 2010Article
- Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53.BMC bioinformatics · 2010Article
- Uracil DNA Glycosylase 2 negatively regulates HIV-1 LTR transcription.Nucleic acids research · 2009Article
- A publish-subscribe model of genetic networks.PloS one · 2008Article
- Comparison of gene regulatory networks via steady-state trajectories.EURASIP journal on bioinformatics & systems biology · 2007Article
- A robust structural PGN model for control of cell-cycle progression stabilized by negative feedbacks.EURASIP journal on bioinformatics & systems biology · 2007Article
- Topology-based cancer classification and related pathway mining using microarray data.Nucleic acids research · 2006Article
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Authors and funding
2 authors at 2 institutions in 1 country.
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Abstract
Transcriptional regulation is a fundamental mechanism of living cells, which allows them to determine their actions and properties, by selectively choosing which proteins to express and by dynamically controlling the amounts of those proteins. In this article, we revisit the problem of mathematically modeling transcriptional regulation. First, we adopt a biologically motivated continuous model for gene transcription and mRNA translation, based on first-order rate equations, coupled with a set of nonlinear equations that model cis-regulation. Then, we view the processes of transcription and translation as being discrete, which, together with the need to use computational techniques for large-scale analysis and simulation, motivates us to model transcriptional regulation by means of a nonlinear discrete dynamical system. Classical arguments from chemical kinetics allow us to specify the nonlinearities underlying cis-regulation and to include both activators and repressors as well as the notion of regulatory modules in our formulation. We show that the steady-state behavior of the proposed discrete dynamical system is identical to that of the continuous model. We discuss several aspects of our model, related to homeostatic and epigenetic regulation as well as to Boolean networks, and elaborate on their significance. Simulations of transcriptional regulation of a hypothetical metabolic pathway illustrate several properties of our model, and demonstrate that a nonlinear discrete dynamical system may be effectively used to model transcriptional regulation in a biologically relevant way.
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