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Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control).…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Cells may control fluctuations in protein levels by means of negative autoregulation, where transcription factors bind DNA sites to repress their own production. Theoretical studies have assumed a single binding site for the repressor,…
We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…
In this work we propose a model for gene expression based on the theory of random dynamical systems (RDS) and show that it has a "modularity property" in the following sense: given any collection of genes that are linked in a…
Transcription factors (TFs) regulate gene expression through complex and co-operative mechanisms. While many TFs act together, the logic underlying TFs binding and their interactions is not fully understood yet. Most current approaches for…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Expression of the Drosophila segment polarity genes is initiated by a prepattern of pair-rule gene products and maintained by a network of regulatory interactions throughout several stages of embryonic development. Analysis of a model of…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
Based on the phosphorelay kinetics operative within BvgAS two component system we propose a mathematical framework for signal transduction and gene regulation of phenotypic phases in Bordetella pertussis. The proposed model identifies a…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…