Related papers: On three genetic repressilator topologies
In 2000, Elowitz and Leibler introduced the repressilator--a synthetic gene circuit with three genes that cyclically repress transcription of the next gene--as well as a corresponding mathematical model. Experimental data and model…
A repressilator consists of a loop made up of three repressively interacting genes. We construct a hexagonal lattice with repressilators on each triangle, and use this as a model system for multiple interacting feedback loops. Using…
The genetic repressilator circuit consists of three transcription factors, or repressors, which negatively regulate each other in a cyclic manner. This circuit was synthetically constructed on plasmids in {\it Escherichia coli} and was…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
We present a simple low-cost electronic circuit that is able to show two different dynamical regimens with oscillations of voltages and with constant values of them. This device is designed as a negative feedback three-node network inspired…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
A family of repressor networks is proposed as a simple model of gene regulatory networks. We analytically show three topological classes of the repressor networks, each of which exhibits distinctly growing complexity of spatiotemporal…
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…
The transcription factors, such as activators and repressors, can interact with the promoter of gene either in a competitive or non-competitive way. In this paper, we construct a stochastic model with non-competitive transcriptional…
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological…
We describe an approach to model genetic regulatory networks at the level of promotion-inhibition circuitry through a class of stochastic spin models that includes spatial and temporal density fluctuations in a natural way. The formalism…
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…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…