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Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Mathematical models of gene regulatory networks are widely used to study cell fate changes and transcriptional regulation. When designing such models, it is important to accurately account for sources of stochasticity. However, doing so can…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Stochasticity in gene expression can result in fluctuations in gene product levels. Recent experiments indicated that feedback regulation plays an important role in controlling the noise in gene expression. A quantitative understanding of…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
An important design principle for biological oscillators divides the oscillators into two classes: fixed frequency, variable amplitude and fixed amplitude, variable frequency. Because of the interplay of nonlinearity and feedback, both…
Using an analytically solvable stochastic model, we study the properties of a simple genetic circuit consisting of multiple copies of an self-regulating gene. We analyse how the variation in gene copy number and the mutations changing the…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
A good understanding of how neurons use electrical pulses (i.e, spikes) to encode the signal information remains elusive. Analyzing spike sequences generated by individual neurons and by two coupled neurons (using the stochastic…
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…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Oscillatory systems arise in the different science fields. Complex mathematical formulations with differential equations have been proposed to model the dynamics of these systems. While they have the advantage of having a direct…
This paper is concerned with conditions for the existence of oscillations in gene regulatory networks with negative cyclic feedback, where time delays in transcription, translation and translocation process are explicitly considered. The…
Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the…
Protein mean and variance levels in a simple stochastic gene expression circuit are controlled using proportional integral feedback. It is shown that the protein mean level can be globally and robustly tracked to any desired value using a…