Related papers: Measuring the Degree of Modularity from Gene Expre…
The correlated variability in the responses of a neural population to the repeated presentation of a sensory stimulus is a universally observed phenomenon. Such correlations have been studied in much detail, both with respect to their…
Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the…
Gene regulatory circuits must contend with intrinsic noise that arises due to finite numbers of proteins. While some circuits act to reduce this noise, others appear to exploit it. A striking example is the competence circuit in Bacillus…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
We study the stochastic resonance phenomenon occurring in electronic Chua circuits operating in the chaotic regime when the forcing signal is modulated at relatively high frequency, of the order of magnitude of the main Chua frequency in…
Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been…
A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other, and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we…
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions all gene circuits draw resources in the form of…
Gene Regulatory Networks(GRNs) with feedback are essential components of many cellular processes and may exhibit oscillatory behavior. Analyzing such systems becomes increasingly complex as the number of components increases. Since gene…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising…
Gene expression and its regulation is a nonequilibrium stochastic process. Different molecules are involved in several biochemical steps in this process with low copies. It is observed that the stochasticity in biochemical processes is…
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We…
Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
Fluctuations and noise may alter the behavior of dynamical systems considerably. For example, oscillations may be sustained by demographic fluctuations in biological systems where a stable fixed point is found in the absence of noise. We…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
We study the oscillatory behaviour of a gene regulatory network with interlinked positive and negative feedback loop. Frequency and amplitude are two important properties of oscillation. Studied network produces two different modes of…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
Gene expression (GE) is an inherently random or stochastic or noisy process. The randomness in different steps of GE, e.g., transcription, translation, degradation, etc., leading to cell-to-cell variations in mRNA and protein levels. This…