Related papers: Graded and Binary Responses in Stochastic Gene Exp…

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…

Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (i) non-quantitative (or data-based)…

Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task, examples include ecosystems, financial markets, complex diseases, etc. In this paper, we…

Stochastic resonance is a well established phenomenon, which proves relevant for a wide range of applications, of broad trans-disciplinary breath. Consider a one dimensional bistable stochastic system, characterized by a deterministic…

While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…

MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…

Longitudinal studies with binary or ordinal responses are widely encountered in various disciplines, where the primary focus is on the temporal evolution of the probability of each response category. Traditional approaches build from the…

Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…

The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate,…

In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…

Stochastic fluctuations in the copy number of gene products have perceivable effects on the functioning of gene regulatory networks (GRN). The Master equation (ME) provides a theoretical basis for studying such effects. However, solving the…

We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…

Genetic switch systems with mutual repression of two transcription factors are studied using deterministic and stochastic methods. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of…

Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling.…

Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…

Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…

Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…

Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…

We study a reaction model that presents stochastic resonance purely due to internal noise. This means that the only source of fluctuations comes from the discrete character of the reactants, and no more noises enter into the system. Our…

Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…