Related papers: Modeling stochastic gene expression under repressi…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
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…
After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a genetic network. The influence of intrinsic and extrinsic noises on genetic…
Switching of the direction of flagella rotations is the key control mechanism governing the chemotactic activity of E. coli and many other bacteria. Power-law distributions of switching times are most peculiar because their emergence cannot…
Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…
This article presents tractable and recursively feasible optimization-based controllers for stochastic linear systems with bounded controls. The stochastic noise in the plant is assumed to be additive, zero mean and fourth moment bounded,…
It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNAs or ceRNAs) that could prove to be crucial for…
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…
Neurons in the nervous system are submitted to distinct sources of noise, such as ionic-channel and synaptic noise, which introduces variability in their responses to repeated presentations of identical stimuli. This motivates the use of…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
We develop an approximate theoretical method to study discrete stochastic birth and death models that include a delay time. We analyze the effect of the delay in the fluctuations of the system and obtain that it can qualitatively alter…
RNA molecules follow a succession of enzyme-mediated processing steps from transcription until maturation. The participating enzymes, for example the spliceosome for mRNAs and Drosha and Dicer for microRNAs, are also produced in the cell…
In a previous work, we presented a model that integrates cancer cell differentiation and immunotherapy, analysing a particular therapy against cancer stem cells by cytotoxic cell vaccines. As every biological system is exposed to random…
This paper considers the behavior of discrete and continuous mathematical models for gene expression in the presence of transcriptional/translational bursting. We treat this problem in generality with respect to the distribution of the…
The bulk of stochastic gene expression models in the literature do not have an explicit description of the age of a cell within a generation and hence they cannot capture events such as cell division and DNA replication. Instead, many…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
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…
In this paper, we study the dynamics of a linear control system with given state feedback control law in the presence of fast periodic sampling at temporal frequency $1/\delta$ ($0 < \delta \ll 1$), together with small white noise…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…