相关论文: Using Fano factors to determine certain types of g…

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…

Expression of cellular genes is regulated by binding of transcription factors to their promoter, either activating or inhibiting transcription of a gene. Particularly interesting is the case when the expressed protein regulates its own…

This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of…

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…

Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…

A detailed stochastic model of single-gene auto-regulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness…

Gene expression is a random or noisy process. The process consists of several random events among which the reinitiation of transcription by RNAP is an important one. The RNAP molecules can bind the gene only after the promoter gets…

Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…

From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…

We investigate a conjecture used in recent experiments to reconstruct the complete dynamics of Fano autoionisation processes out of measured spectral amplitudes [Gruson et al, Science 354 734 (2016); Beaulieu el al, Science 358 1288 (2017);…

We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…

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…

Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human…

Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…

In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as…

MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to…

Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…

Gene expression in response to stimuli is regulated by transcription factors (TFs) through feedback loop motifs, aimed at maintaining the desired TF concentration despite uncertainties and perturbations. In this work, we consider a…

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…