Related papers: Gene activity fully predicts transcriptional burst…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Gene transcription is a stochastic process that involves thousands of reactions. The first set of these reactions, which happen near a gene promoter, are considered to be the most important in the context of stochastic noise. The most…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare…
Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be…
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i)…
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…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
The rate of mRNA translation depends on the initiation, elongation, and termination rates of ribosomes along the mRNA. These rates depend on many "local" factors like the abundance of free ribosomes and tRNA molecules in the vicinity of the…
We study a stochastic model of biosynthesis of proteins in generic bacterial operons. The stochasticity arises from two different processes, namely from `bursting' production of either mRNA and/or protein (in the transcription/translation…
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…
Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding…