相关论文: Stochastic resonances in a distributed genetic bro…
The structure of a stochastic nonlinear gene regulatory network is uncovered by studying its response to input signal generators. Four applications are studied in detail: a nonlinear connection of two linear systems, the design of a logic…
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…
The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects the phase of biochemical oscillations. We provide a theoretical framework for…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
The NF-kB signalling system is involved in a variety of cellular processes including immune response, inflammation, and apoptosis. Recent experiments have found oscillations in the nuclear-cytoplasmic translocation of the NF-kB…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…
Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
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…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
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…
We propose the concepts of distributed robustness and r-robustness, well adapted to functional genetics. Then we discuss the robustness of the relaxation time using a chemical reaction description of genetic and signalling networks. First,…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many…
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…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…