Related papers: Optimizing information flow in small genetic netwo…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
Even under constant external conditions, the expression levels of genes fluctuate. Much emphasis has been placed on the components of this noise that are due to randomness in transcription and translation; here we analyze the role of noise…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Genetic regulatory circuits universally cope with different sources of noise that limit their ability to coordinate input and output signals. In many cases, optimal regulatory performance can be thought to correspond to configurations of…
With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…
Cell type-specific gene expression patterns are represented as memory states of a Hopfield neural network model. It is shown that order parameters of this model can be interpreted as concentrations of master transcription regulators that…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
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…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Using the formalism of information theory, we analyze the mechanism of information transduction in a simple one-step signaling cascade S$\rightarrow$X representing the gene regulatory network. Approximating the signaling channel to be…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
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…