Related papers: Optimizing information flow in small genetic netwo…
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…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
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…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
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…
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…
Cells in natural environments like tissue or soil sense and respond to extracellular ligands with intricately structured and non-monotonic spatial distributions that are sculpted by processes such as fluid flow and substrate adhesion.…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
During embryonic development, differentiating cells respond via gene expression to positional cues from morphogen gradients. While gene expression is often highly erratic, embryonic development is precise. We show by theory and simulations…
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…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…