Related papers: Information capacity of genetic regulatory element…
Neurons and networks in the cerebral cortex must operate reliably despite multiple sources of noise. To evaluate the impact of both input and output noise, we determine the robustness of single-neuron stimulus selective responses, as well…
Information of relevance to the organism often is represented by the concentrations of particular molecules inside a cell. As outside observers we can now measure these concentrations precisely, but the cell's own mechanisms must be…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
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…
Estimating the information transmission capability of a quantum channel remains one of the fundamental problems in quantum information processing. In contrast to classical channels, the information-carrying capability of quantum channels is…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling.…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
The exponential growth in the rate at which information can be communicated through an optical fiber is a key element in the so called information revolution. However, like all exponential growth laws, there are physical limits to be…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
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…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
A Network Control System (NCS) consists of control components that interact with the plant over a shared network. The system dynamics of a NCS could be subject to noise arising from randomness in the times at which the data is transmitted…
In both natural and engineered systems, communication often occurs dynamically over networks ranging from highly structured grids to largely disordered graphs. To use, or comprehend the use of, networks as efficient communication media…
Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the…
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits: sets…
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…
We investigate the capacity of noisy frequency-based channels, motivated by DNA data storage in the short-molecule regime, where information is encoded in the frequency of items types rather than their order. The channel output is a…