Related papers: Information capacity of genetic regulatory element…
Neurons in the brain represent information in their collective activity. The fidelity of this neural population code depends on whether and how variability in the response of one neuron is shared with other neurons. Two decades of studies…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
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…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in…
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…
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…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Bistable biological regulatory systems need to cope with stochastic noise to fine-tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative…
One of the primary computational requirements of a cellular system is the ability to transfer information between spatially separated components. To accomplish this, biology uses diverse physical channels including production or release of…
Individual neurons often produce highly variable responses over nominally identical trials, reflecting a mixture of intrinsic "noise" and systematic changes in the animal's cognitive and behavioral state. Disentangling these sources of…
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and…
Computation in the brain involves multiple types of neurons, yet the organizing principles for how these neurons work together remain unclear. Information theory has offered explanations for how different types of neurons can optimize the…
We theoretically describe how weak signals may be efficiently transmitted throughout more than one frequency range in noisy excitable media by kind of stochastic multiresonance. This serves us here to reinterpret recent experiments in…
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…
Bounded agents are limited by intrinsic constraints on their ability to process information that is available in their sensors and memory and choose actions and memory updates. In this dissertation, we model these constraints as…
The amount of information transmissible through a communications channel is determined by the noise characteristics of the channel and by the quantities of available transmission resources. In classical information theory, the amount of…
While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that…
It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…
We propose an information-theoretic framework for analyzing control systems based on the close relationship of controllers to communication channels. A communication channel takes an input state and transforms it into an output state. A…