相关论文: Information transmission in a two-step cascade: In…
We present a stochastic framework to study signal transmission in a generic two-step cascade $\text{S} \rightarrow \text{X} \rightarrow \text{Y}$. Starting from a set of Langevin equations obeying Gaussian noise processes we calculate the…
Signal propagation in biochemical networks is characterized by the inherent randomness in gene expression and fluctuations of the environmental components, commonly known as intrinsic and extrinsic noise, respectively. We present a…
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…
Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…
In this paper, we relate the philosophical literature on pessimism traps to information cascades, a formal model derived from the economics and mathematics literature. A pessimism trap is a social pattern in which individuals in a…
Biochemical signal transduction, a form of molecular communication, can be modeled using graphical Markov channels with input-modulated transition rates. Such channel models are strongly non-Gaussian. In this paper we use a linear noise…
Research on information diffusion generally assumes complete knowledge of the underlying network. However, in the presence of factors such as increasing privacy awareness, restrictions on application programming interfaces (APIs) and…
We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between…
A cell has the ability to convert an environmental change into the expression of genetic information through a chain of intracellular signal transduction reactions. Here, we aimed to develop a method for quantifying this signal…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
Based on the measurements of noise in gene expression performed during the last decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON…
We evaluate the mutual information between the input and the output of a two layer network in the case of a noisy and non-linear analogue channel. In the case where the non-linearity is small with respect to the variability in the noise, we…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Traditional works on community detection from observations of information cascade assume that a single adjacency matrix parametrizes all the observed cascades. However, in reality the connection structure usually does not stay the same…
Studies on the role of fluctuations in signal propagation and on gene regulation in monoclonal bacterial population have been extensively pursued based on the machinery of two-component system. The bacterial two-component system shows noise…
Information cascades are ubiquitous in both physical society and online social media, taking on large variations in structures, dynamics and semantics. Although the dynamics and semantics of information cascades have been studied, the…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
We employ a unified framework for computing the information capacity of biological signaling systems using Fisher Information. By deriving closed-form or easily computable information capacity formulas, we quantify how well different…
In a previous report we have evaluated analytically the mutual information between the firing rates of N independent units and a set of multi-dimensional continuous+discrete stimuli, for a finite population size and in the limit of large…