Related papers: Noise Filtering and Prediction in Biological Signa…
Cellular signaling involves the transmission of environmental information through cascades of stochastic biochemical reactions, inevitably introducing noise that compromises signal fidelity. Each stage of the cascade often takes the form of…
One major challenge for living cells is the measurement and prediction of signals corrupted by noise. In general, cells need to make decisions based on their compressed representation of noisy, time-varying signals. Strategies for signal…
Cells are constantly exposed to fluctuating environmental conditions. External signals are sensed, processed and integrated by cellular signal transduction networks, which translate input signals into specific cellular responses by means of…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
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…
Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising…
Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…
A modelling framework, based on the theory of signal processing, for characterising the dynamics of systems driven by the unravelling of information is outlined, and is applied to describe the process of decision making. The model input of…
Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of…
Stochastic resonance is a phenomenon in which noise enhances the response of a system to an input signal. The brain is an example of a system that has to detect and transmit signals in a noisy environment, suggesting that it is a good…
Understanding cell function requires an accurate description of how noise is transmitted through biochemical networks. We present an analytical result for the power spectrum of the output signal of a biochemical network that takes into…
When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in a environment that changes over time, past measurements may…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
It has been generally recognized that stochasticity can play an important role in the information processing accomplished by reaction networks in biological cells. Most treatments of that stochasticity employ Gaussian noise even though it…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
Living cells can leverage correlations in environmental fluctuations to predict the future environment and mount a response ahead of time. To this end, cells need to encode the past signal into the output of the intracellular network from…
We describe how noise propagates through a network by calculating the variance of the outputs. Using stochastic calculus and dynamical systems theory, we study the network topologies that accentuate or alleviate the effect of random…