Related papers: Optimal temporal patterns for dynamical cellular s…
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…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
For biological experiments aiming at calibrating models with unknown parameters, a good experimental design is crucial, especially for those subject to various constraints, such as financial limitations, time consumption and physical…
Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…
A recurrent idea in the study of complex systems is that optimal information processing is to be found near bifurcation points or phase transitions. However, this heuristic hypothesis has few (if any) concrete realizations where a standard…
Biological systems display impressive capabilities in effectively responding to environmental signals in real time. There is increasing evidence that organisms may indeed be employing near optimal Bayesian calculations in their…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…
Causal ordering of key events in the cell cycle is essential for proper functioning of an organism. Yet, it remains a mystery how a specific temporal program of events is maintained despite ineluctable stochasticity in the biochemical…
Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here we review some of this recent evidence, focusing on both the molecular mechanisms that potentially underlie such dynamical behavior, and the potential…
This work clarifies the relation between network circuit (topology) and behavior (information transmission and synchronization) in active networks, e.g. neural networks. As an application, we show how to determine a network topology that is…
We show that when cells communicate by contact-mediated interactions, heterogeneity in cell shapes and sizes leads to qualitatively distinct collective behavior in the tissue. For inter-cellular coupling that implements lateral inhibition,…
Biological systems represent time from microseconds to years. An important gap in our knowledge concerns the mechanisms for encoding time intervals of hundreds of milliseconds to minutes that matter for tasks like navigation, communication,…
Populations of cells regulate gene expression in response to external signals, but their ability to make reliable collective decisions is limited by both intrinsic noise in molecular signaling and variability between individual cells. In…
Time plays an essential role in the diffusion of information, influence and disease over networks. In many cases we only observe when a node copies information, makes a decision or becomes infected -- but the connectivity, transmission…
This paper considers the optimum single cell power-control maximizing the aggregate (uplink) communication rate of the cell when there are peak power constraints at mobile users, and a low-complexity data decoder (without successive…
Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the…
Deep learning is the backbone of artificial intelligence technologies, and it can be regarded as a kind of multilayer feedforward neural network. An essence of deep learning is information propagation through layers. This suggests that…
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…