Related papers: Single cells can resolve graded stimuli
Many plants, such as Mimosa pudica (the sensitive plant), employ electrochemical signals known as action potentials (APs) for rapid intercellular communication. In this paper, we consider a reaction diffusion model of individual AP signals…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Various molecules exclusively accumulate at the front or back of migrating eukaryotic cells in response to a shallow gradient of extracellular signals. Directional sensing and signal amplification highlight the essential properties in the…
In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators…
Understanding a neural code requires knowledge both of the elementary symbols that transmit information and of the algorithm for translating these symbols into sensory signals or motor actions. We show that these questions can be separated:…
The spread of a particular trait in a cell population often is modelled by an appropriate system of ordinary differential equations describing how the sizes of subpopulations of the cells with the same genome change in time. On the other…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
Many cells use calcium signalling to carry information from the extracellular side of the plasma membrane to targets in their interior. Since virtually all cells employ a network of biochemical reactions for Ca2+ signalling, much effort has…
Collective sensing by interacting cells is observed in a variety of biological systems, and yet a quantitative understanding of how sensory information is collectively encoded is lacking. Here we investigate the ATP-induced calcium dynamics…
Spike patterns have been reported to encode sensory information in several brain areas. Here we assess the role of specific patterns in the neural code, by comparing the amount of information transmitted with different choices of the…
The brain's diversity of neurons enables a rich behavioral repertoire and flexible adaptation to new situations. Assuming that the ecological pressure has optimized this neuronal variety, we propose exploiting na\"ive behavior to map the…
Understanding computational capabilities of simple biological circuits, such as the regulatory circuits of single-cell organisms, remains an active area of research. Recent theoretical work has shown that a simple regulatory architecture…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
We present a systematic evaluation framework - thirty-seven analyses, 153 statistical tests, four cell types, two perturbation modalities - for assessing mechanistic interpretability in single-cell foundation models. Applying this framework…
Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex…
Populations of mammalian stem cells commonly exhibit considerable cell-cell variability. However, the functional role of this diversity is unclear. Here, we analyze expression fluctuations of the stem cell surface marker Sca1 in mouse…
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…
Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically…
Various biological cells secrete diffusing chemical compounds into their environment for communication purposes. Secretion usually takes place over the cell membrane in a spatially heterogeneous manner. Mathematical models of these…