Related papers: Finding the last bits of positional information
We explain the principles of gene expression pattern stabilization in systems of interacting, diffusible morphogens, with dynamically established source regions. Using a reaction-diffusion model with step-function production term, we…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
Epiboly, during which a tissue closes around the surface of the egg, pervades animal development. This epithelial gap closure involves cell intercalations at the edge of the gap. Here, inspired by serosa closure in the beetle Tribolium, we…
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…
This work aims at providing a mathematical and numerical framework for the analysis on the effects of pulsed electric fields on biological media. Biological tissues and cell suspensions are described as having a heteregeneous permittivity…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…
Mammalian spatial navigation relies on specialized neurons, such as place and grid cells, which encode position based on self-motion and environmental cues. While extensive research has explored the computational role of grid cells, the…
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for…
In processes such as embryo shaping, wound healing, and malignant cell invasion, epithelial cells transition between dispersed phases, where the cells move independently, and condensed phases, where they aggregate and deform to close gaps,…
Transcription factor concentrations provide signals to cells that allow them to regulate gene expression to make correct cell fate decisions. Calculations for noise bounds in gene regulation suggest that clustering or cooperative binding of…
Individual components such as cells, particles, or agents within a larger system often require detailed understanding of their relative position to act accordingly, enabling the system as a whole to function in an organised and efficient…
We study fixed points of cellular automata with $N$ sites on random sparse graphs. In the large $N$ limit such models are known to exhibit phase transitions, from a ``frozen'' phase, where at most a finite number of sites fluctuate at long…
In addition to their self-renewal capabilities, hematopoietic stem cells guarantee the continuous supply of fully differentiated, functional cells of various types in the peripheral blood. The process which controls differentiation into the…
Establishing sharp and correctly positioned boundaries in spatial gene expression patterns is a central task, both in developmental and synthetic biology. We consider situations where a global morphogen gradient provides positional…
The metaphor of a potential epigenetic differentiation landscape broadly suggests that during differentiation a stem cell follows the steepest descending gradient toward a stable equilibrium state which represents the final cell type. It…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
Recent evidence suggests that neural information is encoded in packets and may be flexibly routed from region to region. We have hypothesized that neural circuits are split into sub-circuits where one sub-circuit controls information…
Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict…