Related papers: Finding the last bits of positional information
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to…
We posit that hippocampal place cells encode information about future locations under a transition distribution observed as an agent explores a given (physical or conceptual) space. The encoding of information about the current location,…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
We use laser hole-drilling to assess the mechanics of an embryonic epithelium during development - in vivo and with subcellular resolution. We ablate a subcellular cylindrical hole clean through the epithelium, and track the subsequent…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and…
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…
Information theory is gaining popularity as a tool to characterize performance of biological systems. However, information is commonly quantified without reference to whether or how a system could extract and use it; as a result,…
Positional encodings enable Transformers to incorporate sequential information, yet their theoretical understanding remains limited to two properties: distance attenuation and translation invariance. Because natural language lacks purely…
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…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
Gene expression patterns (GEPs) are established by cross-regulating target genes that interpret morphogen gradients. However, as development progresses, morphogen activity is reduced, leaving the emergent GEP without stabilizing positional…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
Communicating cells can coordinate their gene expressions to form spatial patterns. 'Secrete-and-sense cells' secrete and sense the same molecule to do so and are ubiquitous. Here we address why and how these cells, from disordered…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
The mushroom body of the fruit fly brain is one of the best studied systems in neuroscience. At its core it consists of a population of Kenyon cells, which receive inputs from multiple sensory modalities. These cells are inhibited by the…
The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been…