Related papers: Finding the last bits of positional information
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of…
Analyses of transformer-based models have shown that they encode a variety of linguistic information from their textual input. While these analyses have shed a light on the relation between linguistic information on one side, and internal…
Recent methods have been developed to map single-cell lineage statistics to population growth. Because population growth selects for exponentially rare phenotypes, these methods inherently depend on sampling large deviations from finite…
Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell…
In a recent article [Vetter and Iber, Nat. Commun. 13, 1145 (2022)], we demonstrated that single morphogen gradients in the developing mouse neural tube can carry sufficient positional accuracy to explain the patterning precision of…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
A qualitative model is presented, suggesting gravitational information is transduced into biological systems primarily by its effect on spatially organised membrane and cytoplasmic flows. Continuous low affinity interactions between…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
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…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
In metazoans, cells collectively polarize and align along the tissue plane. This phenomenon is called Planar cell polarity (PCP). Polarization means asymmetric segregation of molecules and sub-cellular structures within a cell. In PCP,…
Cell shape has long been used to discern cell phenotypes and states, but the underlying premise has not been quantitatively tested. Here, we show that a single cell image can be used to discriminate its migration behavior by analyzing a…
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…
Single-cell gene expression data are often characterized by large matrices, where the number of cells may be lower than the number of genes of interest. Factorization models have emerged as powerful tools to condense the available…
The brain anticipates future events using internal models that specify not only what will occur, but also when it will occur and with what probability. We refer to this joint specification of identity, timing, and likelihood as a complete…
Accurate sensing of chemical concentrations is essential for numerous biological processes. The accuracy of this sensing, for small numbers of molecules, is limited by shot noise. Corresponding theoretical limits on sensing precision, as a…
Most decisions require information gathering from a stimulus presented with different gaps. Indeed, the brain process of this integration is rarely ambiguous. Recently, it has been claimed that humans can optimally integrate the information…
Eukaryotic cell development has been optimized by natural selection to obey maximal intracellular flux of messenger proteins. This, in turn, implies maximum Fisher information on angular position about a target nuclear pore complex (NPR).…