Related papers: Positional information, in bits
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 fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
There is little doubt in scientific circles that--counting from the origin of life towards today--evolution has led to an increase in the amount of information stored within the genomes of the biosphere. This trend of increasing information…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
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…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Cellular phones are now offering an ubiquitous means for scientists to observe life: how people act, move and respond to external influences. They can be utilized as measurement devices of individual persons and for groups of people of the…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Gene expression is a stochastic process in which cells produce biomolecules essential to the function of life. Modern experimental methods allow for the measurement of biomolecules at single-cell and single-molecule resolution over time.…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
Gradient sensing requires at least two measurements at different points in space. These measurements must then be communicated to a common location to be compared, which is unavoidably noisy. While much is known about the limits of…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external…
A novel definition of the stimulus-specific information is presented, which is particularly useful when the stimuli constitute a continuous and metric set, as for example, position in space. The approach allows one to build the spatial…
To study how a zygote develops into an embryo with different tissues, large-scale 4D confocal movies of C. elegans embryos have been produced recently by experimental biologists. However, the lack of principled statistical methods for the…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…