Related papers: Finding the last bits of positional information
A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to…
During development, cell fates are determined through a combination of intracellular transcriptional regulations and extracellular signaling. As a result, spatial patterns of different cell types arise. We investigate the decision between…
Self-organization is a fundamental process of complex biological systems, particularly during the early stages of development. In the mammalian embryo, blastocyst formation exemplifies a self-organized system, involving the correct…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand…
Multicellular organisms exhibit a high degree of structural organization with specific cell types always occurring in characteristic locations. The conventional framework for describing the emergence of such consistent spatial patterns is…
Morphogens are secreted signaling molecules that mediate tissue patterning and growth of embryonic tissues. They are secreted in a localized region and spread through the tissue to form a graded concentration profile. We present a…
Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
Living cells respond to spatial signals. Signal transmission to the cell interior often involves the release of second messengers like $Ca^{2+}$ . They will eventually trigger a physiological response by activating kinases that in turn…
Chemical gradients can be used by a particle to determine its position. This \textit{positional information} is of crucial importance, for example in developmental biology in the formation of patterns in an embryo. The central goal of this…
Assessing where and how information is stored in biological networks (such as neuronal and genetic networks) is a central task both in neuroscience and in molecular genetics, but most available tools focus on the network's structure as…
The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for…
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…
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…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
Gene regulatory networks (GRNs) perform a wide range of biological functions. It is, however, often challenging to reveal their functioning mechanism with the conventional approach focusing on the network topological structure from a…
In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…