相关论文: How to Color a French Flag--Biologically Inspired …
During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process…
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…
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…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries,…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Graph coloring, also known as vertex coloring, considers the problem of assigning colors to the nodes of a graph such that adjacent nodes do not share the same color. The optimization version of the problem concerns the minimization of the…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Networks are abundant in biological systems. Small sized over-represented network motifs have been discovered, and it has been suggested that these constitute functional building blocks. We ask whether larger dynamical network motifs exist…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Motivated by a new way of visualizing hypergraphs, we study the following problem. Consider a rectangular grid and a set of colors $\chi$. Each cell $s$ in the grid is assigned a subset of colors $\chi_s \subseteq \chi$ and should be…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
Despite fluorescent cell-labelling being widely employed in biomedical studies, some of its drawbacks are inevitable, with unsuitable fluorescent probes or probes inducing a functional change being the main limitations. Consequently, the…
The degree splitting problem requires coloring the edges of a graph red or blue such that each node has almost the same number of edges in each color, up to a small additive discrepancy. The directed variant of the problem requires…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such…
All cognitive agents are composite beings. Specifically, complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behavior science, evolutionary developmental biology,…
Biological systems can form complex three-dimensional structures through the collective behavior of agents that share a common update rule and operate without central control. How such distributed control gives rise to precise global…
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…
Understanding how cells respond to external stimuli is a central challenge in biomedical research and drug development. Current computational frameworks for modelling cellular responses remain restricted to two-dimensional representations,…