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We consider a cellular monolayer, described using a vertex-based model, for which cells form a spatially disordered array of convex polygons that tile the plane. Equilibrium cell configurations are assumed to minimize a global energy…
A stereotype is an over-generalized belief about a particular group of people, e.g., Asians are good at math or Asians are bad drivers. Such beliefs (biases) are known to hurt target groups. Since pretrained language models are trained on…
Cancer progression and monotonic accumulation models were developed to discover dependencies in the irreversible acquisition of binary traits from cross-sectional data. They have been used in computational oncology and virology but also in…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
Elasticity is a fundamental cellular property that is related to the anatomy, functionality and pathological state of cells and tissues. However, current techniques based on cell deformation, atomic force microscopy or Brillouin scattering…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
The phenomenological model for cell shape deformation and cell migration (Chen et.al. 2018; Vermolen and Gefen 2012) is extended with the incorporation of cell traction forces and the evolution of cell equilibrium shapes as a result of cell…
Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal…
Contact networks are heterogeneous. People with similar characteristics are more likely to interact, a phenomenon called assortative mixing or homophily. While age-assortativity is well-established and social contact matrices for…
Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that…
Human mobility is an important characteristic of human behavior, but since tracking personalized position to high temporal and spatial resolution is difficult, most studies on human mobility patterns rely largely on mathematical models.…
Checklists are simple decision aids that are often used to promote safety and reliability in clinical applications. In this paper, we present a method to learn checklists for clinical decision support. We represent predictive checklists as…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
Cancer is increasingly perceived as a systems-level, network phenomenon. The major trend of malignant transformation can be described as a two-phase process, where an initial increase of network plasticity is followed by a decrease of…
Many cell types display random motility on two-dimensional substrates, but crawl persistently in a single direction when confined in a microchannel or on an adhesive micropattern. Does this imply that the motility mechanism of confined…
In this paper, we consider a series of events observed at spaced time intervals and present a method of representation of the series. To explain an idea, by dealing with a set of gene expression data, which could be obtained from…
Automated cellular instance segmentation is a process utilized for accelerating biological research for the past two decades, and recent advancements have produced higher quality results with less effort from the biologist. Most current…
Cell biologists study in parallel the morphology of cells with the regulation mechanisms that modify this morphology. Such studies are complicated by the inherent heterogeneity present in the cell population. It remains difficult to define…
Automatic detection and segmentation of cells and nuclei in microscopy images is important for many biological applications. Recent successful learning-based approaches include per-pixel cell segmentation with subsequent pixel grouping, or…