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The blastocoel is a fluid-filled cavity characteristic of animal embryos at the blastula stage. Its emergence is commonly described as the result of cleavage patterning, but this historical view conceals a large diversity of mechanisms and…
During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is…
During embryogenesis tissue layers continuously rearrange and fold into specific shapes. Developmental biology identified patterns of gene expression and cytoskeletal regulation underlying local tissue dynamics, but how actions of multiple…
The onset of neural induction in the anterior ectoderm of ascidian embryos is regulated at the extracellular level by FGF signaling molecules, which control the acquisition of neural fate through the activation of the ERK pathway. Among the…
The application of artificial intelligence (AI) in IVF has shown promise in improving consistency and standardization of decisions, but often relies on annotated data and does not make use of the multimodal nature of IVF data. We…
Glioblastoma (GBM) is an aggressive primary brain tumor with a median survival of approximately 15 months. In clinical practice, the Stupp protocol serves as the standard first-line treatment. However, patients exhibit highly heterogeneous…
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,…
Experimental evidence indicates that human brain cancer cells proliferate or migrate, yet do not display both phenotypes at the same time. Here, we present a novel computational model simulating this cellular decision-process leading up to…
This study addresses the issue of leveraging federated learning to improve data privacy and performance in IVF embryo selection. The EM (Expectation-Maximization) algorithm is incorporated into deep learning models to form a federated…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
In a developing embryo, information about the position of cells is encoded in the concentrations of "morphogen" molecules. In the fruit fly, the local concentrations of just a handful of proteins encoded by the gap genes are sufficient to…
Wide-field calcium imaging (WFCI) that records neural calcium dynamics allows for identification of functional brain networks (FBNs) in mice that express genetically encoded calcium indicators. Estimating FBNs from WFCI data is commonly…
The different active roles of neurons and astrocytes during neuronal activation are associated with the metabolic processes necessary to supply the energy needed for their respective tasks at rest and during neuronal activation. Metabolism,…
Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
Many events in the vertebrate immune system are influenced by some element of chance. The objective of the present work is to describe affinity maturation of B lymphocytes (in which random events are perhaps the most characteristic), and to…
Infertility is a major global health issue, and while in-vitro fertilization has improved treatment outcomes, embryo selection remains a critical bottleneck. Time-lapse imaging enables continuous, non-invasive monitoring of embryo…
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…
Cryo-electron microscopy (cryo-EM) is unique among tools in structural biology in its ability to image large, dynamic protein complexes. Key to this ability is image processing algorithms for heterogeneous cryo-EM reconstruction, including…
Embryo selection is one of multiple crucial steps in in-vitro fertilization, commonly based on morphological assessment by clinical embryologists. Although artificial intelligence methods have demonstrated their potential to support embryo…