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A fundamental question in biology is to understand how patterns and shapes emerge from the collective interplay of large numbers of cells. Cells forming two-dimensional epithelial tissues behave as active materials that undergo remodeling…
Morphogenesis is the biological process that causes the emergence and changes of patterns (tissues and organs) in living organisms. It is a robust, self-organising mechanism, governed by Genetic Regulatory Networks (GRN), that hasn't been…
Early detection of developmental disorders can be aided by analyzing infant craniofacial morphology, but modeling infant faces is challenging due to limited data and frequent spontaneous expressions. We introduce BabyFlow, a generative AI…
Gene regulatory network inference uses genome-wide transcriptome measurements in response to genetic, environmental or dynamic perturbations to predict causal regulatory influences between genes. We hypothesized that evolution also acts as…
The growth rate of material interfaces is an important proxy for mixing and reaction rates in fluid dynamics, and can also be used to identify regions of coherence. Estimating such growth rates can be difficult, since they depend on…
We develop a data-driven characterization of the pilot-wave hydrodynamic system in which a bouncing droplet self-propels along the surface of a vibrating bath. We consider drop motion in a confined one-dimensional geometry, and apply the…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation models is identifying the recipes for scaling the model. In this…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
We present a vector field method for obtaining the spatial organization of 3D patterns of gene expression based on gradients and lines of force obtained by numerical integration. The convergence of these lines of force in local maxima are…
Accurate fetal brain segmentation is crucial for extracting biomarkers and assessing neurodevelopment, especially in conditions such as corpus callosum dysgenesis (CCD), which can induce drastic anatomical changes. However, the rarity of…
Concentration gradients play a critical role in embryogenesis, bacterial locomotion, as well as the motility of active particles. Particles develop concentration profiles around them by dissolution, adsorption, or the reactivity of surface…
The "developmental hourglass" describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the "phylotypic stage").…
Agglomeration is an industrially relevant process for the production of bulk materials in which the product properties depend on the morphology of the agglomerates, e.g., on the distribution of size and shape descriptors. Thus, accurate…
How can diffusion models process 3D geometries in a coarse-to-fine manner, akin to our multiscale view of the world? In this paper, we address the question by focusing on a fundamental biochemical problem of generating 3D molecular…
The BCF theory of crystal growth has been successful in describing a wide range of phenomena in surface physics. Typical crystal surfaces are slightly misoriented with respect to a facet plane; thus, the BCF theory views such systems as…
Tissue deformations during morphogenesis can be active, driven by internal processes, or passive, resulting from stresses applied at their boundaries. Here, we introduce the Drosophila hindgut primordium as a model for studying…
Bacterial biofilms play a significant role in various fields that impact our daily lives, from detrimental public health hazards to beneficial applications in bioremediation, biodegradation, and wastewater treatment. However,…
In non-viral gene delivery, the variance of transgenic expression stems from the low number of plasmids successfully transferred. Here, we experimentally determine Lipofectamine- and PEI-mediated exogenous gene expression distributions from…