Related papers: Epigenetic Tracking, a Method to Generate Arbitrar…
Understanding cell fate patterning and morphogenesis in the mammalian embryo remains a formidable challenge. Recently, in vivo models based on embryonic stem cells (ESCs) have emerged as complementary methods to quantitatively dissect the…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
A common developmental process, called branching morphogenesis, generates the epithelial trees in a variety of organs, including the lungs, kidneys, and glands. How branching morphogenesis can create epithelial architectures of very…
Myocardial motion and deformation are rich descriptors that characterize cardiac function. Image registration, as the most commonly used technique for myocardial motion tracking, is an ill-posed inverse problem which often requires prior…
Stem cell regeneration is a crucial biological process for most self-renewing tissues during the development and maintenance of tissue homeostasis. In developing the mathematical models of stem cell regeneration and tissue development, cell…
This paper presents a method for time-lapse 3D cell analysis. Specifically, we consider the problem of accurately localizing and quantitatively analyzing sub-cellular features, and for tracking individual cells from time-lapse 3D confocal…
Methods allowing the synthesis of realistic cell shapes could help generate training data sets to improve cell tracking and segmentation in biomedical images. Deep generative models for cell shape synthesis require a light-weight and…
Data-driven approaches have become a dominant paradigm for robotic grasp planning. However, the performance of these approaches is enormously influenced by the quality of the available training data. In this paper, we propose a framework to…
We present Bionic Tracking, a novel method for solving biological cell tracking problems with eye tracking in virtual reality using commodity hardware. Using gaze data, and especially smooth pursuit eye movements, we are able to track cells…
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…
Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental…
Epigenetics is most often reduced to chromatin marking in the current literature, whereas this notion was initially defined in a more general context. This restricted view ignores that epigenetic memories are in fact more robustly ensured…
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.…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
Tip-driven growth processes underlie the development of many plants. To date, tip-driven growth processes have been modelled as an elongating path or series of segments without taking into account lateral expansion during elongation.…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
Microelectronic morphogenesis is the creation and maintenance of complex functional structures by microelectronic information within shape-changing materials. Only recently has in-built information technology begun to be used to reshape…
The emergence of complex behaviors in cellular automata is an area that has been widely developed in recent years with the intention to generate and analyze automata that produce space-moving patterns or gliders that interact in a periodic…