Related papers: Morphogenesis Software based on Epigenetic Code Co…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
Model-driven engineering is the automatic production of software artefacts from abstract models of structure and functionality. By targeting a specific class of system, it is possible to automate aspects of the development process, using…
During epithelial wound healing, cell morphology near the healed wound and the healing rate vary strongly among different developmental stages even for a single species like \textit{Drosophila}. We develop deformable particle (DP) model…
Deciphering cell type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach estimating cell type abundances from a variety of…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
"Self-organization" has become a watchword in developmental biology, characterizing observations in which embryonic or induced stem cells of animals replicate morphological steps and outcomes seen in intact embryos. While the term was…
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…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
Evolutionary robotics aims to automatically design autonomous adaptive morphological robots that can evolve to accomplish a specific task while adapting to environmental changes. Soft robotics have demonstrated the feasibility of…
In this article, I put forward the idea that the neoplastic process (NP) has deep evolutionary roots and make specific predictions about the connection between cancer and the formation of the first embryo, which allowed for the evolutionary…
Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a central challenge in developmental biology. This is particularly intriguing in early mammalian development, where early cell-lineage differentiation…
During morphogenesis, the shape of a tissue emerges from collective cellular behaviors, which are in part regulated by mechanical and biochemical interactions between cells. Quantification of force and stress is therefore necessary to…
Biological tissues exhibit diverse mechanical and rheological behaviors during morphogenesis. While much is known about tissue phase transitions controlled by structural order and cell mechanics, key questions regarding how tissue-scale…
T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralise infected and cancerous cells. However, there is limited quantitative understanding of the migration process in 3D extracellular matrices (ECMs) and…
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…
Morphogenesis is a developmental process in which cells organize into shapes and patterns. Complex, multi-factorial models are commonly used to study morphogenesis. It is difficult to understand the relation between the uncertainty in the…
Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those…