Related papers: Modeling mammalian gastrulation with embryonic ste…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
We perform a detailed analysis of the migratory motion of human embryonic stem cells in two-dimensions, both when isolated and in close proximity to another cell, recorded with time-lapse microscopic imaging. We show that isolated cells…
The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth,…
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…
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…
We consider cell line classification using multivariate time series data obtained from electric cell-substrate impedance sensing (ECIS) technology. The ECIS device, which monitors the attachment and spreading of mammalian cells in real time…
The minimal requirements for life are autopoiesis and cognition. We propose autopoietic models with cognition and perform three classes of evolutionary simulation. In our models the plasticity of the metabolic cycle and the regulation…
Reliable evaluation of blastocyst quality is critical for the success of in vitro fertilization (IVF) treatments. Current embryo grading practices primarily rely on visual assessment of morphological features, which introduces subjectivity,…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
We describe a generative network model of the architecture of the enteric nervous system (ENS) in the colon employing data from images of human and mouse tissue samples obtained through confocal microscopy. Our models combine spatial point…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
As a first approximation, early embryos may be modeled as foams whose shape depends on the surface tensions of each cell. However it has been remarked that exist line tensions at polarized exterior cellular interfaces (apical). In order to…
We investigate expressiveness, a parameter of one-dimensional cellular automata, in the context of simulated biological systems. The development of elementary cellular automata is interpreted in terms of biological systems, and biologically…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
Living soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set-point. This phenomenon is often referred to as mechanical homeostasis. In contradiction…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…