Related papers: Epigenetic Tracking: Implementation Details
In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…
Creating the best possible conditions is essential for proper cell growth. Incubators, a type of biotechnological instrument, are used to simulate this condition and maintain the cells within them. The processes involved in creating a…
We introduce a comprehensive data-driven framework aimed at enhancing the modeling of physical systems, employing inference techniques and machine learning enhancements. As a demonstrative application, we pursue the modeling of cathodic…
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…
Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…
Evolvability refers to the ability of an individual genotype (solution) to produce offspring with mutually diverse phenotypes. Recent research has demonstrated that divergent search methods, particularly novelty search, promote evolvability…
One of the major goals of nanobionics and bottom-up synthetic biology is the development of artificial cell organelles for the creation of cell-like structures operating similar to biological systems with a minimalistic set of building…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
The timing of cell divisions in early embryos during the In-Vitro Fertilization (IVF) process is a key predictor of embryo viability. However, observing cell divisions in Time-Lapse Monitoring (TLM) is a time-consuming process and highly…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…
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…
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…
Establishing the emergence of evolutionary behavior as a defining characteristic of 'life' is a major step in the Artificial life (ALife) studies. We present here an abstract formal framework for this aim based upon the notion of high-level…
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for…
Biomaterial systems have allowed for the in vitro production of complex, emergent tissue behaviors that were not possible with conventional 2D culture systems allowing for analysis of the normal development as well as disease processes. We…
Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…
Arabidopsis is a widely used model plant to gain basic knowledge on plant physiology and development. Live imaging is an important technique to visualize and quantify elemental processes in plant development. To uncover novel theories…
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…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…