Related papers: Epigenetic Tracking: Implementation Details
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
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…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Automatic cell tracking in dense environments is plagued by inaccurate correspondences and misidentification of parent-offspring relationships. In this paper, we introduce a novel cell tracking algorithm named DenseTrack, which integrates…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
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…
Time series classification is an important analytical task across diverse domains. However, its practical application is often hindered by the scarcity of labeled data and the requirement for substantial computational resources. To address…
In this paper we propose an approach for measuring growth of complexity of emerging patterns in complex systems such as cellular automata. We discuss several ways how a metric for measuring the complexity growth can be defined. This…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Design - especially of physical objects - can be understood as creative acts solving practical problems. In this paper we describe a biologically-inspired developmental model as the basis of a generative form-finding system. Using local…
Unlike other tissue types, like epithelial tissue, which consist of cells with a much more homogeneous structure and function, the nervous tissue spans in a complex multilayer environment whose topographical features display a large…
Epigenetics is the study of how people's behavior and environments influence the way their genes are expressed, even though their DNA sequence is itself unchanged. By aggregating age-related epigenetic markers, epigenetic 'clocks' have…
The detection of cell shape changes in 3D time-lapse images of complex tissues is an important task. However, it is a challenging and tedious task to establish a comprehensive dataset to improve the performance of deep learning models. In…
Cellular automata are discrete and computational models thatcan be shown as general models of complexity. They are used in varied applications to derive the generalized behavior of the presented model. In this paper we have took one such…
We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell…
How does growth encode form in developing organisms? Many different spatiotemporal growth profiles may sculpt tissues into the same target 3D shapes, but only specific growth patterns are observed in animal and plant development. In…
A key process in the life of any multicellular organism is its development from a single egg into a full grown adult. The first step in this process often consists of forming a tissue layer out of randomly placed cells on the surface of the…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
Reprogramming is a process of transforming differentiated cells into pluripotent stem cells by inducing specific modifying factors in the cells. Reprogramming is a non-equilibrium process involving a collaboration at levels separated by…