Related papers: Epigenetic Tracking: Towards a Project for an Arti…
Substantial efforts have been applied to engineer CA with desired emergent properties, such as supporting gliders. Recent work in continuous CA has generated a wide variety of compelling bioreminiscent patterns, and the expansion of CA…
During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is…
We present feature finding and tracking algorithms in 3D in living cells, and demonstrate their utility to measure metrics important in cell biological processes. We developed a computational imaging hybrid approach that combines automated…
This paper reports on patterns exhibiting self-replication with spontaneous, inheritable mutations and exponential genetic drift in Neural Cellular Automata. Despite the models not being explicitly trained for mutation or inheritability,…
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…
Gene regulatory network (GRN) modeling is a well-established theoretical framework for the study of cell-fate specification during developmental processes. Recently, dynamical models of GRNs have been taken as a basis for formalizing the…
Artificial Intelligence has looked into biological systems as a source of inspiration. Although there are many aspects of the brain yet to be discovered, neuroscience has found evidence that the connections between neurons continuously grow…
The "developmental hourglass" describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the "phylotypic stage").…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification, a gene expression pattern that achieves greater cell…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
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…
Cell detection and tracking are paramount for bio-analysis. Recent approaches rely on the tracking-by-model evolution paradigm, which usually consists of training end-to-end deep learning models to detect and track the cells on the frames…
Natural plants are exemplars of adaptation through self-organisation and collective decision making. As such, they provide a rich source of inspiration for adaptive mechanisms in artificial systems. Plant growth - a structure development…
Although deep learning has made significant progress on fixed large-scale datasets, it typically encounters challenges regarding improperly detecting unknown/unseen classes in the open-world scenario, over-parametrized, and overfitting…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…
Artificial neurons built on synthetic gene networks have potential applications ranging from complex cellular decision-making to bioreactor regulation. Furthermore, due to the high information throughput of natural systems, it provides an…
A one-dimensional cellular automaton with a probabilistic evolution rule can generate stochastic surface growth in $(1 + 1)$ dimensions. Two such discrete models of surface growth are constructed from a probabilistic cellular automaton…
Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing,…