Related papers: Epigenetic Tracking: a Model for Multicellular Bio…
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated…
This paper presents a comprehensive survey of various established mathematical models pertaining to Somitogenesis, a biological process. The study begins by revisiting and replicating the findings from prominent research papers in this…
The hierarchical organisation of cell identity is a fundamental feature of animal development with rich and well-characterized experimental phenomenology, yet the mechanisms driving its emergence remain unknown. The regulation of cell…
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins and widespread disruptions in brain function. Computational modeling has advanced our understanding of these processes, but efforts have traditionally…
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…
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…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
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…
Neural development represents not only an exciting and complex field of study, with ongoing progress, but it also became the epicentre of neuroscience and developmental biology, as it strives to describe the underlying cellular and…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
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…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
The majority of solid tumours arise in epithelia and therefore much research effort has gone into investigating the growth, renewal and regulation of these tissues. Here we review different mathematical and computational approaches that…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such…
Developing epithelial tissues coordinate cell proliferation and mechanical forces to achieve proper size and shape. As epithelial cells tightly adhere together to form the confluent tissue, the distribution of cell areas significantly…
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…
Development from egg to embryo to adult is a fascinating instance of biological self-organization for which genetics has supplied us with a parts list. It remains to find the principles organizing the assembly of those parts. In the last…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…