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The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
Measurements on embryonic epithelial tissues in a diverse range of organisms have shown that the statistics of cell neighbor numbers are universal in tissues where cell proliferation is the primary cell activity. Highly simplified…
Cells segmentation shows rapid growth in biology. Indeed, using the classical segmentation methods only is not enough to segment this type of images. In this manuscript, we will present a new method of ribosomes segmentation. A…
In general Evolutionary Computation (EC) includes a number of optimization methods inspired by biological mechanisms of evolution. The methods catalogued in this area use the Darwinian principles of life evolution to produce algorithms that…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Spherical embryos of the algal genus $Volvox$ must turn themselves inside out to complete their embryogenesis. This `inversion', which shares important features with morphological events such as gastrulation in animals, is perhaps the…
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…
In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists. Of interest…
In order to describe two-dimensionally packed cells in epithelial tissues both mathematically and physically, there have been developed several sorts of geometrical models, such as the vertex model, the finite element model, the…
Cellular Potts models are broadly applied across developmental biology and cancer research. We overcome limitations of the traditional approach, which reinterprets a modified Metropolis sampling as ad hoc dynamics, by introducing a physical…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Experimental studies are prevalent in Evolutionary Computation (EC), and concerns about the reproducibility and replicability of such studies have increased in recent times, reflecting similar concerns in other scientific fields. In this…
The accurate modeling of biological processes allows to predict the spatio-temporal behavior of living tissues by computer-aided (in-silico) testing, a useful tool for the development of medical strategies, avoiding the expenses and…
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…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells…