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Challenges of assessing complexity and clonality in populations of mixed species arise in diverse areas of modern biology, including estimating diversity and clonality in microbiome populations, measuring patterns of T and B cell clonality,…
Clonal interference, competition between multiple co-occurring beneficial mutations, has a major role in adaptation of asexual populations. We provide a simple individual based stochastic model of clonal interference taking into account a…
Populations of mammalian stem cells commonly exhibit considerable cell-cell variability. However, the functional role of this diversity is unclear. Here, we analyze expression fluctuations of the stem cell surface marker Sca1 in mouse…
Recent theoretical studies have shown that demographic stochasticity can greatly increase the tendency of asexually reproducing phenotypically diverse organisms to spontaneously evolve into localised clusters, suggesting a simple mechanism…
Scalable manufacturing of human induced pluripotent stem cells (iPSCs) is essential for industrial-scale production of cell therapies and regenerative medicines. However, the 3D aggregate cultures used in manufacturing exhibit substantial…
Many imaging techniques for biological systems -- like fixation of cells coupled with fluorescence microscopy -- provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the…
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) derived from somatic cells (SCs) provide promising resources for regenerative medicine and medical research, leading to a daily identification of new cell lines.…
We consider a spatial version of the classical Moran model with seed-banks where the constituent populations have finite sizes. Individuals live in colonies labelled by $\mathbb{Z}^d$, $d\geq 1$, playing the role of a geographic space,…
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…
We review recent progress in the understanding of the role of multiple- and simultaneous multiple merger coalescents as models for the genealogy in idealised and real populations with exceptional reproductive behaviour. In particular, we…
Human bone marrow stromal cells (BMSC) include skeletal stem cells with ground-breaking therapeutic potential. However, BMSC colonies have very heterogeneous in vivo behaviour, due to their different potency; this unpredictability is the…
When confronted with an undesired cell population, such as bacterial infections or tumors, we seek the most effective treatment, designed to eliminate the population as rapidly as possible. A common practice is to monitor the cells…
Two powerful and complementary experimental approaches are commonly used to study the cell cycle and cell biology: One class of experiments characterizes the statistics (or demographics) of an unsynchronized exponentially-growing…
In large clonal populations, several clones generally compete which results in complex evolutionary and ecological dynamics: experiments show successive selective sweeps of favorable mutations as well as long-term coexistence of multiple…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
We consider the problem of jointly modeling and clustering populations of tensors by introducing a high-dimensional tensor mixture model with heterogeneous covariances. To effectively tackle the high dimensionality of tensor objects, we…
Hematopoietic stem cells in mammals are known to reside mostly in the bone marrow, but also transitively passage in small numbers in the blood. Experimental findings have suggested that they exist in a dynamic equilibrium, continuously…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…