Related papers: Mutation frequencies in a birth-death branching pr…
Cancer progression and monotonic accumulation models were developed to discover dependencies in the irreversible acquisition of binary traits from cross-sectional data. They have been used in computational oncology and virology but also in…
Tumors are defined by their intense proliferation, but sometimes cancer cells turn senescent and stop replicating. In the stochastic cancer model in which all cells are tumorigenic, senescence is seen as the result of random mutations,…
Objectives: In this study, we quantify the growth variability of tumour cell clones from a human leukemia cell line. Materials and methods: We have used microplate spectrophotometry to measure the growth kinetics of hundreds of individual…
We investigate a partial differential equation model of a cancer cell population, which is structured with respect to age and telomere length of cells. We assume a continuous telomere length structure, which is applicable to the clonal…
For the model of periodic chronic myelogenous leukemia considered by Pujo-Menjouet, Mackey et al., model consisting of two delay differential equations, the equation for the density of so-called "resting cells" was studied from numerical…
A general multi-type population model is considered, where individuals live and reproduce according to their age and type, but also under the influence of the size and composition of the entire population. We describe the dynamics of the…
We propose a new deterministic growth model which captures certain features of both the Gompertz and Korf laws. We investigate its main properties, with special attention to the correction factor, the relative growth rate, the inflection…
We model the growth of a cell population using a piecewise deterministic Markov branching tree. In this model, each cell splits into two offspring at a division rate $B(x)$, which depends on its size $x$. The size of each cell increases…
We consider a stationary continuous model of random size population with non-neutral mutations using a continuous state branching process with non-homogeneous immigration. We assume the type (or mutation) of the immigrants is random given…
In this paper we study a class of stochastic individual-based models that describe the evolution of haploid populations where each individual is characterised by a phenotype and a genotype. The phenotype of an individual determines its…
A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…
A two-type two-sex branching process is introduced with the aim of describing the interaction of predator and prey populations with sexual reproduction and promiscuous mating. In each generation and in each species the total number of…
We consider a model of random permutations of the sites of the cubic lattice. Permutations are weighted so that sites are preferably sent onto neighbors. We present numerical evidence for the occurrence of a transition to a phase with…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
Consider a random permutation of $\{1, \ldots, \lfloor n^{t_2}\rfloor\}$ drawn according to the Ewens measure with parameter $t_1$ and let $K(n, t)$ denote the number of its cycles, where $t\equiv (t_1, t_2)\in\mathbb [0, 1]^2$. Next,…
Under mild non-degeneracy assumptions on branching rates in each generation, we provide a criterion for almost-sure extinction of a multi-type branching process with time-dependent branching rates. We also provide a criterion for the total…
A two-variable stochastic model for diffusion-limited nucleation is developed using a formalism derived from fluctuating hydrodynamics. The model is a direct generalization of the standard Classical Nucleation Theory. The nucleation rate…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
The problem of estimating the growth rate of a birth and death processes based on the coalescence times of a sample of $n$ individuals has been considered by several authors (\cite{stadler2009incomplete, williams2022life,…