Related papers: A probabilistic model for gene content evolution w…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Understanding how knowledge is created and propagates within groups is crucial to explain how human populations have evolved through time. Anthropologists have relied on different theoretical models to address this question. In this work,…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
We propose a type-dependent branching model with mutation and competition for modeling phylogenies of a virus population. The competition kernel depends for any two virus particles on the particles' types, the total mass of the population…
We consider a branching model in discrete time where each individual has a trait in some general state space. Both the reproduction law and the trait inherited by the offsprings may depend on the trait of the mother and the environment. We…
We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping…
In this work, we develop a stochastic model of gene gain and loss with the aim of inferring when (if at all) in evolutionary history and association between two genes arises. The data we consider is a species tree along with information on…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
Cancer results from genetic alterations that disturb the normal cooperative behavior of cells. Recent high-throughput genomic studies of cancer cells have shown that the mutational landscape of cancer is complex and that individual cancers…
We present two data-driven procedures to estimate the transition density of an homogeneous Markov chain. The first yields to a piecewise constant estimator on a suitable random partition. By using an Hellinger-type loss, we establish…
Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the…
We construct a family of genealogy-valued Markov processes that are induced by a continuous-time Markov population process. We derive exact expressions for the likelihood of a given genealogy conditional on the history of the underlying…
We present a genetic algorithm which is distributed in two novel ways: along genotype and temporal axes. Our algorithm first distributes, for every member of the population, a subset of the genotype to each network node, rather than a…
Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly…
General birth-and-death as well as hopping stochastic dynamics of infinite particle systems in the continuum are considered. We derive corresponding evolution equations for correlation functions and generating functionals. General…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…
The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss and lateral gene transfer (LGT). The extent of LGT,…
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case count data. The coalescent is used to model the genealogy that…
The paper deals with a certain class of random evolutions. We develop a construction that yields an invariant measure for a continuous-time Markov process with random transitions. The approach is based on a particular way of constructing…