Related papers: Distortion of genealogical properties when the sam…
Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population…
The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…
Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic…
Assume that individuals alive at time $t$ in some population can be ranked in such a way that the coalescence times between consecutive individuals are i.i.d. The ranked sequence of these branches is called a coalescent point process. We…
The Wright-Fisher model describes a biological population containing a finite number of individuals. In this work we consider a Wright-Fisher model for a randomly mating population, where selection and mutation act at an unlinked locus. The…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
We construct a reliable estimation of evolutionary parameters within the Wright-Fisher model, which describes changes in allele frequencies due to selection and genetic drift, from time-series data. Such data exists for biological…
When identical particles on a line collide, they merge and continue as one. Exact determinantal formulas have long been available for particles conditioned never to collide, but collisions change the number of particles, and exact…
Man-made communications signals are typically modelled as continuous-time (CT) wide-sense cyclostationary (WSCS) processes. As modern processing is digital, it operates on sampled versions of the CT signals. When sampling is applied to a CT…
Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
A branching process in random environment $(Z_n, n \in \N)$ is a generalization of Galton Watson processes where at each generation the reproduction law is picked randomly. In this paper we give several results which belong to the class of…
We consider a family of models describing the evolution under selection of a population whose dynamics can be related to the propagation of noisy traveling waves. For one particular model, that we shall call the exponential model, the…
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,…
Deep Gaussian processes (DGP) have appealing Bayesian properties, can handle variable-sized data, and learn deep features. Their limitation is that they do not scale well with the size of the data. Existing approaches address this using a…
Consider a haploid population of fixed finite size with a finite number of allele types and having Cannings exchangeable genealogy with neutral mutation. The stationary distribution of the Markov chain of allele counts in each generation is…
Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and…
We consider population dynamics as implemented by the cloning algorithm for analysis of large deviations of time-averaged quantities. Using the simple symmetric exclusion process as a prototypical example, we investigate the convergence of…
Wright-Fisher diffusions describe the evolution of the type composition of an infinite haploid population with two types (say type $0$ and type $1$) subject to neutral reproductions, and possibly selection and mutations. In the present…
Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…