Related papers: An empirical approach to demographic inference wit…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
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…
We introduce a modified spatial $\Lambda$-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective…
Large-scale statistical analysis of data sets associated with genome sequences plays an important role in modern biology. A key component of such statistical analyses is the computation of $p$-values and confidence bounds for statistics…
Census data provide detailed information about population characteristics at a coarse resolution. Nevertheless, fine-grained, high-resolution mappings of population counts are increasingly needed to characterize population dynamics and to…
We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…
We provide a general mathematical framework based on the theory of graphical models to study admixture graphs. Admixture graphs are used to describe the ancestral relationships between past and present populations, allowing for population…
Data on historical populations often extends no further than numbers of people by broad age-sex group, with nothing on numbers of births or deaths. Demographers studying these populations have experimented with methods that use the data on…
In an extant population, how much information do extant individuals provide on the pedigree of their ancestors? Recent work by Kim, Mossel, Ramnarayan and Turner (2020) studied this question under a number of simplifying assumptions,…
We analyse a model consisting of a population of individuals which is subdivided into a finite set of demes, each of which has a fixed but differing number of individuals. The individuals can reproduce, die and migrate between the demes…
The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial,…
We address the problem of performing regression while ensuring demographic parity, even without access to sensitive attributes during inference. We present a general-purpose post-processing algorithm that, using accurate estimates of the…
The coalescent revolutionised theoretical population genetics, simplifying, or making possible for the first time, many analyses, proofs, and derivations, and offering crucial insights about the way in which the structure of data in samples…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…
Covariance matrix estimation is a fundamental statistical task in many applications, but the sample covariance matrix is sub-optimal when the sample size is comparable to or less than the number of features. Such high-dimensional settings…
Recovery of population size history from molecular sequence data is an important problem in population genetics. Inference commonly relies on a coalescent model linking the population size history to genealogies. The high computational cost…
Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of…
Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…
In the case of informative sampling the sampling scheme explicitly or implicitly depends on the response variable. As a result, the sample distribution of response variable can- not be used for making inference about the population. In this…