Related papers: Reconstructing pedigrees: a stochastic perspective

Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…

The dynamics of a population exhibiting exponential growth can be modelled as a birth-death process, which naturally captures the stochastic variation in population size over time. In this article, we consider a supercritical birth-death…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…

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…

A set of independence statements may define the independence structure of interest in a family of joint probability distributions. This structure is often captured by a graph that consists of nodes representing the random variables and of…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

Driven by the popularity of television shows such as Who Do You Think You Are? many millions of users have uploaded their family tree to web projects such as WikiTree. Analysis of this corpus enables us to investigate genealogy…

A density-dependent branching process is a particle system in which individuals reproduce independently, but in a way that depends on the current population size. This feature can model a wide range of ecological interactions at the cost of…

Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of how we expect…

Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recombination from sequencing data is a very challenging problem,…

Online genealogy datasets contain extensive information about millions of people and their past and present family connections. This vast amount of data can assist in identifying various patterns in human population. In this study, we…

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…

We investigate a simple quantitative genetics model subjet to a gradual environmental change from the viewpoint of the phylogenies of the living individuals. We aim to understand better how the past traits of their ancestors are shaped by…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

Record linkage is the process of identifying records that refer to the same entities from several databases. This process is challenging because commonly no unique entity identifiers are available. Linkage therefore has to rely on partially…

We linked names and contact information to publicly available profiles in the Personal Genome Project. These profiles contain medical and genomic information, including details about medications, procedures and diseases, and demographic…

Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…