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We propose a Bayesian nonparametric model to infer population admixture, extending the Hierarchical Dirichlet Process to allow for correlation between loci due to Linkage Disequilibrium. Given multilocus genotype data from a sample of individuals, the model allows inferring classifying individuals as unadmixed or admixed, inferring the number of subpopulations ancestral to an admixed population and the population of origin of chromosomal regions. Our model does not assume any specific mutation process and can be applied to most of the commonly used genetic markers. We present a MCMC algorithm to perform posterior inference from the model and discuss methods to summarise the MCMC output for the analysis of population admixture. We demonstrate the performance of the proposed model in simulations and in a real application, using genetic data from the EDAR gene, which is considered to be ancestry-informative due to well-known variations in allele frequency as well as phenotypic effects across ancestry. The structure analysis of this dataset leads to the identification of a rare haplotype in Europeans.
We propose a hierarchical Bayesian model to estimate the proportional contribution of source populations to a newly founded colony. Samples are derived from the first generation offspring in the colony, but mating may occur preferentially among migra
We propose a general Bayesian approach to modeling epidemics such as COVID-19. The approach grew out of specific analyses conducted during the pandemic, in particular an analysis concerning the effects of non-pharmaceutical interventions (NPIs) in re
Studying the determinants of adverse pregnancy outcomes like stillbirth and preterm birth is of considerable interest in epidemiology. Understanding the role of both individual and community risk factors for these outcomes is crucial for planning app
How should social scientists understand and communicate the uncertainty of statistically estimated causal effects? It is well-known that the conventional significance-vs.-insignificance approach is associated with misunderstandings and misuses. Behav
When a latent shoeprint is discovered at a crime scene, forensic analysts inspect it for distinctive patterns of wear such as scratches and holes (known as accidentals) on the source shoes sole. If its accidentals correspond to those of a suspects sh