相关论文: Efficient moment-based inference of admixture para…
Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele…
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…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Over the last fifty years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, 'The…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model…
The MIXANDMIX (mixtures by Anderson mixing) tool for the computation of the empirical spectral distribution of random matrices generated by mixtures of populations is described. Within the population mixture model the mapping between the…
The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…
Inference of individual admixture coefficients, which is important for population genetic and association studies, is commonly performed using compute-intensive likelihood algorithms. With the availability of large population genomic data…
Admixture mapping is a popular tool to identify regions of the genome associated with traits in a recently admixed population. Existing methods have been developed primarily for identification of a single locus influencing a dichotomous…
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…
In genetically admixed populations, admixed individuals possess ancestry from multiple source groups. Studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
Mixture models are a fundamental tool in applied statistics and machine learning for treating data taken from multiple subpopulations. The current practice for estimating the parameters of such models relies on local search heuristics…
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…
Mixture models are often used to identify meaningful subpopulations (i.e., clusters) in observed data such that the subpopulations have a real-world interpretation (e.g., as cell types). However, when used for subpopulation discovery,…
The Mapper algorithm is an essential tool for visualizing complex, high dimensional data in topology data analysis (TDA) and has been widely used in biomedical research. It outputs a combinatorial graph whose structure implies the shape of…
Communication and networking research introduces new protocols and standards with an increasing number of researchers relying on real experiments rather than simulations to evaluate the performance of their new protocols. A number of…