Related papers: Estimating heterozygosity from a low-coverage geno…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
Revealing relationships between genes and disease phenotypes is a critical problem in biomedical studies. This problem has been challenged by the heterogeneity of diseases. Patients of a perceived same disease may form multiple subgroups,…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
DNA sequencing is becoming increasingly commonplace, both in medical and direct-to-consumer settings. To promote discovery, collected genomic data is often de-identified and shared, either in public repositories, such as OpenSNP, or with…
The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic which is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods,…
When testing for the association of a single SNP with a phenotypic response, one usually considers an additive genetic model, assuming that the mean of of the response for the heterozygous state is the average of the means for the two…
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation…
Estimates of population size for hidden and hard-to-reach individuals are of particular interest to health officials when health problems are concentrated in such populations. Efforts to derive these estimates are often frustrated by a…
The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in…
In this paper, we consider the problem of answering count queries for genomic data subject to perfect privacy constraints. Count queries are often used in applications that collect aggregate (population-wide) information from biomedical…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
DNA databases are widely used in forensic science to identify unknown offenders. When no exact match is found, familial DNA searches can help by identifying first-degree relatives using likelihood ratios. If multiple subpopulations are…
The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated…
The standard paradigm for the analysis of genome-wide association studies involves carrying out association tests at both typed and imputed SNPs. These methods will not be optimal for detecting the signal of association at SNPs that are not…
When a sample frequency table is published, disclosure risk arises when some individuals can be identified on the basis of their values in certain attributes in the table called key variables, and then their values in other attributes may…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…