Related papers: Detection of selective sweeps in cattle using geno…
Training population selection for genomic selection has captured a great deal of interest in animal and plant breeding. In this article, we derive a computationally efficient statistic to measure the reliability of estimates of genetic…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
The aim of this paper was to develop statistical models to estimate individual breed composition based on the previously proposed idea of regressing discrete random variables corresponding to counts of reference alleles of biallelic…
Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the…
SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and…
High-dimensional variable selection has emerged as one of the prevailing statistical challenges in the big data revolution. Many variable selection methods have been adapted for identifying single nucleotide polymorphisms (SNPs) linked to…
Pedigree data contain family history information that is used to analyze hereditary diseases. These clinical data sets may contain duplicate records due to the same family visiting a clinic multiple times or a clinician entering multiple…
Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions.…
We investigate saddlepoint approximations applied to the score test statistic in genome-wide association studies with binary phenotypes. The inaccuracy in the normal approximation of the score test statistic increases with increasing sample…
We suggest a simple deterministic approximation for the growth of the favoured-allele frequency during a selective sweep. Using this approximation we introduce an accurate model for genetic hitch-hiking. Only when Ns < 10 (N is the…
The exploration of selected single nucleotide polymorphisms (SNPs) to identify genetic diversity between different sequencing population pools (Pool-seq) is a fundamental task in genetic research. As underlying sequence reads and their…
Modern maize breeding relies upon selection in inbreeding populations to improve the performance of cross-population hybrids. The United States Department of Agriculture - Agricultural Research Service reciprocal recurrent selection…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Sex difference in allele frequency is an emerging topic that is critical to our understanding of ascertainment bias, as well as data quality particularly of the largely overlooked X chromosome. To detect sex difference in allele frequency…
Plant domestication involved a process of selection through human agency of a series of traits collectively termed the domestication syndrome. Current debate concerns the pace at which domesticated plants emerged from cultivated wild…
Genomic regions (or loci) displaying outstanding correlation with some environmental variables are likely to be under selection and this is the rationale of recent methods of identifying selected loci and retrieving functional information…
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely…
Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele…
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, human harvesting, and changes in fish-host prevalence. Currently, over 70% of species are threatened, endangered or extinct. To…
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The…