Related papers: The dissection of expression quantitative trait lo…
We analyse interactions of Quantitative Trait Loci (QTL) in heat selected yeast by comparing them to an unselected pool of random individuals. Here we re-examine data on individual F12 progeny selected for heat tolerance, which have been…
The distribution and heritability of many traits depends on numerous loci in the genome. In general, the astronomical number of possible genotypes makes the system with large numbers of loci difficult to describe. Multilocus evolution,…
While covariance matrices have been widely studied in many scientific fields, relatively limited progress has been made on estimating conditional covariances that permits a large covariance matrix to vary with high-dimensional subject-level…
Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a…
Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In simple cases, single polymorphic loci explain a significant fraction of the phenotype variability. However, many traits of…
Although many phenotypic traits are determined by a large number of genetic variants, the behavior of allele frequencies in a polygenic trait is not completely understood. The problem is especially challenging when the quantitative trait of…
In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in QTL mapping have begun to elucidate the genetic architectures underlying vast numbers of…
This paper describes a Bayesian statistical method for determining the genetic basis of a complex genetic trait. The method uses a sample of unrelated individuals classified into two groups, for example cases and controls. Each group is…
Genome-wide eQTL mapping explores the relationship between gene expression values and DNA variants to understand genetic causes of human disease. Due to the large number of genes and DNA variants that need to be assessed simultaneously,…
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 recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression…
The evolutionary effect of recombination depends crucially on the epistatic interactions between linked loci. A paradigmatic case where recombination is known to be strongly disadvantageous is a two-locus fitness landscape dis- playing…
Genetic variation affecting gene regulation is a central driver of phenotypic differences between individuals and can be used to uncover how biological processes are organized in a cell. Although detecting cis-eQTLs is now routine,…
In an empirical Bayesian setting, we provide a new multiple testing method, useful when an additional covariate is available, that influences the probability of each null hypothesis being true. We measure the posterior significance of each…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population-genetic test for…
Understanding the genetic underpinnings of complex traits and diseases has been greatly advanced by genome-wide association studies (GWAS). However, a significant portion of trait heritability remains unexplained, known as ``missing…
Obtaining a closed-form sampling distribution for the coalescent with recombination is a challenging problem. In the case of two loci, a new framework based on asymptotic series has recently been developed to derive closed-form results when…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…