Related papers: The dissection of expression quantitative trait lo…
This paper explores the genotype-phenotype relationship. It outlines conditions under which the dependence of a quantitative trait on the genome might be predictable, based on measurement of a limited subset of genotypes. It uses the theory…
Adaptation to local environments often occurs through natural selection acting on a large number of loci, each having a weak phenotypic effect. One way to detect these loci is to identify genetic polymorphisms that exhibit high correlation…
With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a…
We consider an infinitely large population under stabilising selection and mutation in which the allelic effects determining a polygenic trait vary between loci. We obtain analytical expressions for the stationary genetic variance as a…
Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their…
Suppose we have a set $X$ consisting of $n$ taxa and we are given information from $k$ loci from which to construct a phylogeny for $X$. Each locus offers information for only a fraction of the taxa. The question is whether this data…
Generative, temporal network models play an important role in analyzing the dependence structure and evolution patterns of complex networks. Due to the complicated nature of real network data, it is often naive to assume that the underlying…
The random coefficients model is an extension of the linear regression model that allows for unobserved heterogeneity in the population by modeling the regression coefficients as random variables. Given data from this model, the statistical…
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and…
To understand the effect of assortative mating on the genetic evolution of a population, we consider a finite population in which each individual has a type, determined by a sequence of n diallelic loci. We assume that the population…
The Genotype-Tissue Expression (GTEx) project collects samples from multiple human tissues to study the relationship between genetic variation or single nucleotide polymorphisms (SNPs) and gene expression in each tissue. However, most…
Causal inference approaches in systems genetics exploit quantitative trait loci (QTL) genotypes to infer causal relationships among phenotypes. The genetic architecture of each phenotype may be complex, and poorly estimated genetic…
Gene-gene and gene-environment interactions are widely believed to play significant roles in explaining the variability of complex traits. While substantial research exists in this area, a comprehensive statistical framework that addresses…
In order to deal with the systematic verification with uncertain infromation in possibility theory, Li and Li \cite{li12} introduced model checking of linear-time properties in which the uncertainty is modeled by possibility measures. Xue,…
Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection…
There is a growing interest in cell-type-specific analysis from bulk samples with a mixture of different cell types. A critical first step in such analyses is the accurate estimation of cell-type proportions in a bulk sample. Although many…
The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention,…
We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with population growth, and use this function to construct…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
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…