Related papers: Detection of correlation between genotypes and env…
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…
High-throughput pheno-, geno-, and envirotyping allows characterization of plant genotypes and the trials they are evaluated in, producing different types of data. These different data modalities can be integrated into statistical or…
Motivation. Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly…
In genetic association studies, detecting phenotype-genotype association is a primary goal. We assume that the relationship between the data -phenotype, genetic markers and environmental covariates - can be modelled by a generalized linear…
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…
Ecological systems are governed by complex interactions which are mainly nonlinear. In order to capture this complexity and nonlinearity, statistical models recently gained popularity. However, although these models are commonly applied in…
Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either…
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…
Many diseases and traits involve a complex interplay between genes and environment, generating significant interest in studying gene-environment interaction through observational data. However, for lifestyle and environmental risk factors,…
Interactions between genes and environmental factors may play a key role in the etiology of many common disorders. Several regularized generalized linear models (GLMs) have been proposed for hierarchical selection of gene by environment…
In plant breeding and variety testing, there is an increasing interest in making use of environmental information to enhance predictions for new environments. Here, we will review linear mixed models that have been proposed for this…
Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current challenges of the field mainly involve processing large numbers of models and…
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…
Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that…
Modern methods for quantifying and predicting species distribution play a crucial part in biodiversity conservation. Occupancy models are a popular choice for analyzing species occurrence data as they allow to separate the observational…
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…
The spatial panel regression model has shown great success in modelling econometric and other types of data that are observed both spatially and temporally with associated predictor variables. However, model checking via testing for spatial…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
In statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been…
In recent years we have been able to gather large amounts of genomic data at a fast rate, creating situations where the number of variables greatly exceeds the number of observations. In these situations, most models that can handle a…