Tests for Hardy-Weinberg equilibrium (HWE) have been used to detect genotyping error, but those tests have low power unless the sample size is very large. We assessed the performance of measures of departure from HWE as an alternative way of screening for genotyping error. Three measures of the...

The term "epistasis" is sometimes used to describe some form of statistical interaction between genetic factors and is alternatively sometimes used to describe instances in which the effect of a particular genetic variant is masked by a variant at another locus. In general statistical tests for...

Recent applications of principal components analysis (PCA) and multidimensional scaling (MDS) in human population genetics have found that "statistical maps" based on the genotypes in population-genetic samples often resemble geographic maps of the underlying sampling locations. To provide...

We wish to suggest the categorical analysis of variance as a means of quantifying the proportion of total genetic variation attributed to different sources of variation. This method potentially challenges researchers to rethink conclusions derived from a well-known method known as the analysis...

In this work we deal with parameter estimation in a latent variable model, namely the multiple-hidden i.i.d. model, which is derived from multiple alignment algorithms. We first provide a rigorous formalism for the homology structure of k sequences related by a star-shaped phylogenetic tree in...

Nuisance factors in a protein-array study add obfuscating variation to spot intensity measurements, diminishing the accuracy and precision of protein concentration predictions. The effects of nuisance factors may be reduced by design of experiments, and by estimating and then subtracting...

In Genomewide association (GWA) studies investigating thousands of SNPs, large sample sizes are needed to obtain a reasonable power after correction for multiple testing. To obtain the necessary sample sizes, data from different populations/cohorts are combined. The problem of pooling evidence...

Klebanov et al. (2006) proposed a new type of stochastic dependence, Type A dependence, between gene expression levels. They estimated the abundance of Type A pairs by testing the correlation coefficients of gene pairs. We propose a new model, hidden regulator dependence, as an alternative to...

Granger causality (GC) tests are ideally suited to investigate time series data generated by bivariate vector autoregressive (VAR) processes. Recent studies have applied GC analysis and its extensions for modeling functional relationships and network structure from temporal gene expression...

The recent emergence of massively parallel sequencing technologies has enabled an increasing number of human genome re-sequencing studies, notable among them being the 1000 Genomes Project. The main aim of these studies is to identify the yet unknown genetic variants in a genomic region, mostly...