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Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
The attributable risk, often called the population attributable risk, is in many epidemiological contexts a more relevant measure of exposure-disease association than the excess risk, relative risk, or odds ratio. When estimating…
Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…
In the search for genetic factors that are associated with complex heritable human traits, considerable attention is now being focused on rare variants that individually have small effects. In response, numerous recent papers have proposed…
Genetic association studies are becoming an important component of medical research. To cite one instance, pharmacogenomics which is gaining prominence as a useful tool for personalized medicine is heavily reliant on results from genetic…
Replication helps ensure that a genotype-phenotype association observed in a genome-wide association (GWA) study represents a credible association and is not a chance finding or an artifact due to uncontrolled biases. We discuss…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
Detecting anomalies in large sets of observations is crucial in various applications, such as epidemiological studies, gene expression studies, and systems monitoring. We consider settings where the units of interest result in multiple…
Risk prediction that capitalizes on emerging genetic findings holds great promise for improving public health and clinical care. However, recent risk prediction research has shown that predictive tests formed on existing common genetic…
Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is…
Matched case-control studies are commonly employed in epidemiological research for their convenience and efficiency. Analysis of secondary outcomes can yield valuable insights into biological pathways and help identify genetic variants of…
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…
Background: Selecting feature genes to predict phenotypes is one of the typical tasks in analyzing genomics data. Though many general-purpose algorithms were developed for prediction, dealing with highly correlated genes in the prediction…
The development of next generation sequencing (NGS) technology and genotype imputation methods enabled researchers to measure both common and rare variants in genome-wide association studies (GWAS). Statistical methods have been proposed to…
In genetic association studies, rare variants with extremely small allele frequency play a crucial role in complex traits, and the set-based testing methods that jointly assess the effects of groups of single nucleotide polymorphisms (SNPs)…
We propose and study a fully efficient method to estimate associations of an exposure with disease incidence when both, incident cases and prevalent cases, i.e. individuals who were diagnosed with the disease at some prior time point and…
Studying the effects of groups of Single Nucleotide Polymorphisms (SNPs), as in a gene, genetic pathway, or network, can provide novel insight into complex diseases, above that which can be gleaned from studying SNPs individually. Common…
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…