Related papers: An efficient strategy to characterize alleles and …
Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…
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…
Genomic regions (or loci) displaying outstanding correlation with some environmental variables are likely to be under selection and this is the rationale of recent methods of identifying selected loci and retrieving functional information…
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…
There are a number of vectors for attack when trying to link an individual to a certain DNA sequence. Phenotypic prediction is one such vector; linking DNA to an individual based on their traits. Current approaches are not overly effective,…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
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,…
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…
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…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for…
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…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
The standard paradigm for the analysis of genome-wide association studies involves carrying out association tests at both typed and imputed SNPs. These methods will not be optimal for detecting the signal of association at SNPs that are not…
Research on the localization of the genetic basis associated with diseases or traits has been widely conducted in the last a few decades. Scan methods have been developed for region-based analysis in whole-genome association studies,…
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…
Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…
In a case-control study aimed at localizing disease variants, association between a marker and the disease status is often tested by comparing the marker allele frequencies among cases and controls. These marker allele frequencies are…
Heritability is a central parameter in quantitative genetics, both from an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within and between genotype variability. This approach…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…