Related papers: Replication in Genome-Wide Association Studies
When testing for the association of a single SNP with a phenotypic response, one usually considers an additive genetic model, assuming that the mean of of the response for the heterozygous state is the average of the means for the two…
Genome-wide association studies (GWAS) suggests that a complex disease is typically affected by many genetic variants with small or moderate effects. Identification of these risk variants remains to be a very challenging problem.…
Matching is a widely used causal inference design that aims to approximate a randomized experiment using observational data by forming matched sets of treated and control units based on similarities in their covariates. Ideally, treated…
Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…
The vast majority of connections between complex disease and common genetic variants were identified through meta-analysis, a powerful approach that enables large samples sizes while protecting against common artifacts due to population…
Rerandomization is a modern experimental design technique that repeatedly randomizes treatment assignments until covariates are deemed balanced between treatment groups. This enhances the precision and coherence of causal effect estimators,…
Genetic association study is an essential step to discover genetic factors that are associated with a complex trait of interest. In this paper we present a novel generalized quasi-likelihood score (GQLS) test that is suitable for a study…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…
Genomic data arising from a genome-wide association study (GWAS) are often not only of large-scale, but also incomplete. A specific form of their incompleteness is missing values with non-ignorable missingness mechanism. The intrinsic…
Let $W_1,\ldots,W_N$ be a sample of $\mathrm{Pareto}(\alpha)$ random variables normalized by their sum, such that $\sum_i W_i=1$. The $W_i$ may represent the weights of valleys in a spin glass (if $0<\alpha<1$), or the frequency of…
Multi-model inference covers a wide range of modern statistical applications such as variable selection, model confidence set, model averaging and variable importance. The performance of multi-model inference depends on the availability of…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Reproducibility has been increasingly encouraged by communities of science in order to validate experimental conclusions, and replication studies represent a significant opportunity to vision scientists wishing contribute new perceptual…
Diffusion models have emerged as a powerful framework for generative modeling, with guidance techniques playing a crucial role in enhancing sample quality. Despite their empirical success, a comprehensive theoretical understanding of the…
Traditional GWAS has advanced our understanding of complex diseases but often misses nonlinear genetic interactions. Deep learning offers new opportunities to capture complex genomic patterns, yet existing methods mostly depend on feature…
Reproducibility is central to the credibility of scientific findings, yet complete replication studies are costly and infrequent. However, many biological experiments contain internal replication, which is defined as repetition across…
Gene interaction graphs aim to capture various relationships between genes and represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality by…
We calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…