Related papers: Estimating Reproducibility in Genome-Wide Associat…
Many published research results are false, and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework…
Two-sample summary-data Mendelian randomization (MR) has become a popular research design to estimate the causal effect of risk exposures. With the sample size of GWAS continuing to increase, it is now possible to utilize genetic…
Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by…
Background: The standard regulatory approach to assess replication success is the two-trials rule, requiring both the original and the replication study to be significant with effect estimates in the same direction. The sceptical p-value…
We combine two important ideas in the analysis of large-scale genomics experiments (e.g. experiments that aim to identify genes that are differentially expressed between two conditions). The first is use of Empirical Bayes (EB) methods to…
Multiple hypothesis testing is a fundamental problem in high dimensional inference, with wide applications in many scientific fields. In genome-wide association studies, tens of thousands of tests are performed simultaneously to find if any…
Through genome-wide association studies (GWAS), disease susceptible genetic variables can be identified by comparing the genetic data of individuals with and without a specific disease. However, the discovery of these associations poses a…
The large-scale multiple testing inherent to high throughput biological data necessitates very high statistical stringency and thus true effects in data are difficult to detect unless they have high effect sizes. One promising approach for…
The cell biology literature is littered with erroneously tiny P values, often the result of evaluating individual cells as independent samples. Because readers use P values and error bars to infer whether a reported difference would likely…
Large-scale genome-wide association studies (GWAS) have offered an exciting opportunity to discover putative causal genes or risk factors associated with diseases by using SNPs as instrumental variables (IVs). However, conventional…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are…
This paper describes and tests a method for carrying out quantified reproducibility assessment (QRA) that is based on concepts and definitions from metrology. QRA produces a single score estimating the degree of reproducibility of a given…
The regularized random forest (RRF) was recently proposed for feature selection by building only one ensemble. In RRF the features are evaluated on a part of the training data at each tree node. We derive an upper bound for the number of…
The ongoing replication crisis in science has increased interest in the methodology of replication studies. We propose a novel Bayesian analysis approach using power priors: The likelihood of the original study's data is raised to the power…
Genetic variants identified to date by genome-wide association studies only explain a small fraction of total heritability. Gene-by-gene interaction is one important potential source of unexplained heritability. In the first part of this…
Given a real-world graph, how can we measure relevance scores for ranking and link prediction? Random walk with restart (RWR) provides an excellent measure for this and has been applied to various applications such as friend recommendation,…
A new standard is proposed for the evidential assessment of replication studies. The approach combines a specific reverse-Bayes technique with prior-predictive tail probabilities to define replication success. The method gives rise to a…
The variance component tests used in genomewide association studies of thousands of individuals become computationally exhaustive when multiple traits are analysed in the context of omics studies. We introduce two high-throughput algorithms…
In genome-wide association studies (GWASs) of common diseases/traits, we often analyze multiple GWASs with the same phenotype together to discover associated genetic variants with higher power. Since it is difficult to access data with…