Related papers: Smaller $p$-values in genomics studies using disti…

In an empirical Bayesian setting, we provide a new multiple testing method, useful when an additional covariate is available, that influences the probability of each null hypothesis being true. We measure the posterior significance of each…

Bayes factors for composite hypotheses have difficulty in encoding vague prior knowledge, as improper priors cannot be used and objective priors may be subjectively unreasonable. To address these issues I revisit the posterior Bayes factor,…

Motivation: Modern biobanks, with unprecedented sample sizes and phenotypic diversity, have become foundational resources for genomic studies, enabling powerful cross-phenotype and population-scale analyses. As studies grow in complexity,…

We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…

Statistical hypothesis testing, as formalized by 20th Century statisticians and taught in college statistics courses, has been a cornerstone of 100 years of scientific progress. Nevertheless, the methodology is increasingly questioned in…

Massively parallel DNA sequencing techniques are rapidly changing the dynamics of phylogenetic study design by exponentially increasing the discovery of phylogenetically useful loci. This increase in the number of phylogenetic markers…

The features in high dimensional biomedical prediction problems are often well described with lower dimensional manifolds. An example is genes that are organised in smaller functional networks. The outcome can then be described with the…

In high-throughput genetics studies, an important aim is to identify gene-environment interactions associated with the clinical outcomes. Recently, multiple marginal penalization methods have been developed and shown to be effective in…

Many methods have been developed to estimate the set of relevant variables in a sparse linear model Y= XB+e where the dimension p of B can be much higher than the length n of Y. Here we propose two new methods based on multiple hypotheses…

This article presents a Conformalized Locally Adaptive Weighting (CLAW) approach to multiple testing with side information. The proposed method employs innovative data-driven strategies to construct pairwise exchangeable scores, which are…

We consider large-scale studies in which thousands of significance tests are performed simultaneously. In some of these studies, the multiple testing procedure can be severely biased by latent confounding factors such as batch effects and…

We study methods for simultaneous analysis of many noisy and biased estimates, each paired with an even noisier estimate of its own bias. The analyst's goal is to construct short calibrated intervals for each parameter. The standard…

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,…

One of the most common analysis tasks in genomic research is to identify genes that are differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) statistical tests using moderated genewise variances have been very…

In multi-center clinical trials, due to various reasons, the individual-level data are strictly restricted to be assessed publicly. Instead, the summarized information is widely available from published results. With the advance of…

Multi-gene panel testing allows many cancer susceptibility genes to be tested quickly at a lower cost making such testing accessible to a broader population. Thus, more patients carrying pathogenic germline mutations in various…

It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…

Large case/control Genome-Wide Association Studies (GWAS) often include groups of related individuals with known relationships. When testing for associations at a given locus, current methods incorporate only the familial relationships…

Identifying signals that replicate across multiple studies is essential for establishing robust scientific evidence, yet existing methods for high-dimensional replicability analysis either rely on restrictive modeling assumptions, are…

Tens of thousands of simultaneous hypothesis tests are routinely performed in genomic studies to identify differentially expressed genes. However, due to unmeasured confounders, many standard statistical approaches may be substantially…