ArticleGenome biology2019
A practical guide to methods controlling false discoveries in computational biology.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 257 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
257 citing papers in PubMed, 3 syntheses or guidelines pooled it.
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- Identification of key proteins and pathways in myocardial infarction using machine learning approaches.Scientific reports · 2025Pooled it
- The Contribution of Lipidomics in Ovarian Cancer Management: A Systematic Review.International journal of molecular sciences · 2023Pooled it
- Sleeping for Two: a randomized controlled trial of cognitive behavioral therapy for insomnia in pregnancy.Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine · 2025Trial
- Stratification of responses to tDCS intervention in a healthy pediatric population based on resting-state EEG profiles.Scientific reports · 2023Trial
- Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-treatment DNA Methylation From Peripheral Blood.International journal of radiation oncology, biology, physics · 2023Trial
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- Plasma proteomics framework predicts metabolic dysfunction-associated steatotic liver disease up to 16 years before onset.Nature aging · 2026Article
- Age differences in spontaneous cerebrovascular reactivity at rest.GeroScience · 2026Article
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- Microbial predictors of sustained clinical remission following the Crohn's disease exclusion diet in adults and microbiome shifts toward healthy pediatric controls.Crohn's & colitis 360 · 2026Article
- Gut microbial genetic variations are associated with exploratory behavior via SNV-driven metabolic regulation in a sheep model.Science China. Life sciences · 2026Article
- Interpersonal Synchronization of Autonomic Physiology via Mere Visual Contact.Annals of the New York Academy of Sciences · 2026Article
- Early-Life DNA methylation at TRIM6 and TTC23 promoters associates with respiratory infections at one year.Pediatric research · 2026Article
- Accelerometer-Measured Sedentary Behavior, Future Disease, and Cardiovascular-Kidney-Metabolic Health.JACC. Advances · 2026Article
- Circulating Lipid Traits and Ovarian Cancer Risk: A Systematic Review and Meta-Analysis with Mendelian Randomization Integration.Metabolites · 2026Review
- Quantifying the contribution of the rare biosphere and functional potential to the compacted clay baseliner of sanitary landfill.World journal of microbiology & biotechnology · 2026Article
197 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
backgroundIn high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have emerged as popular and powerful tools for error rate control. While classic FDR methods use only p values as input, more modern FDR methods have been shown to increase power by incorporating complementary information as informative covariates to prioritize, weight, and group hypotheses. However, there is currently no consensus on how the modern methods compare to one another. We investigate the accuracy, applicability, and ease of use of two classic and six modern FDR-controlling methods by performing a systematic benchmark comparison using simulation studies as well as six case studies in computational biology.
resultsMethods that incorporate informative covariates are modestly more powerful than classic approaches, and do not underperform classic approaches, even when the covariate is completely uninformative. The majority of methods are successful at controlling the FDR, with the exception of two modern methods under certain settings. Furthermore, we find that the improvement of the modern FDR methods over the classic methods increases with the informativeness of the covariate, total number of hypothesis tests, and proportion of truly non-null hypotheses.
conclusionsModern FDR methods that use an informative covariate provide advantages over classic FDR-controlling procedures, with the relative gain dependent on the application and informativeness of available covariates. We present our findings as a practical guide and provide recommendations to aid researchers in their choice of methods to correct for false discoveries.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.