ArticleBioinformatics (Oxford, England)2024
Bayesian gene set benchmark dose estimation for "omic" responses.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
2 citing papers in PubMed.
- BayesCurveFit: Enhancing Curve Fitting for Early-Stage Compound Screening Using Bayesian Inference.bioRxiv : the preprint server for biology · 2025Article
- Modeling omics dose-response at the pathway level with DoseRider.Computational and structural biotechnology journal · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
motivationEstimating a toxic reference point using tools like the benchmark dose (BMD) is a critical step in setting policy to regulate pollution and ensure safe environments. Toxicity can be measured for different endpoints, including changes in gene expression and histopathology for various tissues, and is typically explored one gene or tissue at a time in a univariate setting that ignores correlation. In this work, we develop a multivariate estimation procedure to estimate the BMD for specified gene sets. Our approach extends the foundational univariate approach by accounting for correlation in a statistically principled way.
resultsWe illustrate the method using data from a 5-day rat study and Hallmark gene sets and compare to existing BMD results computed by the EPA for both gene sets and apical histopathology endpoints. In contrast to previous ad-hoc methods, our principled approach provides the needed extension to bring the foundational univariate method into the multivariate world of transcriptomics. In addition to use in a regulatory setting, our method can provide hypothesis generation when gene sets correspond to mechanistic pathways. AVAILABILITY AND IMPLEMENTATION: BS-BMD is implemented in R and C++ and available at https://github.com/NIEHS/BS-BMD.
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Registered trials
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.