ArticleMolecular systems biology2024
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability.
Article in Molecular systems biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- The phenotypic landscape of the model firmicuteProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Elevated temperature undermines the efficacy ofmSphere · 2026Article
- Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro.Nature microbiology · 2025Article
- Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis.Nature communications · 2025Article
- Comprehensive mutational characterization of the calcium-sensing STIM1 EF-hand reveals residues essential for structure and function.Genetics · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
Chemical genomics is a powerful and increasingly accessible technique to probe gene function, gene-gene interactions, and antibiotic synergies and antagonisms. Indeed, multiple large-scale pooled datasets in diverse organisms have been published. Here, we identify an artifact arising from uncorrected differences in the number of cell doublings between experiments within such datasets. We demonstrate that this artifact is widespread, show how it causes spurious gene-gene and drug-drug correlations, and present a simple but effective post hoc method for removing its effects. Using several published datasets, we demonstrate that this correction removes spurious correlations between genes and conditions, improving data interpretability and revealing new biological insights. Finally, we determine experimental factors that predispose a dataset for this artifact and suggest a set of experimental and computational guidelines for performing pooled chemical genomics experiments that will maximize the potential of this powerful technique.
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Registered trials
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