ArticleNature chemical biology2022
Combining CRISPRi and metabolomics for functional annotation of compound libraries.
Article in Nature chemical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Multi-omics decodes a defect-interface dual-engineered PtPb@SbOMaterials today. Bio · 2026Article
- Article
- High-Content CRISPR Screening: Methods and Applications.MedComm · 2026Review
- Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics.bioRxiv : the preprint server for biology · 2026Article
- Multi-omics and artificial intelligence for precision drug discovery and potential clinical applications.Signal transduction and targeted therapy · 2026Review
- From CRISPR functional genomics to synthetic interventions: engineering antiviral strategies.Journal of virology · 2026Review
- Targeting metabolism to combat anticancer and antibacterial drug resistance.Trends in pharmacological sciences · 2026Review
- A comprehensive review of cluster methods for drug-drug interaction network.Quantitative biology (Beijing, China) · 2026Review
- Integration of diverse bioactivity data into the Chemical Checker compound universe.Nature protocols · 2025Review
- Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria.Nature communications · 2025Article
- Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability.The Journal of cell biology · 2025Article
- Biological activity of secondary metabolites of actinomycetes and their potential sources as antineoplastic drugs: a review.Frontiers in microbiology · 2025Review
- Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- AI-empowered perturbation proteomics for complex biological systems.Cell genomics · 2024Article
- Review
- Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery.The Biochemical journal · 2024Review
- Chemical Composition of Commercial Cannabis.Journal of agricultural and food chemistry · 2024Article
- Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products.Natural product reports · 2024Review
- A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli.Cell reports methods · 2024Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
Molecular profiling of small molecules offers invaluable insights into the function of compounds and allows for hypothesis generation about small-molecule direct targets and secondary effects. However, current profiling methods are limited in either the number of measurable parameters or throughput. Here we developed a multiplexed, unbiased framework that, by linking genetic to drug-induced changes in nearly a thousand metabolites, allows for high-throughput functional annotation of compound libraries in Escherichia coli. First, we generated a reference map of metabolic changes from CRISPR interference (CRISPRi) with 352 genes in all major essential biological processes. Next, on the basis of the comparison of genetic changes with 1,342 drug-induced metabolic changes, we made de novo predictions of compound functionality and revealed antibacterials with unconventional modes of action (MoAs). We show that our framework, combining dynamic gene silencing with metabolomics, can be adapted as a general strategy for comprehensive high-throughput analysis of compound functionality from bacteria to human cell lines.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.