ArticleNature communications2019
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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
24 citing papers in PubMed, 49 citations in OpenAlex.
- Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways.bioRxiv : the preprint server for biology · 2026Article
- Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis.Nature communications · 2026Article
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- Systematic genome-wide mapping of host determinants of bacteriophage infectivity.Cell systems · 2025Article
- Review
- Dissecting host-microbe interactions with modern functional genomics.Current opinion in microbiology · 2024Review
- Community standards and future opportunities for synthetic communities in plant-microbiota research.Nature microbiology · 2024Review
- High-throughput protein characterization by complementation using DNA barcoded fragment libraries.Molecular systems biology · 2024Article
- Advancing quantitative PCR with color cycle multiplex amplification.Nucleic acids research · 2024Article
- The rise and future of CRISPR-based approaches for high-throughput genomics.FEMS microbiology reviews · 2024Review
- Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.Nature communications · 2024Article
- Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery.The Biochemical journal · 2024Review
- High-throughput microbial culturomics using automation and machine learning.Nature biotechnology · 2023Article
- Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins.Nature chemical biology · 2023Article
- Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains.Nature microbiology · 2023Article
- A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens.iScience · 2022Review
- The genetic basis of phage susceptibility, cross-resistance and host-range inMicrobiology (Reading, England) · 2021Article
- Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.Communications biology · 2021Article
- Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins.The ISME journal · 2021Article
- Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.
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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.