ArticleNature protocols2017
Rapid curation of gene disruption collections using Knockout Sudoku.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Cobalt and nickel ion synergy promotes gene amplification and stable metal resistance inApplied and environmental microbiology · 2026Article
- Oligonucleotide genetics forbioRxiv : the preprint server for biology · 2026Article
- CauloKO: an ordered transposon mutant library inJournal of bacteriology · 2026Article
- Review
- Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans.PLoS biology · 2025Article
- Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching.Communications biology · 2025Article
- ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.Nucleic acids research · 2024Article
- Genomic characterization of rare earth binding by Shewanella oneidensis.Scientific reports · 2023Article
- Optimized Replication of Arrayed Bacterial Mutant Libraries Increases Access to Biological Resources.Microbiology spectrum · 2023Article
- A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression.Nature microbiology · 2023Article
- Optimized replication of arrayed bacterial mutant libraries increase access to biological resources.bioRxiv : the preprint server for biology · 2023Article
- Generation of a Gluconobacter oxydans knockout collection for improved extraction of rare earth elements.Nature communications · 2021Article
- Identification of a pathway for electron uptake in Shewanella oneidensis.Communications biology · 2021Article
- Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of ∼$10,000 for a collection for a single organism. The method uses manual 4D combinatorial pooling, next-generation sequencing, and a Bayesian inference algorithm to rapidly process and then accurately annotate the extremely large progenitor transposon insertion mutant collections needed to achieve saturating coverage of complex microbial genomes. This method is ∼100× faster and 30× lower in cost than the next comparable method (In-seq) for annotating transposon mutant collections by combinatorial pooling and next-generation sequencing. This method facilitates the rapid, algorithmically guided condensation and curation of the progenitor collection into a high-quality, nonredundant collection that is suitable for rapid genetic screening and gene discovery.
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