ArticleNucleic acids research2013
High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed, 139 citations in OpenAlex.
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- Zoonotic Streptococcus imports glucose to inhibit stringent response and promote growth during meningitis.Nature microbiology · 2026Article
- Cross-species phenotypic profiling uncovers functional determinants of bacterial cold shock adaptation.bioRxiv : the preprint server for biology · 2025Article
- The PDZ domain of EpsC is required for extracellular secretion of VesB by the Type II secretion system inJournal of bacteriology · 2025Article
- DnaB and DciA: mechanisms of helicase loading and translocation on ssDNA.Nucleic acids research · 2025Article
- Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites.Science (New York, N.Y.) · 2025Article
- Fine-tuning of a CRISPRi screen in the seventh pandemic Vibrio cholerae.BMC genomics · 2024Article
- LD-transpeptidation is crucial for fitness and polar growth in Agrobacterium tumefaciens.PLoS genetics · 2024Article
- Use of zebrafish to identify host responses specific to type VI secretion system mediated interbacterial antagonism.PLoS pathogens · 2024Article
- Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome.mLife · 2024Article
- Frequent nonhomologous replacement of replicative helicase loaders by viruses inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Temporal genome-wide fitness analysis ofmSystems · 2024Article
- Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.Microbial genomics · 2023Article
- Identification of determinants for entering into a viable but nonculturable state in Vibrio alginolyticus by Tn-seq.Applied microbiology and biotechnology · 2023Article
- Advances in cholera research: from molecular biology to public health initiatives.Frontiers in microbiology · 2023Review
- Construction of high-density transposon mutant library of Staphylococcus aureus using bacteriophage ϕ11.Journal of microbiology (Seoul, Korea) · 2022Article
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40 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or 'sick'). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data.
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