ArticleNucleic acids research2018
SLING: a tool to search for linked genes in bacterial datasets.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 22 citations in OpenAlex.
- Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.Cell host & microbe · 2023Pooled it
- The role of toxin-antitoxin systems inJournal of bacteriology · 2026Review
- The plasmid-borne hipBA operon of Klebsiella michiganensis encodes a potent plasmid stabilization system.Journal of applied microbiology · 2024Article
- Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages ofmBio · 2024Article
- The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Protein family neighborhood analyzer-ProFaNA.PeerJ · 2023Article
- Genome mining reveals the prevalence and extensive diversity of toxin-antitoxin systems inFrontiers in microbiology · 2023Article
- Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings.Current research in microbial sciences · 2023Review
- Characterization of qnrB-carrying plasmids from ESBL- and non-ESBL-producing Escherichia coli.BMC genomics · 2022Article
- Article
- Emergence of Hybrid Resistance and Virulence Plasmids Harboring New Delhi Metallo-β-Lactamase inAntibiotics (Basel, Switzerland) · 2021Article
- Article
- Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems inFrontiers in microbiology · 2021Article
- A widespread toxin-antitoxin system exploiting growth control via alarmone signaling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population.Nucleic acids research · 2020Article
- Survey of Toxin⁻Antitoxin Systems inToxins · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Gene arrays and operons that encode functionally linked proteins form the most basic unit of transcriptional regulation in bacteria. Rules that govern the order and orientation of genes in these systems have been defined; however, these were based on a small set of genomes that may not be representative. The growing availability of large genomic datasets presents an opportunity to test these rules, to define the full range and diversity of these systems, and to understand their evolution. Here we present SLING, a tool to Search for LINked Genes by searching for a single functionally essential gene, along with its neighbours in a rule-defined proximity (https://github.com/ghoresh11/sling/wiki). Examining this subset of genes enables us to understand the basic diversity of these genetic systems in large datasets. We demonstrate the utility of SLING on a clinical collection of enteropathogenic Escherichia coli for two relevant operons: toxin antitoxin (TA) systems and RND efflux pumps. By examining the diversity of these systems, we gain insight on distinct classes of operons which present variable levels of prevalence and ability to be lost or gained. The importance of this analysis is not limited to TA systems and RND pumps, and can be expanded to understand the diversity of many other relevant gene arrays.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.