ArticleBriefings in bioinformatics2024
PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Revealing Functional Traits of Insect Pest Suppressive Rhizobacterial Strains Through Comparative Genomics.Environmental microbiology · 2026Article
- plsMD: a plasmid reconstruction tool from short-read assemblies.BMC bioinformatics · 2026Article
- Conserved protein sequence-structure signatures identify antibiotic resistance genes from the human microbiome.Microbiome · 2026Article
- From Wild to Farm: Gut Bacteriome Differences and Probiotic Potential of Pantoea Agglomerans in Two-Spotted Cricket (Gryllus Bimaculatus) Rearing.Probiotics and antimicrobial proteins · 2026Article
- Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.BMC genomics · 2026Article
- Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.Current microbiology · 2026Article
- Genomic and proteomic analyses of the maize root isolateApplied and environmental microbiology · 2026Article
- Population structure, antimicrobial resistance, and virulence factors of diabetic foot-associatedMicrobiology spectrum · 2026Article
- Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases.The ISME journal · 2026Article
- Integrative phenotypic and functional genomic characterization of virulence and antimicrobial resistance inFrontiers in microbiology · 2026Article
- Genomic epidemiology ofFrontiers in microbiology · 2026Article
- Genomic surveillance reveals escalating antimicrobial resistance and plasmid diversity in clinicalFrontiers in microbiology · 2026Article
- Analyzing multidrug resistance patterns across the food supply chain using association rule mining.Preventive veterinary medicine · 2026Article
- Biological control ofFrontiers in microbiology · 2026Article
- Characterization ofApplied and environmental microbiology · 2025Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- High-quality genome assemblies of 152 root commensal bacteria from the model legume Lotus japonicus.Scientific data · 2025Article
- Genetic exchange networks bridge mobile DNA vehicles in the bacterial pathogen Listeria monocytogenes.Nature communications · 2025Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Soil microbial responses to multiple global change factors as assessed by metagenomics.Nature communications · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Plasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be difficult to identify plasmid sequences from chromosomal sequences in genomic and metagenomic data. Here, we have developed a new tool called PlasmidHunter, which uses machine learning to predict plasmid sequences based on gene content profile. PlasmidHunter can achieve high accuracies (up to 97.6%) and high speeds in benchmark tests including both simulated contigs and real metagenomic plasmidome data, outperforming other existing tools.
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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.