ArticleNucleic acids research2018
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures.
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 296 papers.
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Who cites it
296 citing papers in PubMed, 605 citations in OpenAlex.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
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- Convergence of Plasmid-Mediated tmexCD-toprJ With Critical Resistance Genes Fuels Spread of Multidrug Resistant Bacteria.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Combined Marbofloxacin-Geraniol-Tris-EDTA Exposure Delays Marbofloxacin Resistance Escalation inAntibiotics (Basel, Switzerland) · 2026Article
- A genomic framework for tracking antibiotic resistance genes: global dissemination ofAntimicrobial agents and chemotherapy · 2026Article
- Genomic and functional characterization of Rhizobium metallidurans NS41, a heavy-metal-resistant, non-legume-associated endophyte that reduces oxidative stress in metal-exposed maize.Molecular genetics and genomics : MGG · 2026Article
- Contrasting Roles of Mobile Genetic Elements and Metal Resistance Genes in Shaping the Gut Resistome of Wild Fish from the Qiantang River.Animals : an open access journal from MDPI · 2026Article
- Metagenomic analysis reveals resistome characteristics and high-risk resistance genes in the pig nasal cavities, feces, and farm dust.Animal microbiome · 2026Article
- National genomic surveillance reveals global plasmid and chromosomal dissemination routes of blanpj antimicrobials and resistance · 2026Article
- Evidence for Genotype-Associated Differences in Disease Severity and Limitations of Serotype-Based Classification inPathogens (Basel, Switzerland) · 2026Article
- Experimental evolution under colistin selection increases colistin minimum inhibitory concentration (MIC) without detectable collateral MIC shifts in Escherichia coli ATCC 25922.Scientific reports · 2026Article
- Emerging Dissemination of blaMicrobiologyOpen · 2026Article
- Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.Infectious medicine · 2026Article
- Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Complete Genome of an Alkali-Resistant Rhizobium anhuiense Symbiont of Pea Reveals Species-Specific Plasmid Fusion and Genomic Plasticity.Environmental microbiology reports · 2026Article
- Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products.Antibiotics (Basel, Switzerland) · 2026Article
- Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms.Nature communications · 2026Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
236 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions.
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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.