ArticleDatabase : the journal of biological databases and curation2017
FARME DB: a functional antibiotic resistance element database.
Article in Database : the journal of biological databases and curation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems.Briefings in bioinformatics · 2026Pooled it
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Targeting Horizontal Gene Transfer to Combat Antimicrobial Resistance: A Review of Mechanisms, Drivers, and Multi-Omics Strategies.Infection and drug resistance · 2026Review
- Dental devices and antimicrobial resistance: challenges, innovations, and regulatory compliances.Frontiers in medical technology · 2026Review
- ProtAlign-ARG: antibiotic resistance gene characterization integrating protein language models and alignment-based scoring.Scientific reports · 2025Article
- DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.Microbiome · 2025Article
- Mitigating Health Risks Through Environmental Tracking of Pseudomonas aeruginosa.Current microbiology · 2024Review
- What role do biocontrol agents with MgmSystems · 2024Article
- ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics.Nucleic acids research · 2023Article
- Antibiotic resistance genes are differentially mobilized according to resistance mechanism.GigaScience · 2022Article
- Review and Comparison of Antimicrobial Resistance Gene Databases.Antibiotics (Basel, Switzerland) · 2022Review
- Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.Frontiers in microbiology · 2022Review
- Text mining for identification of biological entities related to antibiotic resistant organisms.PeerJ · 2022Article
- Phylum barrier andMicrobial genomics · 2021Article
- Interkingdom Gut Microbiome and Resistome of the CockroachmSystems · 2021Article
- Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria.Cellular and molecular life sciences : CMLS · 2021Review
- Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data.Journal of microbiology (Seoul, Korea) · 2021Review
- Microbial retention and resistances in stormwater quality improvement devices treating road runoff.FEMS microbes · 2021Article
- The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health.MicrobiologyOpen · 2020Review
- CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.Nucleic acids research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates.Database URL: http://staff.washington.edu/jwallace/farme.
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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.