{"doi":"10.1099/mgen.0.001290","title":"Towards quantifying plasmid similarity","abstract":"<jats:p>Plasmids are extrachromosomal replicons which can quickly spread resistance and virulence genes between clinical pathogens. From the tens of thousands of currently available plasmid sequences we know that overall plasmid diversity is structured, with related plasmids sharing a largely conserved ‘backbone’ of genes while being able to carry very different genetic cargo. Moreover, plasmid genomes can be structurally plastic and undergo frequent rearrangements. So, how can we quantify plasmid similarity? Answering this question requires practical efforts to sample natural variation as well as theoretical considerations of what defines a group of related plasmids. Here we consider the challenges of analysing and rationalising the current plasmid data deluge to define appropriate similarity thresholds.</jats:p>","journal":"Microbial Genomics","year":2024,"id":613424,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":305630,"name":"Liam P. 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So, how can we quantify plasmid similarity? Answering this question requires practical efforts to sample natural variation as well as theoretical considerations of what defines a group of related plasmids. Here we consider the challenges of analysing and rationalising the current plasmid data deluge to define appropriate similarity thresholds.</jats:p>","is_dataset_classified":null,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39264704","pmcid":"PMC11392043","openalex_id":"https://openalex.org/W4402478765","authors":[],"funders":[{"funder_name":"National Institute for Health Research Health Protection Research Unit","grant_id":"NIHR200915","title":null},{"funder_name":"Wellcome Trust","grant_id":"220422/Z/20/Z","title":null},{"funder_name":"Wellcome Trust","grant_id":"220422","title":"The evolution of mobile genetic elements in Gram-negative bacteria"},{"funder_name":"Wellcome Trust","grant_id":"","title":null}],"total_grants":4,"fwci":3.2282,"citation_percentile":0.91395646,"influential_citations":0,"citation_trend":[{"year":2025,"count":5},{"year":2026,"count":2}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1099/mgen.0.001290","host_type":"journal"},{"url":"https://doi.org/10.1099/mgen.0.001290","host_type":"publisher"},{"url":"https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001290?crawler=true&mimetype=application/pdf","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39264704","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11392043","host_type":"repository"},{"url":"https://ora.ox.ac.uk/objects/uuid:044b4d0a-93e5-41f5-89c0-98b097cc68e1","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11392043/pdf/mgen-10-01290.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11392043","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11392043?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1099/mgen.0.001290","host_type":""}],"fields_of_study":["Plant Pathogenic Bacteria Studies","Genomics and Phylogenetic Studies","Antibiotic Resistance in Bacteria","0301 basic medicine","03 medical and health sciences"],"mesh_terms":["Bacteria","Phylogeny","Plasmids","Genetic Variation"],"keywords":["Plasmid","Replicon","Extrachromosomal DNA","Biology","Genetics","Genome","Similarity (geometry)","Gene","Computational biology","Virulence","Computer science","Artificial intelligence","Antimicrobial resistance","Mobile genetic elements","Genomic Epidemiology","Bacteria","Genetic Variation","Pathogens and Epidemiology","Phylogeny","Plasmids"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T08:03:14.736749Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}