{"id":"https://openalex.org/W7161715923","doi":"https://doi.org/10.1093/bib/bbag240","title":"On using clustering statistics for assessing plasmid binning tools accuracy","display_name":"On using clustering statistics for assessing plasmid binning tools accuracy","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7161715923","doi":"https://doi.org/10.1093/bib/bbag240","pmid":"https://pubmed.ncbi.nlm.nih.gov/42153317"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag240","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag240","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064046379","display_name":"Victor Epain","orcid":"https://orcid.org/0000-0003-0049-0954"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Victor Epain","raw_affiliation_strings":["Department of Mathematics, Simon Fraser University , 8888 University Drive, Burnaby, V5A 1S6 BC ,"],"raw_orcid":"https://orcid.org/0000-0003-0049-0954","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Simon Fraser University , 8888 University Drive, Burnaby, V5A 1S6 BC ,","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136483785","display_name":"Aniket Mane","orcid":"https://orcid.org/0000-0002-0130-7149"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Aniket Mane","raw_affiliation_strings":["Department of Mathematics, Simon Fraser University , 8888 University Drive, Burnaby, V5A 1S6 BC ,"],"raw_orcid":"https://orcid.org/0000-0002-0130-7149","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Simon Fraser University , 8888 University Drive, Burnaby, V5A 1S6 BC ,","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063811688","display_name":"C\u00e9dric Chauve","orcid":"https://orcid.org/0000-0001-9837-1878"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Cedric Chauve","raw_affiliation_strings":["Department of Mathematics, Simon Fraser University , 8888 University Drive, Burnaby, V5A 1S6 BC ,"],"raw_orcid":"https://orcid.org/0000-0001-9837-1878","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Simon Fraser University , 8888 University Drive, Burnaby, V5A 1S6 BC ,","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063811688"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.39559823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11331","display_name":"Fecal contamination and water quality","score":0.20909999310970306,"subfield":{"id":"https://openalex.org/subfields/2312","display_name":"Water Science and Technology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11331","display_name":"Fecal contamination and water quality","score":0.20909999310970306,"subfield":{"id":"https://openalex.org/subfields/2312","display_name":"Water Science and Technology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12282","display_name":"Mineral Processing and Grinding","score":0.10649999976158142,"subfield":{"id":"https://openalex.org/subfields/2210","display_name":"Mechanical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12012","display_name":"Diatoms and Algae Research","score":0.04830000177025795,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8532000184059143},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.760200023651123},{"id":"https://openalex.org/keywords/homogeneity","display_name":"Homogeneity (statistics)","score":0.5339000225067139},{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.3456000089645386},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.31220000982284546}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8532000184059143},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.760200023651123},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6966000199317932},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5741999745368958},{"id":"https://openalex.org/C142259097","wikidata":"https://www.wikidata.org/wiki/Q5891314","display_name":"Homogeneity (statistics)","level":2,"score":0.5339000225067139},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34869998693466187},{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.3456000089645386},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.31220000982284546},{"id":"https://openalex.org/C67226441","wikidata":"https://www.wikidata.org/wiki/Q1665389","display_name":"Robust statistics","level":3,"score":0.273499995470047},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.25040000677108765}],"mesh":[{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbag240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag240","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42153317","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42153317","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:HAL:hal-05567472v1","is_oa":false,"landing_page_url":"https://hal.science/hal-05567472","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2026","raw_type":"info:eu-repo/semantics/preprint"},{"id":"pmh:oai:pubmedcentral.nih.gov:13184515","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13184515/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag240","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.4508059620857239}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":2,"referenced_works":["https://openalex.org/W4404722864","https://openalex.org/W4416137589"],"related_works":[],"abstract_inverted_index":{"We":[0],"discuss":[1],"the":[2,12,25],"drawbacks":[3],"of":[4,14],"using":[5],"homogeneity":[6],"and":[7,36],"completeness,":[8],"statistics":[9],"defined":[10],"for":[11,17,39],"evaluation":[13],"clustering":[15],"accuracy,":[16,22],"evaluating":[18],"plasmid":[19,34],"binning":[20],"tools":[21,38],"motivated":[23],"by":[24,45],"recently":[26],"published":[27],"paper":[28],"\"Circling":[29],"in":[30],"on":[31],"plasmids:":[32],"benchmarking":[33],"detection":[35],"reconstruction":[37],"short-read":[40],"data":[41],"from":[42],"diverse":[43],"species,\"":[44],"Teixeira":[46],"et":[47],"al.":[48]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-05-20T00:00:00"}
