{"id":"https://openalex.org/W7165018443","doi":"https://doi.org/10.1093/bib/bbag317","title":"Response to \u2018On using clustering statistics for assessing plasmid binning tools accuracy\u2019","display_name":"Response to \u2018On using clustering statistics for assessing plasmid binning tools accuracy\u2019","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7165018443","doi":"https://doi.org/10.1093/bib/bbag317","pmid":"https://pubmed.ncbi.nlm.nih.gov/42308417"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag317","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":null,"license_id":null,"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/bbag317","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102811871","display_name":"Marco Teixeira","orcid":"https://orcid.org/0000-0002-7219-0478"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Marco Teixeira","raw_affiliation_strings":["Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628XE, Zuid Holland ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,"],"raw_orcid":"https://orcid.org/0000-0002-7219-0478","affiliations":[{"raw_affiliation_string":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628XE, Zuid Holland ,","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012355338","display_name":"Colin J. Worby","orcid":"https://orcid.org/0000-0002-9132-7249"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin J Worby","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,"],"raw_orcid":"https://orcid.org/0000-0002-9132-7249","affiliations":[{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002088014","display_name":"Thomas Abeel","orcid":"https://orcid.org/0000-0002-7205-7431"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Thomas Abeel","raw_affiliation_strings":["Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628XE, Zuid Holland ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,"],"raw_orcid":"https://orcid.org/0000-0002-7205-7431","affiliations":[{"raw_affiliation_string":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628XE, Zuid Holland ,","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079515502","display_name":"Ashlee M. Earl","orcid":"https://orcid.org/0000-0001-7857-9145"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashlee M Earl","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,"],"raw_orcid":"https://orcid.org/0000-0001-7857-9145","affiliations":[{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088129247","display_name":"Abigail L. Manson","orcid":"https://orcid.org/0000-0002-3800-0714"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abigail L Manson","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,"],"raw_orcid":"https://orcid.org/0000-0002-3800-0714","affiliations":[{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.6248676,"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":0.25780001282691956,"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":0.25780001282691956,"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/T10753","display_name":"Microplastics and Plastic Pollution","score":0.0989999994635582,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"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":0.0925000011920929,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8450000286102295},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.767799973487854},{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.6766999959945679},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.6362000107765198},{"id":"https://openalex.org/keywords/homogeneity","display_name":"Homogeneity (statistics)","score":0.40220001339912415}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8450000286102295},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.767799973487854},{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.6766999959945679},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6608999967575073},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.6362000107765198},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46070000529289246},{"id":"https://openalex.org/C142259097","wikidata":"https://www.wikidata.org/wiki/Q5891314","display_name":"Homogeneity (statistics)","level":2,"score":0.40220001339912415},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.30809998512268066},{"id":"https://openalex.org/C2989134064","wikidata":"https://www.wikidata.org/wiki/Q288510","display_name":"Execution time","level":2,"score":0.3068000078201294},{"id":"https://openalex.org/C17231256","wikidata":"https://www.wikidata.org/wiki/Q5156540","display_name":"Completeness (order theory)","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28999999165534973},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.27900001406669617},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2736000120639801},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2549999952316284}],"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag317","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42308417","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42308417","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:pubmedcentral.nih.gov:13275021","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13275021/","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/bbag317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag317","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7149703821","display_name":null,"funder_award_id":"U19AI110818","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W3048606227","https://openalex.org/W3157575185","https://openalex.org/W4319599390","https://openalex.org/W4399139567","https://openalex.org/W4404722864","https://openalex.org/W4416137589"],"related_works":[],"abstract_inverted_index":{"This":[0],"response":[1,29],"addresses":[2],"the":[3,15,52,63,74,98,106,114,123],"comments":[4],"raised":[5],"by":[6],"Dr.":[7],"Epain":[8],"and":[9,40,58,76,103,111],"colleagues":[10],"in":[11,28,34,143],"their":[12,50],"Letter":[13],"to":[14,30,61,70,73,83,166],"Editor":[16],"titled":[17],"'On":[18],"using":[19,56,120],"clustering":[20,164],"statistics":[21],"for":[22,43,156],"assessing":[23],"plasmid":[24,38,66,86,117,137,157,168],"binning":[25,67,87],"tools":[26,42,68,119,139],"accuracy'":[27],"our":[31,109,144],"paper":[32],"'Circling":[33],"on":[35,105],"plasmids:":[36],"benchmarking":[37,115],"detection":[39],"reconstruction":[41,118,138],"short-read":[44],"data":[45,158],"from":[46],"diverse":[47],"species'.":[48],"In":[49,94],"letter,":[51],"authors":[53],"caution":[54],"against":[55],"homogeneity":[57],"completeness":[59],"measures":[60],"evaluate":[62,167],"accuracy":[64],"of":[65,78,100,108,116,126],"due":[69],"issues":[71],"related":[72],"length":[75],"content":[77,104],"contigs.":[79],"They":[80],"also":[81,112],"refer":[82],"PlasEval,":[84],"a":[85],"evaluation":[88],"tool":[89],"that":[90],"they":[91],"recently":[92],"developed.":[93],"response,":[95],"we":[96,131],"evaluated":[97],"impact":[99],"contig":[101],"size":[102],"results":[107],"study,":[110,145],"repeated":[113],"PlasEval.":[121],"Though":[122],"absolute":[124],"values":[125],"metrics":[127,165],"differed":[128],"across":[129],"tests,":[130],"observed":[132],"nearly":[133],"identical":[134],"rankings":[135],"among":[136],"as":[140],"originally":[141],"reported":[142],"with":[146],"gplas2":[147],"outperforming":[148],"all":[149],"other":[150],"tools.":[151],"Nevertheless,":[152],"approaches":[153],"specifically":[154],"designed":[155],"may":[159],"be":[160],"better":[161],"suited":[162],"than":[163],"reconstruction.":[169]},"counts_by_year":[],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2026-06-18T00:00:00"}
