{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T20:58:01Z","timestamp":1781729881284,"version":"3.54.5"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"vor","delay-in-days":47,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000016","name":"Department of Health and Human Services","doi-asserted-by":"publisher","award":["U19AI110818"],"award-info":[{"award-number":["U19AI110818"]}],"id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of California Irvine and the Broad Institute","award":["U19AI172725"],"award-info":[{"award-number":["U19AI172725"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>This response addresses the comments raised by Dr. Epain and colleagues in their Letter to the Editor titled \u2018On using clustering statistics for assessing plasmid binning tools accuracy\u2019 in response to our paper \u2018Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species\u2019. In their letter, the authors caution against using homogeneity and completeness measures to evaluate the accuracy of plasmid binning tools due to issues related to the length and content of contigs. They also refer to PlasEval, a plasmid binning evaluation tool that they recently developed. In response, we evaluated the impact of contig size and content on the results of our study, and also repeated the benchmarking of plasmid reconstruction tools using PlasEval. Though the absolute values of metrics differed across tests, we observed nearly identical rankings among plasmid reconstruction tools as originally reported in our study, with gplas2 outperforming all other tools. Nevertheless, approaches specifically designed for plasmid data may be better suited than clustering metrics to evaluate plasmid reconstruction.<\/jats:p>","DOI":"10.1093\/bib\/bbag317","type":"journal-article","created":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T11:47:52Z","timestamp":1779882472000},"source":"Crossref","is-referenced-by-count":0,"title":["Response to \u2018On using clustering statistics for assessing plasmid binning tools accuracy\u2019"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7219-0478","authenticated-orcid":false,"given":"Marco","family":"Teixeira","sequence":"first","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]},{"name":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628XE, Zuid Holland ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9132-7249","authenticated-orcid":false,"given":"Colin J","family":"Worby","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7205-7431","authenticated-orcid":false,"given":"Thomas","family":"Abeel","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]},{"name":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628XE, Zuid Holland ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7857-9145","authenticated-orcid":false,"given":"Ashlee M","family":"Earl","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3800-0714","authenticated-orcid":false,"given":"Abigail L","family":"Manson","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,17]]},"reference":[{"key":"2026061716444400400_ref1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaf589","article-title":"Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species","volume":"26","author":"Teixeira","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026061716444400400_ref3","doi-asserted-by":"publisher","first-page":"e14779","DOI":"10.7717\/peerj.14779","article-title":"Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering","volume":"11","author":"Nguyen","year":"2023","journal-title":"PeerJ"},{"key":"2026061716444400400_ref4","doi-asserted-by":"publisher","first-page":"102096","DOI":"10.1016\/j.artmed.2021.102096","article-title":"Evaluation of clustering and topic modeling methods over health-related tweets and emails","volume":"117","author":"Lossio-Ventura","year":"2021","journal-title":"Artif Intell Med"},{"key":"2026061716444400400_ref2","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1186\/s12859-024-05941-0","article-title":"Plaseval: a framework for comparing and evaluating plasmid detection tools","volume":"25","author":"Mane","year":"2024","journal-title":"BMC Bioinform"},{"key":"2026061716444400400_ref5","doi-asserted-by":"publisher","first-page":"4555","DOI":"10.1038\/s41467-024-48352-8","article-title":"The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages","volume":"15","author":"Wang","year":"2024","journal-title":"Nat Commun"},{"key":"2026061716444400400_ref6","doi-asserted-by":"publisher","first-page":"3841","DOI":"10.1016\/j.cub.2020.07.019","article-title":"Antibiotics interfere with the evolution of plasmid stability","volume":"30","author":"Wein","year":"2020","journal-title":"Curr Biol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/3\/bbag317\/68542056\/bbag317.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/3\/bbag317\/68542056\/bbag317.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T20:44:50Z","timestamp":1781729090000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag317\/8709878"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5]]},"references-count":6,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag317","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,5]]},"published":{"date-parts":[[2026,5]]},"article-number":"bbag317"}}