{"id":"https://openalex.org/W4416137589","doi":"https://doi.org/10.1093/bib/bbaf589","title":"Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species","display_name":"Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4416137589","doi":"https://doi.org/10.1093/bib/bbaf589","pmid":"https://pubmed.ncbi.nlm.nih.gov/41214871"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf589","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf589","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf589/65266503/bbaf589.pdf","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://academic.oup.com/bib/article-pdf/26/6/bbaf589/65266503/bbaf589.pdf","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 2628 XE, Zuid Holland ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, Zuid Holland, The Netherlands","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"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 2628 XE, 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"]},{"raw_affiliation_string":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, Zuid Holland, The Netherlands","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, United States","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083034206","display_name":"C\u00e9lia Souque","orcid":"https://orcid.org/0000-0001-7194-4322"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I2801543288","display_name":"Lemuel Shattuck Hospital","ror":"https://ror.org/01wpqwr25","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801543288"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C\u00e9lia Souque","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , 10 Shattuck St, Boston, MA 02115 ,","Laboratory of Systems Pharmacology, Harvard Medical School , 200 Longwood Ave, Boston, MA 02115 ,","Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, United States"],"raw_orcid":"https://orcid.org/0000-0001-7194-4322","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , 10 Shattuck St, Boston, MA 02115 ,","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I2801543288"]},{"raw_affiliation_string":"Laboratory of Systems Pharmacology, Harvard Medical School , 200 Longwood Ave, Boston, MA 02115 ,","institution_ids":["https://openalex.org/I4210155419"]},{"raw_affiliation_string":"Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, United States","institution_ids":["https://openalex.org/I4210155419"]}]},{"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 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006796623","display_name":"Terrance Shea","orcid":null},"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":"Terrance Shea","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"raw_orcid":null,"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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Nicoletta Commins","orcid":"https://orcid.org/0000-0002-0562-9735"},"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":"Nicoletta Commins","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"raw_orcid":"https://orcid.org/0000-0002-0562-9735","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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Joshua T Smith","orcid":"https://orcid.org/0000-0001-5511-8717"},"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":"Joshua T Smith","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"raw_orcid":"https://orcid.org/0000-0001-5511-8717","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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025561682","display_name":"Arjun M. Miklos","orcid":"https://orcid.org/0009-0000-9221-4556"},"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":"Arjun M Miklos","raw_affiliation_strings":["Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"raw_orcid":"https://orcid.org/0009-0000-9221-4556","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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","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 2628 XE, Zuid Holland ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, Zuid Holland, The Netherlands","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"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 2628 XE, 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"]},{"raw_affiliation_string":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft 2628 XE, Zuid Holland, The Netherlands","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, United States","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 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","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 ,","Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States"],"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"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St, Cambridge, MA 02142, United States","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"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":4.2772,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.95134965,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"26","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.3091000020503998,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.3091000020503998,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.24250000715255737,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.1379999965429306,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.955299973487854},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.8608999848365784},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5422000288963318},{"id":"https://openalex.org/keywords/enterobacteriaceae","display_name":"Enterobacteriaceae","score":0.4251999855041504},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.3912000060081482},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.3538999855518341},{"id":"https://openalex.org/keywords/virulence","display_name":"Virulence","score":0.33329999446868896}],"concepts":[{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.955299973487854},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8608999848365784},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6157000064849854},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5591999888420105},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5422000288963318},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5133000016212463},{"id":"https://openalex.org/C2778910516","wikidata":"https://www.wikidata.org/wiki/Q380136","display_name":"Enterobacteriaceae","level":4,"score":0.4251999855041504},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.3912000060081482},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.3538999855518341},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.33329999446868896},{"id":"https://openalex.org/C2889275","wikidata":"https://www.wikidata.org/wiki/Q7316313","display_name":"Restriction digest","level":4,"score":0.3230000138282776},{"id":"https://openalex.org/C80343103","wikidata":"https://www.wikidata.org/wiki/Q7667796","display_name":"T-DNA Binary system","level":5,"score":0.31790000200271606},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.29840001463890076},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.28060001134872437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27300000190734863},{"id":"https://openalex.org/C40767141","wikidata":"https://www.wikidata.org/wiki/Q285697","display_name":"Recombinant DNA","level":3,"score":0.2651999890804291},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2644999921321869},{"id":"https://openalex.org/C128319531","wikidata":"https://www.wikidata.org/wiki/Q219715","display_name":"Restriction enzyme","level":3,"score":0.25440001487731934}],"mesh":[{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016983","descriptor_name":"Enterococcus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016983","descriptor_name":"Enterococcus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016983","descriptor_name":"Enterococcus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016983","descriptor_name":"Enterococcus","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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},{"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},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf589","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf589","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf589/65266503/bbaf589.pdf","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:41214871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41214871","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":null},{"id":"pmh:oai:europepmc.org:11410649","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12602193","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf589","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf589","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf589/65266503/bbaf589.pdf","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":[],"awards":[{"id":"https://openalex.org/G10969003","display_name":null,"funder_award_id":"U19 AI110818","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5307995909","display_name":null,"funder_award_id":"U19 AI172725","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"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"},{"id":"https://openalex.org/G8323817331","display_name":null,"funder_award_id":"R35 GM133700","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"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/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4416137589.pdf"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W313236425","https://openalex.org/W1982855075","https://openalex.org/W1999979510","https://openalex.org/W2055043387","https://openalex.org/W2119902463","https://openalex.org/W2128964206","https://openalex.org/W2131681506","https://openalex.org/W2143325926","https://openalex.org/W2149452073","https://openalex.org/W2401005551","https://openalex.org/W2579703015","https://openalex.org/W2784788330","https://openalex.org/W2805609941","https://openalex.org/W2883838322","https://openalex.org/W2893355352","https://openalex.org/W2942757983","https://openalex.org/W2945501761","https://openalex.org/W2950530458","https://openalex.org/W2951160681","https://openalex.org/W2951254987","https://openalex.org/W2951325968","https://openalex.org/W2951563276","https://openalex.org/W2952167528","https://openalex.org/W2987650093","https://openalex.org/W3003395627","https://openalex.org/W3008821393","https://openalex.org/W3014345701","https://openalex.org/W3037415594","https://openalex.org/W3043497582","https://openalex.org/W3048606227","https://openalex.org/W3117016494","https://openalex.org/W3141815669","https://openalex.org/W3173711206","https://openalex.org/W3179720352","https://openalex.org/W3194892958","https://openalex.org/W3196145281","https://openalex.org/W3199421355","https://openalex.org/W3209528471","https://openalex.org/W3214798457","https://openalex.org/W3214956918","https://openalex.org/W3215940488","https://openalex.org/W4221044588","https://openalex.org/W4226064126","https://openalex.org/W4255659575","https://openalex.org/W4306871314","https://openalex.org/W4376641675","https://openalex.org/W4378071169","https://openalex.org/W4382631507","https://openalex.org/W4383709533","https://openalex.org/W4383816978","https://openalex.org/W4386923826","https://openalex.org/W4387402854","https://openalex.org/W4390904364","https://openalex.org/W4391519057","https://openalex.org/W4391986951","https://openalex.org/W4392231323","https://openalex.org/W4393114531","https://openalex.org/W4399139567","https://openalex.org/W4400007690","https://openalex.org/W4403393008","https://openalex.org/W4404722864","https://openalex.org/W4408540876"],"related_works":[],"abstract_inverted_index":{"The":[0,158],"ability":[1,112],"to":[2,51,113],"detect":[3],"and":[4,16,21,96,126,132,143,156],"reconstruct":[5],"plasmids":[6,32,116,172,202],"from":[7,47,104,117,137,179],"genome":[8,39],"assemblies":[9,40,80,119],"is":[10],"crucial":[11],"for":[12,153,187,194,210],"studying":[13],"the":[14,37,42,105,146],"evolution":[15],"spread":[17],"of":[18,36,67,124,162,201,216],"antimicrobial":[19],"resistance":[20],"virulence":[22],"in":[23,41,64,94,168,213],"bacteria.":[24],"Though":[25],"long-read":[26],"sequencing":[27],"technologies":[28],"have":[29],"made":[30],"reconstructing":[31],"easier,":[33],"most":[34],"(97%)":[35],"bacterial":[38],"public":[43],"domain":[44],"are":[45],"generated":[46],"short-read":[48,118],"data.":[49],"Work":[50],"compare":[52],"plasmid":[53,87,92,98,107,148,164,169,189,195],"reconstruction":[54,99],"tools":[55,71,89,100],"has":[56],"focused":[57],"primarily":[58],"on":[59,73],"Escherichia":[60],"coli,":[61],"leaving":[62],"gaps":[63],"our":[65],"understanding":[66],"how":[68],"well":[69,152],"these":[70],"perform":[72],"other,":[74],"less":[75,198],"well-characterized,":[76],"taxa.":[77],"Using":[78],"high-quality":[79],"as":[81],"ground":[82],"truth,":[83],"we":[84],"benchmarked":[85],"12":[86],"detection":[88,149,165],"(which":[90,101],"identify":[91],"contigs":[93,103],"assemblies)":[95],"four":[97],"group":[102],"same":[106],"together).":[108],"We":[109],"tested":[110],"their":[111],"characterize":[114],"diverse":[115],"representing":[120],"a":[121],"wide":[122],"range":[123],"Enterobacterales":[125,155,171],"Enterococcus":[127],"species,":[128],"including":[129],"newly":[130],"discovered":[131],"poorly":[133],"characterized":[134],"species":[135],"collected":[136],"nonhuman":[138],"hosts.":[139],"Plasmer,":[140],"PlasmidEC,":[141],"PlaScope,":[142],"gplas2":[144],"were":[145,166,203],"highest-scoring":[147],"tools,":[150],"performing":[151],"both":[154],"enterococci.":[157],"two":[159],"major":[160],"determinants":[161],"accurate":[163],"representation":[167],"databases-with":[170],"being":[173],"more":[174],"easily":[175],"detected":[176],"than":[177,199],"those":[178],"enterococci-and":[180],"assembly":[181],"contiguity,":[182],"which":[183],"was":[184],"also":[185],"key":[186],"successful":[188],"reconstruction.":[190],"Gplas2":[191],"performed":[192],"best":[193],"reconstruction;":[196],"however,":[197],"half":[200],"perfectly":[204],"reconstructed,":[205],"suggesting":[206],"that":[207],"substantial":[208],"room":[209],"improvement":[211],"remains":[212],"this":[214],"class":[215],"tools.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":6}],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2025-11-11T00:00:00"}
