{"id":"https://openalex.org/W3173385890","doi":"https://doi.org/10.1186/s12859-021-04270-w","title":"PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets","display_name":"PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets","publication_year":2021,"publication_date":"2021-06-26","ids":{"openalex":"https://openalex.org/W3173385890","doi":"https://doi.org/10.1186/s12859-021-04270-w","mag":"3173385890","pmid":"https://pubmed.ncbi.nlm.nih.gov/34174810"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04270-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04270-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04270-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04270-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011931659","display_name":"L\u00e9a Pradier","orcid":"https://orcid.org/0000-0002-1545-3585"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I208215962","display_name":"Universit\u00e9 Paul-Val\u00e9ry Montpellier","ror":"https://ror.org/00qhdy563","country_code":"FR","type":"education","lineage":["https://openalex.org/I208215962"]},{"id":"https://openalex.org/I4210089824","display_name":"Centre d'\u00c9cologie Fonctionnelle et \u00c9volutive","ror":"https://ror.org/008rywf59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210088668","https://openalex.org/I4210089824","https://openalex.org/I4210090127","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210117091","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4399657933","https://openalex.org/I4405257220","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"L\u00e9a Pradier","raw_affiliation_strings":["Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France. lea.pradier@cefe.cnrs.fr","Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France"],"raw_orcid":"https://orcid.org/0000-0002-1545-3585","affiliations":[{"raw_affiliation_string":"Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France. lea.pradier@cefe.cnrs.fr","institution_ids":["https://openalex.org/I159885104","https://openalex.org/I4210089824","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France","institution_ids":["https://openalex.org/I4210089824","https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I208215962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044582052","display_name":"Tazzio Tissot","orcid":"https://orcid.org/0000-0002-2035-8216"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]},{"id":"https://openalex.org/I4210122226","display_name":"Centre de Recerca Matem\u00e0tica","ror":"https://ror.org/020s51w82","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210122226","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Tazzio Tissot","raw_affiliation_strings":["Centre de Recerca Matem\u00e0tica, 08193, Cerdanyola del Vall\u00e8s, Spain","Genomics, Bioinformatics and Evolution. Departament de Gen\u00e8tica i Microbiologia, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre de Recerca Matem\u00e0tica, 08193, Cerdanyola del Vall\u00e8s, Spain","institution_ids":["https://openalex.org/I4210122226"]},{"raw_affiliation_string":"Genomics, Bioinformatics and Evolution. Departament de Gen\u00e8tica i Microbiologia, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088642653","display_name":"Anna-Sophie Fiston-Lavier","orcid":"https://orcid.org/0000-0002-7306-6532"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anna-Sophie Fiston-Lavier","raw_affiliation_strings":["Institut des Sciences de l'Evolution de Montpellier (ISE-M), Equipe Evolution, Vecteurs, Adaptation et Symbiose, UMR 5554, CNRS-Universit\u00e9 Montpellier, 34090, Montpellier Cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut des Sciences de l'Evolution de Montpellier (ISE-M), Equipe Evolution, Vecteurs, Adaptation et Symbiose, UMR 5554, CNRS-Universit\u00e9 Montpellier, 34090, Montpellier Cedex 05, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210105943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024965499","display_name":"St\u00e9phanie Bedhomme","orcid":"https://orcid.org/0000-0001-8075-0968"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I208215962","display_name":"Universit\u00e9 Paul-Val\u00e9ry Montpellier","ror":"https://ror.org/00qhdy563","country_code":"FR","type":"education","lineage":["https://openalex.org/I208215962"]},{"id":"https://openalex.org/I4210089824","display_name":"Centre d'\u00c9cologie Fonctionnelle et \u00c9volutive","ror":"https://ror.org/008rywf59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210088668","https://openalex.org/I4210089824","https://openalex.org/I4210090127","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210117091","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4399657933","https://openalex.org/I4405257220","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"St\u00e9phanie Bedhomme","raw_affiliation_strings":["Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France. stephanie.bedhomme@cefe.cnrs.fr","Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France. stephanie.bedhomme@cefe.cnrs.fr","institution_ids":["https://openalex.org/I4210089824","https://openalex.org/I159885104","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Universit\u00e9 de Montpellier, Universit\u00e9 Paul Val\u00e9ry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche Pour le D\u00e9veloppement, 34000, Montpellier, France","institution_ids":["https://openalex.org/I4210089824","https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I208215962"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5011931659","https://openalex.org/A5024965499"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I208215962","https://openalex.org/I4210089824"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.0126,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.92597043,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"22","issue":"1","first_page":"349","last_page":"349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.16660000383853912,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.16660000383853912,"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"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.15049999952316284,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.1200999990105629,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.9127849340438843},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.8464358448982239},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7177746295928955},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6846634149551392},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6626764535903931},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6164209246635437},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.612635612487793},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5861687064170837},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.5533865094184875},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.5027017593383789},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.4178480803966522},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35370832681655884},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.21726617217063904},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16991344094276428}],"concepts":[{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.9127849340438843},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8464358448982239},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7177746295928955},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6846634149551392},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6626764535903931},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6164209246635437},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.612635612487793},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5861687064170837},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.5533865094184875},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5027017593383789},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.4178480803966522},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35370832681655884},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.21726617217063904},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16991344094276428}],"mesh":[{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","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":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-021-04270-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04270-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04270-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34174810","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34174810","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-03421526v1","is_oa":true,"landing_page_url":"https://hal.science/hal-03421526","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ddd.uab.cat:247490","is_oa":true,"landing_page_url":"https://ddd.uab.cat/record/247490","pdf_url":null,"source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:12a908723de64bbfbcd0a8f8a95717ec","is_oa":true,"landing_page_url":"https://doaj.org/article/12a908723de64bbfbcd0a8f8a95717ec","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-17 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8236179","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8236179","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04270-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04270-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04270-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7599999904632568,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G6690816222","display_name":null,"funder_award_id":"ERC-2015-CoG-682819","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"}],"funders":[{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3173385890.pdf","grobid_xml":"https://content.openalex.org/works/W3173385890.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W38301456","https://openalex.org/W1604674059","https://openalex.org/W1970995838","https://openalex.org/W1989348205","https://openalex.org/W1997463836","https://openalex.org/W2014846709","https://openalex.org/W2033024573","https://openalex.org/W2043031449","https://openalex.org/W2104704801","https://openalex.org/W2114850508","https://openalex.org/W2119902463","https://openalex.org/W2123658138","https://openalex.org/W2140647036","https://openalex.org/W2142678478","https://openalex.org/W2143325926","https://openalex.org/W2282919575","https://openalex.org/W2620760558","https://openalex.org/W2738855940","https://openalex.org/W2782623083","https://openalex.org/W2796402930","https://openalex.org/W2883838322","https://openalex.org/W2912883243","https://openalex.org/W2942757983","https://openalex.org/W2949831026","https://openalex.org/W2977723904","https://openalex.org/W3014345701","https://openalex.org/W3104596207","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2330186985","https://openalex.org/W2950447380","https://openalex.org/W2055448750","https://openalex.org/W2345730070","https://openalex.org/W2107854630","https://openalex.org/W4319294554","https://openalex.org/W3134563641","https://openalex.org/W1986608492","https://openalex.org/W4394186879","https://openalex.org/W1973931558"],"abstract_inverted_index":{"BACKGROUND:":[0],"Plasmids":[1],"are":[2,12,75,86,183],"mobile":[3],"genetic":[4],"elements":[5],"that":[6,85],"often":[7],"carry":[8],"accessory":[9],"genes,":[10],"and":[11,32,39,74,91,147,174,192],"vectors":[13],"for":[14],"horizontal":[15],"transfer":[16],"between":[17],"bacterial":[18,103],"genomes.":[19,109],"Plasmid":[20],"detection":[21,201],"in":[22,36,41,82,106,202],"large":[23],"genomic":[24,168],"datasets":[25,169],"is":[26],"crucial":[27],"to":[28,50,79],"analyze":[29],"their":[30,34],"spread":[31],"quantify":[33],"role":[35],"bacteria":[37],"adaptation":[38],"particularly":[40],"antibiotic":[42],"resistance":[43],"propagation.":[44],"Bioinformatics":[45],"methods":[46,69],"have":[47],"been":[48],"developed":[49,95],"detect":[51,134],"plasmids.":[52],"However,":[53],"they":[54],"suffer":[55],"from":[56],"low":[57,65],"sensitivity":[58],"(i.e.,":[59,67],"most":[60],"plasmids":[61,81,122],"remain":[62],"undetected)":[63],"or":[64,123],"precision":[66],"these":[68],"identify":[70,80],"chromosomes":[71,124],"as":[72,121],"plasmids),":[73],"overall":[76],"not":[77,87],"adapted":[78],"whole":[83],"genomes":[84],"fully":[88],"assembled":[89,108],"(contigs":[90],"scaffolds).":[92],"RESULTS:":[93],"We":[94],"PlasForest,":[96],"a":[97,126],"homology-based":[98,196],"random":[99],"forest":[100],"classifier":[101],"identifying":[102],"plasmid":[104,137,150,200],"sequences":[105],"partially":[107],"Without":[110],"knowing":[111],"the":[112,116],"taxonomical":[113],"origin":[114],"of":[115,129,136,144,149,157,178,188],"samples,":[117],"PlasForest":[118,161,179],"identifies":[119],"contigs":[120,138,151],"with":[125,142,155],"F1":[127],"score":[128],"0.950.":[130],"Notably,":[131],"it":[132],"can":[133],"77.4%":[135],"below":[139,186],"1":[140],"kb":[141,154],"2.8%":[143],"false":[145,158],"positives":[146],"99.9%":[148],"over":[152],"50":[153],"2.2%":[156],"positives.":[159],"CONCLUSIONS:":[160],"outperforms":[162],"other":[163,189],"currently":[164,184],"available":[165],"tools":[166],"on":[167,180],"by":[170],"being":[171],"both":[172],"sensitive":[173],"precise.":[175],"The":[176],"performance":[177],"metagenomic":[181],"assemblies":[182],"well":[185],"those":[187],"k-mer-based":[190],"methods,":[191],"we":[193],"discuss":[194],"how":[195],"approaches":[197],"could":[198],"improve":[199],"such":[203],"datasets.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
