{"id":"https://openalex.org/W4413050685","doi":"https://doi.org/10.3233/shti251083","title":"Plasmidity: A Novel Pipeline for Plasmid Sequence Prediction","display_name":"Plasmidity: A Novel Pipeline for Plasmid Sequence Prediction","publication_year":2025,"publication_date":"2025-08-07","ids":{"openalex":"https://openalex.org/W4413050685","doi":"https://doi.org/10.3233/shti251083","pmid":"https://pubmed.ncbi.nlm.nih.gov/40776101"},"language":"en","primary_location":{"id":"doi:10.3233/shti251083","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti251083","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.3233/shti251083","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013458454","display_name":"Rosal\u00eda Palomino\u2010Cabrera","orcid":"https://orcid.org/0000-0002-6423-4821"},"institutions":[{"id":"https://openalex.org/I4210113075","display_name":"Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla","ror":"https://ror.org/025gxrt12","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210113075"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Rosalia Palomino-Cabrera","raw_affiliation_strings":["Servicio de Microbiolog\u00eda H. U. Marqu\u00e9s de Valdecilla \u2013 IDIVAL, Santander, Spain","Servicio de Microbiolog\u00eda H. U. Marqu\u00e9s de Valdecilla - IDIVAL, Santander, Spain"],"raw_orcid":"https://orcid.org/0000-0002-6423-4821","affiliations":[{"raw_affiliation_string":"Servicio de Microbiolog\u00eda H. U. Marqu\u00e9s de Valdecilla \u2013 IDIVAL, Santander, Spain","institution_ids":["https://openalex.org/I4210113075"]},{"raw_affiliation_string":"Servicio de Microbiolog\u00eda H. U. Marqu\u00e9s de Valdecilla - IDIVAL, Santander, Spain","institution_ids":["https://openalex.org/I4210113075"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089697393","display_name":"Inmaculada Garc\u00eda\u2010Romero","orcid":"https://orcid.org/0000-0002-8939-3271"},"institutions":[{"id":"https://openalex.org/I4210111405","display_name":"Centro Andaluz de Biolog\u00eda del Desarrollo","ror":"https://ror.org/01v5e3436","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210111405","https://openalex.org/I918821925","https://openalex.org/I95013407"]},{"id":"https://openalex.org/I95013407","display_name":"Universidad Pablo de Olavide","ror":"https://ror.org/02z749649","country_code":"ES","type":"education","lineage":["https://openalex.org/I95013407"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Inmaculada Garcia Romero","raw_affiliation_strings":["Centro Andaluz de Biolog\u00eda del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain"],"raw_orcid":"https://orcid.org/0000-0002-8939-3271","affiliations":[{"raw_affiliation_string":"Centro Andaluz de Biolog\u00eda del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain","institution_ids":["https://openalex.org/I4210111405","https://openalex.org/I95013407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041019879","display_name":"Miguel A. Valvano","orcid":"https://orcid.org/0000-0001-8229-3641"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Miguel A. Valvano","raw_affiliation_strings":["Wellcome-Wolfson Institute for Experimental Medicine, Queen\u2019s University Belfast, Belfast, UK","Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK"],"raw_orcid":"https://orcid.org/0000-0001-8229-3641","affiliations":[{"raw_affiliation_string":"Wellcome-Wolfson Institute for Experimental Medicine, Queen\u2019s University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]},{"raw_affiliation_string":"Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001595112","display_name":"Guillermo L\u00f3pez\u2013Campos","orcid":"https://orcid.org/0000-0003-3011-0940"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Guillermo H. Lopez-Campos","raw_affiliation_strings":["Wellcome-Wolfson Institute for Experimental Medicine, Queen\u2019s University Belfast, Belfast, UK","Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK"],"raw_orcid":"https://orcid.org/0000-0003-3011-0940","affiliations":[{"raw_affiliation_string":"Wellcome-Wolfson Institute for Experimental Medicine, Queen\u2019s University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]},{"raw_affiliation_string":"Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34212108,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"329","issue":null,"first_page":"1472","last_page":"1476"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9855999946594238,"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":0.9855999946594238,"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/contig","display_name":"Contig","score":0.8557318449020386},{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.7094482183456421},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.525871992111206},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5248311161994934},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4666125178337097},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4434102475643158},{"id":"https://openalex.org/keywords/gradient-boosting","display_name":"Gradient boosting","score":0.4400142729282379},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4351109564304352},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.37883538007736206},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3666366934776306},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21171924471855164},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.16820693016052246}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8557318449020386},{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.7094482183456421},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.525871992111206},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5248311161994934},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4666125178337097},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4434102475643158},{"id":"https://openalex.org/C70153297","wikidata":"https://www.wikidata.org/wiki/Q5591907","display_name":"Gradient boosting","level":3,"score":0.4400142729282379},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4351109564304352},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37883538007736206},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3666366934776306},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21171924471855164},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.16820693016052246},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.3233/shti251083","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti251083","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:40776101","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40776101","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":"Studies in health technology and informatics","raw_type":null},{"id":"pmh:oai:pure.qub.ac.uk/portal:openaire/805e7188-b565-4176-a446-9c492fd7e50a","is_oa":false,"landing_page_url":"https://pure.qub.ac.uk/en/publications/805e7188-b565-4176-a446-9c492fd7e50a","pdf_url":null,"source":{"id":"https://openalex.org/S4306402319","display_name":"Research Portal (Queen's University Belfast)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126231945","host_organization_name":"Queen's University Belfast","host_organization_lineage":["https://openalex.org/I126231945"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Palomino-Cabrera, R, Garcia Romero, I, Valvano, M A & Lopez-Campos, G H 2025, 'Plasmidity: a novel pipeline for plasmid sequence prediction', Studies in health technology and informatics, vol. 329, pp. 1472-1476. https://doi.org/10.3233/SHTI251083","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:digital.csic.es:10261/422422","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/422422","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.3233/shti251083","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti251083","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1994449010","https://openalex.org/W2074936491","https://openalex.org/W2069489638","https://openalex.org/W4242258765","https://openalex.org/W2044103084","https://openalex.org/W1545755951","https://openalex.org/W2162517701","https://openalex.org/W140544075","https://openalex.org/W2043343084","https://openalex.org/W2360829643"],"abstract_inverted_index":{"We":[0],"have":[1],"built":[2],"PLASMIDITY,":[3],"an":[4,90],"automated":[5],"pipeline":[6],"to":[7],"assemble":[8],"short":[9],"reads":[10,56],"and":[11,50],"characterize":[12],"contigs":[13],"searching":[14],"for":[15,19],"biologically":[16],"relevant":[17],"features":[18],"plasmid":[20,39,48,86],"sequences":[21],"detection":[22],"applying":[23],"machine":[24],"learning":[25],"methods,":[26],"including":[27],"contig":[28],"length,":[29],"multiplicity,":[30],"circularity,":[31],"insertion":[32],"sequence":[33],"composition,":[34],"chromosome":[35],"markers":[36,40],"(rRNA,":[37],"tRNA),":[38],"(OriV,":[41],"Rep,":[42],"Mob/Rlx),":[43],"G+C%":[44],"variation,":[45],"similarity":[46],"with":[47],"references,":[49],"k-mer":[51],"profile.":[52],"Using":[53],"simulated":[54],"WGS":[55],"from":[57],"200":[58],"taxonomically":[59],"diverse":[60],"samples,":[61],"we":[62],"trained":[63],"two":[64],"Gradient":[65],"Boosting":[66],"classifiers,":[67],"achieving":[68],"a":[69],"maximum":[70],"F1":[71],"score":[72],"of":[73,81],"0.901":[74],"in":[75,92],"the":[76,82,93],"test":[77],"dataset.":[78],"The":[79],"comparison":[80],"models":[83],"against":[84],"other":[85],"prediction":[87],"tools":[88],"shows":[89],"improvement":[91],"outcomes.":[94]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
