{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T08:01:40Z","timestamp":1775116900862,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2018,11,5]],"date-time":"2018-11-05T00:00:00Z","timestamp":1541376000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100003221","name":"Oneida Nation Foundation","doi-asserted-by":"publisher","award":["LISBOA-01\u20130145-FEDER-016417"],"award-info":[{"award-number":["LISBOA-01\u20130145-FEDER-016417"]}],"id":[{"id":"10.13039\/100003221","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,8]]},"DOI":"10.1093\/nar\/gky1073","type":"journal-article","created":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T19:19:00Z","timestamp":1539976740000},"page":"D188-D194","source":"Crossref","is-referenced-by-count":46,"title":["Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data"],"prefix":"10.1093","volume":"47","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8054-4136","authenticated-orcid":false,"given":"Tiago F","family":"Jesus","sequence":"first","affiliation":[{"name":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"}]},{"given":"Bruno","family":"Ribeiro-Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"}]},{"given":"Diogo N","family":"Silva","sequence":"additional","affiliation":[{"name":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"}]},{"given":"Valeria","family":"Bortolaia","sequence":"additional","affiliation":[{"name":"National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4084-6233","authenticated-orcid":false,"given":"M\u00e1rio","family":"Ramirez","sequence":"additional","affiliation":[{"name":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5274-2722","authenticated-orcid":false,"given":"Jo\u00e3o A","family":"Carri\u00e7o","sequence":"additional","affiliation":[{"name":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2018,11,5]]},"reference":[{"key":"key\n\t\t\t\t2019010803581368500_B1","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: the agents of open source evolution","volume":"3","author":"Frost","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"key\n\t\t\t\t2019010803581368500_B2","doi-asserted-by":"crossref","first-page":"242","DOI":"10.3389\/fmicb.2015.00242","article-title":"Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy","volume":"6","author":"Shintani","year":"2015","journal-title":"Front. Microbiol."},{"key":"key\n\t\t\t\t2019010803581368500_B3","doi-asserted-by":"crossref","first-page":"20160424","DOI":"10.1098\/rstb.2016.0424","article-title":"Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria","volume":"372","author":"Hall","year":"2017","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"key\n\t\t\t\t2019010803581368500_B4","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1128\/MMBR.00020-10","article-title":"Mobility of plasmids","volume":"74","author":"Smillie","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"key\n\t\t\t\t2019010803581368500_B5","doi-asserted-by":"crossref","first-page":"182","DOI":"10.3389\/fmicb.2017.00182","article-title":"Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology","volume":"8","author":"Orlek","year":"2017","journal-title":"Front. Microbiol."},{"key":"key\n\t\t\t\t2019010803581368500_B6","first-page":"e000128","article-title":"On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data","volume":"3","author":"Arredondo-Alonso","year":"2017","journal-title":"Microb. Genom."},{"key":"key\n\t\t\t\t2019010803581368500_B7","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1093\/bioinformatics\/btq299","article-title":"cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data","volume":"26","author":"Zhou","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581368500_B8","doi-asserted-by":"crossref","first-page":"e1004766","DOI":"10.1371\/journal.pgen.1004766","article-title":"Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences","volume":"10","author":"Lanza","year":"2014","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t2019010803581368500_B9","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1093\/bioinformatics\/btw493","article-title":"plasmidSPAdes: assembling plasmids from whole genome sequencing data","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581368500_B10","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1093\/bioinformatics\/btw651","article-title":"Recycler: an algorithm for detecting plasmids from de novo assembly graphs","volume":"33","author":"Rozov","year":"2017","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581368500_B11","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"key\n\t\t\t\t2019010803581368500_B12","first-page":"e000206","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"key\n\t\t\t\t2019010803581368500_B13","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581368500_B14","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581368500_B15","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581368500_B16","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"key\n\t\t\t\t2019010803581368500_B17","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581368500_B18","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010803581368500_B19","doi-asserted-by":"crossref","first-page":"D5","DOI":"10.1093\/nar\/gkn741","article-title":"Database resources of the National Center for Biotechnology Information","volume":"37","author":"Sayers","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581368500_B20","article-title":"Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates","author":"Laczny","year":"2017","journal-title":"Brief. Bioinform."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/D1\/D188\/27437338\/gky1073.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,6]],"date-time":"2023-09-06T05:49:59Z","timestamp":1693979399000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/D1\/D188\/5160973"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,5]]},"references-count":20,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2018,11,5]]},"published-print":{"date-parts":[[2019,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky1073","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1,8]]},"published":{"date-parts":[[2018,11,5]]}}}