{"id":"https://openalex.org/W2951563276","doi":"https://doi.org/10.1093/bioinformatics/btw493","title":"plasmidSPAdes: assembling plasmids from whole genome sequencing data","display_name":"plasmidSPAdes: assembling plasmids from whole genome sequencing data","publication_year":2016,"publication_date":"2016-07-27","ids":{"openalex":"https://openalex.org/W2951563276","doi":"https://doi.org/10.1093/bioinformatics/btw493","mag":"2951563276","pmid":"https://pubmed.ncbi.nlm.nih.gov/27466620"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3380/16920848/btw493.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3380/16920848/btw493.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024412068","display_name":"Dmitry Antipov","orcid":"https://orcid.org/0000-0002-6087-0660"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Dmitry Antipov","raw_affiliation_strings":["1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia"],"affiliations":[{"raw_affiliation_string":"1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia","institution_ids":["https://openalex.org/I172901346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045757015","display_name":"Nolan T. Hartwick","orcid":"https://orcid.org/0000-0001-7916-7791"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nolan Hartwick","raw_affiliation_strings":["2Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"2Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041272819","display_name":"Max W. Shen","orcid":"https://orcid.org/0000-0002-4226-1861"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Max Shen","raw_affiliation_strings":["3Bioinformatics and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"3Bioinformatics and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111116704","display_name":"Mikhail Raiko","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mikhail Raiko","raw_affiliation_strings":["2Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"2Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025927694","display_name":"Alla Lapidus","orcid":"https://orcid.org/0000-0003-0427-8731"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alla Lapidus","raw_affiliation_strings":["1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia"],"affiliations":[{"raw_affiliation_string":"1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia","institution_ids":["https://openalex.org/I172901346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027480961","display_name":"Pavel A. Pevzner","orcid":"https://orcid.org/0000-0002-0418-165X"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Pavel A. Pevzner","raw_affiliation_strings":["1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia","2Department of Computer Science and Engineering, University of California, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia","institution_ids":["https://openalex.org/I172901346"]},{"raw_affiliation_string":"2Department of Computer Science and Engineering, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5024412068"],"corresponding_institution_ids":["https://openalex.org/I172901346"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":29.6349,"has_fulltext":true,"cited_by_count":550,"citation_normalized_percentile":{"value":0.99777111,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"32","issue":"22","first_page":"3380","last_page":"3387"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9854000210762024,"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":0.8550410270690918},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7046928405761719},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6350084543228149},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.5413702726364136},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5068510174751282},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5041404962539673},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4798983335494995},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4616585671901703},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4482366442680359}],"concepts":[{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.8550410270690918},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7046928405761719},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6350084543228149},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.5413702726364136},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5068510174751282},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5041404962539673},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4798983335494995},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4616585671901703},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4482366442680359},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","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":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3380/16920848/btw493.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27466620","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27466620","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3380/16920848/btw493.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G7935490444","display_name":null,"funder_award_id":"15.61.951.2015","funder_id":"https://openalex.org/F4320322515","funder_display_name":"Saint Petersburg State University"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320322515","display_name":"Saint Petersburg State University","ror":"https://ror.org/023znxa73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951563276.pdf","grobid_xml":"https://content.openalex.org/works/W2951563276.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W313236425","https://openalex.org/W1593142205","https://openalex.org/W1927633768","https://openalex.org/W1969955142","https://openalex.org/W1973593256","https://openalex.org/W1989342781","https://openalex.org/W1996650392","https://openalex.org/W2004416209","https://openalex.org/W2004548026","https://openalex.org/W2017798220","https://openalex.org/W2058598212","https://openalex.org/W2096128575","https://openalex.org/W2099809434","https://openalex.org/W2107772251","https://openalex.org/W2120902911","https://openalex.org/W2124695620","https://openalex.org/W2141137078","https://openalex.org/W2143325926","https://openalex.org/W2162055898","https://openalex.org/W2191563170","https://openalex.org/W2341134505","https://openalex.org/W2735138488"],"related_works":["https://openalex.org/W4388965752","https://openalex.org/W2429129060","https://openalex.org/W2750385014","https://openalex.org/W2378211422","https://openalex.org/W2908588478","https://openalex.org/W2114870167","https://openalex.org/W2409844362","https://openalex.org/W2890718724","https://openalex.org/W1984664666","https://openalex.org/W2114174502"],"abstract_inverted_index":{"plasmidSPAdes":[0],"is":[1],"publicly":[2],"available":[3,12],"at":[4,13],"http://spades.bioinf.spbau.ru/plasmidSPAdes/":[5],"CONTACT:":[6],"d.antipov@spbu.ruSupplementary":[7],"information:":[8],"Supplementary":[9],"data":[10],"are":[11],"Bioinformatics":[14],"online.":[15]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":46},{"year":2024,"cited_by_count":45},{"year":2023,"cited_by_count":57},{"year":2022,"cited_by_count":58},{"year":2021,"cited_by_count":85},{"year":2020,"cited_by_count":74},{"year":2019,"cited_by_count":71},{"year":2018,"cited_by_count":54},{"year":2017,"cited_by_count":31},{"year":2016,"cited_by_count":14}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}