{"id":"https://openalex.org/W2977608376","doi":"https://doi.org/10.1093/bioinformatics/btz735","title":"simurg: simulate bacterial pangenomes in R","display_name":"simurg: simulate bacterial pangenomes in R","publication_year":2019,"publication_date":"2019-09-26","ids":{"openalex":"https://openalex.org/W2977608376","doi":"https://doi.org/10.1093/bioinformatics/btz735","mag":"2977608376","pmid":"https://pubmed.ncbi.nlm.nih.gov/31584605"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz735","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz735","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031983257","display_name":"Ignacio Ferr\u00e9s","orcid":"https://orcid.org/0000-0003-0910-6568"},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":true,"raw_author_name":"Ignacio Ferr\u00e9s","raw_affiliation_strings":["Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay","institution_ids":["https://openalex.org/I4210156231"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033768950","display_name":"Pablo Fresia","orcid":"https://orcid.org/0000-0002-8465-476X"},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":false,"raw_author_name":"Pablo Fresia","raw_affiliation_strings":["Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay","Unidad Mixta UMPI, Institut Pasteur Montevideo + INIA , Montevideo 11400, Uruguay"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay","institution_ids":["https://openalex.org/I4210156231"]},{"raw_affiliation_string":"Unidad Mixta UMPI, Institut Pasteur Montevideo + INIA , Montevideo 11400, Uruguay","institution_ids":["https://openalex.org/I4210156231"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084062750","display_name":"Gregorio Iraola","orcid":"https://orcid.org/0000-0002-6516-3404"},"institutions":[{"id":"https://openalex.org/I116419501","display_name":"Universidad Mayor","ror":"https://ror.org/00pn44t17","country_code":"CL","type":"education","lineage":["https://openalex.org/I116419501"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["CL","GB","UY"],"is_corresponding":true,"raw_author_name":"Gregorio Iraola","raw_affiliation_strings":["Center for Integrative Biology, Universidad Mayor , Santiago de Chile 7510041, Chile","Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay","Wellcome Sanger Institute , Hinxton CB10 1SA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Integrative Biology, Universidad Mayor , Santiago de Chile 7510041, Chile","institution_ids":["https://openalex.org/I116419501"]},{"raw_affiliation_string":"Microbial Genomics Laboratory, Institut Pasteur Montevideo , Uruguay","institution_ids":["https://openalex.org/I4210156231"]},{"raw_affiliation_string":"Wellcome Sanger Institute , Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5031983257","https://openalex.org/A5084062750"],"corresponding_institution_ids":["https://openalex.org/I116419501","https://openalex.org/I2802476451","https://openalex.org/I4210156231"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4143,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.61516855,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"36","issue":"4","first_page":"1273","last_page":"1274"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6299999952316284,"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":0.6299999952316284,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.12020000070333481,"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/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.03629999980330467,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8347800970077515},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7527090907096863},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5876034498214722},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.58035808801651},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5294382572174072},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.5217528939247131},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48227623105049133},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46989700198173523},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.43846654891967773},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4298970103263855},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.38694894313812256},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37792086601257324},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3610023856163025},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31650295853614807},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31215476989746094},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22016751766204834},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19380289316177368}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8347800970077515},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7527090907096863},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5876034498214722},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.58035808801651},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5294382572174072},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5217528939247131},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48227623105049133},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46989700198173523},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.43846654891967773},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4298970103263855},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.38694894313812256},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37792086601257324},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3610023856163025},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31650295853614807},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31215476989746094},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22016751766204834},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19380289316177368},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz735","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz735","pdf_url":null,"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:31584605","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31584605","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2422602140","display_name":null,"funder_award_id":"POS_NAC_2018_1_151494","funder_id":"https://openalex.org/F4320310753","funder_display_name":"Agencia Nacional de Investigaci\u00f3n e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320310753","display_name":"Agencia Nacional de Investigaci\u00f3n e Innovaci\u00f3n","ror":"https://ror.org/03egaj678"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W197896231","https://openalex.org/W1908991493","https://openalex.org/W2041267682","https://openalex.org/W2091328482","https://openalex.org/W2117801354","https://openalex.org/W2122673596","https://openalex.org/W2145369404","https://openalex.org/W2150550043","https://openalex.org/W2151409320","https://openalex.org/W2172179959","https://openalex.org/W2227690683","https://openalex.org/W2243973145","https://openalex.org/W2765684905","https://openalex.org/W2782426614","https://openalex.org/W2803257421","https://openalex.org/W2949102320","https://openalex.org/W4235243453"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W4384009753","https://openalex.org/W4292228088","https://openalex.org/W3080200277","https://openalex.org/W3081674575","https://openalex.org/W4287673983"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,105],"pangenome":[2,38,96],"concept":[3],"describes":[4],"genetic":[5],"variability":[6,39],"as":[7,66],"the":[8,20,77,111],"union":[9],"of":[10,16,26,34,62,82,95],"genes":[11],"shared":[12],"in":[13],"a":[14,32,90],"set":[15],"genomes":[17],"and":[18,40,71,79,114],"constitutes":[19],"current":[21],"paradigm":[22],"for":[23,93,118],"comparative":[24],"analysis":[25],"bacterial":[27,57,83],"populations.":[28],"However,":[29],"there":[30],"is":[31,108,115],"lack":[33],"tools":[35],"to":[36,55],"simulate":[37,56],"structure":[41],"using":[42,59,85],"defined":[43],"evolutionary":[44,63,100],"models.":[45],"RESULTS:":[46],"We":[47],"developed":[48],"simurg,":[49],"an":[50],"R":[51],"package":[52,107],"that":[53],"allows":[54,76],"pangenomes":[58,84],"different":[60],"combinations":[61],"constraints":[64],"such":[65],"gene":[67,69],"gain,":[68],"loss":[70],"mutation":[72],"rates.":[73],"Our":[74],"tool":[75,92],"straightforward":[78],"reproducible":[80],"simulation":[81],"real":[86],"sequence":[87],"data,":[88],"providing":[89],"valuable":[91],"benchmarking":[94],"software":[97],"or":[98],"comparing":[99],"hypotheses.":[101],"AVAILABILITY":[102],"AND":[103],"IMPLEMENTATION:":[104],"simurg":[106],"released":[109],"under":[110],"GPL-3":[112],"license,":[113],"freely":[116],"available":[117,128],"download":[119],"from":[120],"GitHub":[121],"(https://github.com/iferres/simurg).":[122],"SUPPLEMENTARY":[123],"INFORMATION:":[124],"Supplementary":[125],"data":[126],"are":[127],"at":[129],"Bioinformatics":[130],"online.":[131]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
