{"id":"https://openalex.org/W4404945100","doi":"https://doi.org/10.1093/bioinformatics/btae720","title":"Panacus: fast and exact pangenome growth and core size estimation","display_name":"Panacus: fast and exact pangenome growth and core size estimation","publication_year":2024,"publication_date":"2024-11-27","ids":{"openalex":"https://openalex.org/W4404945100","doi":"https://doi.org/10.1093/bioinformatics/btae720","pmid":"https://pubmed.ncbi.nlm.nih.gov/39626271"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae720","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae720","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae720","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065658218","display_name":"Luca Parmigiani","orcid":"https://orcid.org/0000-0002-2139-3259"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Luca Parmigiani","raw_affiliation_strings":["Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615,"],"affiliations":[{"raw_affiliation_string":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615,","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008992371","display_name":"Erik Garrison","orcid":"https://orcid.org/0000-0003-3821-631X"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Garrison","raw_affiliation_strings":["Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163,"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163,","institution_ids":["https://openalex.org/I160606119"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019771245","display_name":"Jens Stoye","orcid":"https://orcid.org/0000-0002-4656-7155"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jens Stoye","raw_affiliation_strings":["Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615,"],"affiliations":[{"raw_affiliation_string":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615,","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067570776","display_name":"Tobias Marschall","orcid":"https://orcid.org/0000-0002-9376-1030"},"institutions":[{"id":"https://openalex.org/I4210089242","display_name":"D\u00fcsseldorf University Hospital","ror":"https://ror.org/006k2kk72","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210089242"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Marschall","raw_affiliation_strings":["Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,"],"affiliations":[{"raw_affiliation_string":"Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","institution_ids":["https://openalex.org/I44260953","https://openalex.org/I4210089242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055740017","display_name":"Daniel Doerr","orcid":"https://orcid.org/0000-0002-3720-6227"},"institutions":[{"id":"https://openalex.org/I4210089242","display_name":"D\u00fcsseldorf University Hospital","ror":"https://ror.org/006k2kk72","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210089242"]},{"id":"https://openalex.org/I4210152419","display_name":"Deutsches Diabetes-Zentrum e.V.","ror":"https://ror.org/04ews3245","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210152419","https://openalex.org/I44260953"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Doerr","raw_affiliation_strings":["Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","Department for Endocrinology and Diabetology, Medical Faculty and University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research , D\u00fcsseldorf 40225,"],"affiliations":[{"raw_affiliation_string":"Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Department for Endocrinology and Diabetology, Medical Faculty and University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225,","institution_ids":["https://openalex.org/I44260953","https://openalex.org/I4210089242"]},{"raw_affiliation_string":"German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research , D\u00fcsseldorf 40225,","institution_ids":["https://openalex.org/I4210152419"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5065658218"],"corresponding_institution_ids":["https://openalex.org/I20121455"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.5588,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.96865902,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"40","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9940999746322632,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9869999885559082,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6664490699768066},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4679360091686249},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4544835090637207},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.43796128034591675},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4331432282924652},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4274601936340332},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.41252970695495605},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3394409120082855},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33247146010398865},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20756855607032776},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09092491865158081}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6664490699768066},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4679360091686249},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4544835090637207},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.43796128034591675},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4331432282924652},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4274601936340332},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.41252970695495605},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3394409120082855},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33247146010398865},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20756855607032776},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09092491865158081}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae720","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae720","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39626271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39626271","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11665632","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11665632","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11665632/pdf/btae720.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae720","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae720","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1974542962","display_name":null,"funder_award_id":"Sk\u0142odowska","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2689612763","display_name":null,"funder_award_id":"Marie","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3345650513","display_name":null,"funder_award_id":"1U01HG010973","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3514550006","display_name":null,"funder_award_id":"Centre","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7440903218","display_name":null,"funder_award_id":"956229","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1964114909","https://openalex.org/W2041391522","https://openalex.org/W2041457600","https://openalex.org/W2093610003","https://openalex.org/W2127901812","https://openalex.org/W2150550043","https://openalex.org/W2603734366","https://openalex.org/W2888300707","https://openalex.org/W3092652421","https://openalex.org/W4280583823","https://openalex.org/W4284884776","https://openalex.org/W4376133202","https://openalex.org/W4395037980","https://openalex.org/W6847042891"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2791776396","https://openalex.org/W2117798581","https://openalex.org/W4384009753","https://openalex.org/W2964820744","https://openalex.org/W4247858078","https://openalex.org/W2378944243"],"abstract_inverted_index":{"Panacus":[0,25],"is":[1,6],"implemented":[2],"in":[3],"Rust":[4],"and":[5,19],"published":[7],"as":[8],"Open":[9],"Source":[10],"software":[11],"under":[12],"the":[13],"MIT":[14],"license.":[15],"The":[16],"source":[17],"code":[18],"documentation":[20],"are":[21],"available":[22],"at":[23,31],"https://github.com/marschall-lab/panacus.":[24],"can":[26],"be":[27],"installed":[28],"via":[29],"Bioconda":[30],"https://bioconda.github.io/recipes/panacus/README.html.":[32]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":19}],"updated_date":"2026-04-03T22:45:19.894376","created_date":"2025-10-10T00:00:00"}
