{"id":"https://openalex.org/W4387965266","doi":"https://doi.org/10.1186/s12859-023-05531-6","title":"Pan-genome de Bruijn graph using the bidirectional FM-index","display_name":"Pan-genome de Bruijn graph using the bidirectional FM-index","publication_year":2023,"publication_date":"2023-10-26","ids":{"openalex":"https://openalex.org/W4387965266","doi":"https://doi.org/10.1186/s12859-023-05531-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/37884897"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05531-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05531-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05531-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05531-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064037172","display_name":"Lore Depuydt","orcid":"https://orcid.org/0000-0001-8517-0479"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Lore Depuydt","raw_affiliation_strings":["Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium. Lore.Depuydt@UGent.be","Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium. Lore.Depuydt@UGent.be","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011288877","display_name":"Luca Renders","orcid":"https://orcid.org/0000-0002-2244-1427"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Luca Renders","raw_affiliation_strings":["Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002088014","display_name":"Thomas Abeel","orcid":"https://orcid.org/0000-0002-7205-7431"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Thomas Abeel","raw_affiliation_strings":["Delft Bioinformatics Lab, Delft University of Technology, 2628 XE, Delft, The Netherlands","Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delft Bioinformatics Lab, Delft University of Technology, 2628 XE, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054831130","display_name":"Jan Fostier","orcid":"https://orcid.org/0000-0002-9994-8269"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Jan Fostier","raw_affiliation_strings":["Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium. Jan.Fostier@UGent.be","Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium. Jan.Fostier@UGent.be","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064037172"],"corresponding_institution_ids":["https://openalex.org/I32597200"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2231,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.79712713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"24","issue":"1","first_page":"400","last_page":"400"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6305000185966492,"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":0.6305000185966492,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.16820000112056732,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.03720000013709068,"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/de-bruijn-graph","display_name":"De Bruijn graph","score":0.7448087930679321},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.549004077911377},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5057082176208496},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.5023887157440186},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.4687158167362213},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4595318138599396},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4412158727645874},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4271343946456909},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3920140266418457},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3748689293861389},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2048613727092743},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19391795992851257},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.14291179180145264},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.13928481936454773},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08865073323249817},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08446323871612549}],"concepts":[{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.7448087930679321},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.549004077911377},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5057082176208496},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.5023887157440186},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.4687158167362213},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4595318138599396},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4412158727645874},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4271343946456909},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3920140266418457},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3748689293861389},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2048613727092743},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19391795992851257},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.14291179180145264},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.13928481936454773},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08865073323249817},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08446323871612549}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":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":"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},{"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-023-05531-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05531-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05531-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37884897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37884897","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:archive.ugent.be:01HEW85AXZ111VK2GW872Z2VWG","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-01HEW85AXZ111VK2GW872Z2VWG","pdf_url":"https://biblio.ugent.be/publication/01HEW85AXZ111VK2GW872Z2VWG/file/01HEW88WE6ZTAN1ZH50K422XVK.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"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":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10605969","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10605969","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10605969/pdf/12859_2023_Article_5531.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:608f41265dd34314802e1e271673d7df","is_oa":true,"landing_page_url":"https://doaj.org/article/608f41265dd34314802e1e271673d7df","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-33 (2023)","raw_type":"article"},{"id":"pmh:oai:tudelft.nl:uuid:32fc5cba-4ef5-48b9-b270-6c4269925c5e","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:32fc5cba-4ef5-48b9-b270-6c4269925c5e","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"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":"","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05531-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05531-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05531-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6173454641","display_name":"Search schemes for sequence alignment","funder_award_id":"1SE7822N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G8837067486","display_name":"Search schemes for sequence alignment to pan-genome graphs.","funder_award_id":"1117322N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4387965266.pdf"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W6247929","https://openalex.org/W17958277","https://openalex.org/W1516502318","https://openalex.org/W1635391495","https://openalex.org/W1813440684","https://openalex.org/W1822485921","https://openalex.org/W1867886327","https://openalex.org/W1991874243","https://openalex.org/W2010361633","https://openalex.org/W2052422622","https://openalex.org/W2056981303","https://openalex.org/W2079497788","https://openalex.org/W2113312463","https://openalex.org/W2119279650","https://openalex.org/W2124249157","https://openalex.org/W2127901812","https://openalex.org/W2129264270","https://openalex.org/W2134199796","https://openalex.org/W2136651963","https://openalex.org/W2150469424","https://openalex.org/W2150550043","https://openalex.org/W2157219052","https://openalex.org/W2158322625","https://openalex.org/W2158874082","https://openalex.org/W2159675211","https://openalex.org/W2170551349","https://openalex.org/W2272733715","https://openalex.org/W2312729946","https://openalex.org/W2474973645","https://openalex.org/W2492182665","https://openalex.org/W2570688240","https://openalex.org/W2613825882","https://openalex.org/W2759261668","https://openalex.org/W2888300707","https://openalex.org/W2889833303","https://openalex.org/W2891275623","https://openalex.org/W2937008344","https://openalex.org/W2950122868","https://openalex.org/W2952366981","https://openalex.org/W2952379095","https://openalex.org/W2953622720","https://openalex.org/W2964849163","https://openalex.org/W2971433408","https://openalex.org/W2971520867","https://openalex.org/W2978078216","https://openalex.org/W2978714755","https://openalex.org/W2992988966","https://openalex.org/W2999295646","https://openalex.org/W3017152484","https://openalex.org/W3020388903","https://openalex.org/W3028658133","https://openalex.org/W3086246013","https://openalex.org/W3088400220","https://openalex.org/W3092652421","https://openalex.org/W3120923229","https://openalex.org/W3167495622","https://openalex.org/W3168724350","https://openalex.org/W4200597270","https://openalex.org/W4206067192","https://openalex.org/W4285079340","https://openalex.org/W4301824356","https://openalex.org/W4322008640","https://openalex.org/W4382632370","https://openalex.org/W4394666350","https://openalex.org/W6966982515"],"related_works":["https://openalex.org/W2562683361","https://openalex.org/W3087469195","https://openalex.org/W2354744388","https://openalex.org/W3125399386","https://openalex.org/W2949121831","https://openalex.org/W2756186577","https://openalex.org/W2735897904","https://openalex.org/W3215786367","https://openalex.org/W1908987670","https://openalex.org/W2025111520"],"abstract_inverted_index":{"BACKGROUND:":[0],"Pan-genome":[1],"graphs":[2,24,46],"are":[3,25,47],"gaining":[4],"importance":[5],"in":[6,50,96,142,153,194,212],"the":[7,41,68,82,126,130,140,172,205,209,213,228,243],"field":[8],"of":[9,52,94,98,132,207,227,240,252],"bioinformatics":[10],"as":[11,31,164,166],"data":[12,76,107],"structures":[13],"to":[14,118,136,171,186],"represent":[15],"and":[16,38,54,100,138,218,235],"jointly":[17],"analyze":[18],"multiple":[19],"genomes.":[20],"Compacted":[21],"de":[22,113],"Bruijn":[23,114],"inherently":[26],"suited":[27],"for":[28,109],"this":[29,88],"purpose,":[30],"their":[32],"graph":[33,60,75,115,141,147,173,230,244],"topology":[34,215],"naturally":[35],"reveals":[36],"similarity":[37],"divergence":[39],"within":[40,189],"pan-genome.":[42],"Most":[43],"state-of-the-art":[44],"pan-genome":[45,229],"represented":[48],"explicitly":[49],"terms":[51,97],"nodes":[53],"edges.":[55],"Recently,":[56],"an":[57],"alternative,":[58],"implicit":[59],"representation":[61,89,226],"was":[62],"proposed":[63],"that":[64,80,116,179,231],"builds":[65],"directly":[66],"upon":[67],"unidirectional":[69,134],"FM-index.":[70],"As":[71],"such,":[72],"a":[73,92,106,110,187,190,195,200,224],"memory-efficient":[74,225],"structure":[77,108],"is":[78,123,257],"obtained":[79],"inherits":[81],"FM-index'":[83],"backward":[84],"search":[85,139,175,246],"functionality.":[86],"However,":[87],"suffers":[90],"from":[91],"number":[93],"shortcomings":[95],"functionality":[99],"algorithmic":[101],"performance.":[102],"RESULTS:":[103],"We":[104,177,222],"present":[105],"pan-genome,":[111],"compacted":[112],"aims":[117],"address":[119],"these":[120,158],"shortcomings.":[121],"It":[122],"built":[124],"on":[125,157],"bidirectional":[127],"FM-index,":[128],"extending":[129],"ability":[131],"its":[133],"counterpart":[135],"navigate":[137],"both":[143],"directions.":[144],"All":[145],"basic":[146],"navigation":[148],"steps":[149],"can":[150,181],"be":[151],"performed":[152],"constant":[154],"time.":[155],"Based":[156],"features,":[159],"we":[160,180,203],"implement":[161],"subgraph":[162,233],"visualization":[163,217,234],"well":[165],"lossless":[167,236],"approximate":[168,237],"pattern":[169,238],"matching":[170,239],"using":[174,245],"schemes.":[176,247],"demonstrate":[178],"retrieve":[182],"all":[183],"occurrences":[184],"corresponding":[185],"read":[188],"certain":[191],"edit":[192],"distance":[193],"very":[196],"efficient":[197],"manner.":[198],"Through":[199],"case":[201],"study,":[202],"show":[204],"potential":[206],"exploiting":[208],"information":[210],"embedded":[211],"graph's":[214],"through":[216],"sequence":[219],"alignment.":[220],"CONCLUSIONS:":[221],"propose":[223],"supports":[232],"reads":[241],"against":[242],"The":[248],"C++":[249],"source":[250],"code":[251],"our":[253],"software,":[254],"called":[255],"Nexus,":[256],"available":[258],"at":[259],"https://github.com/biointec/nexus":[260],"under":[261],"AGPL-3.0":[262],"license.":[263]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
