{"id":"https://openalex.org/W4400140650","doi":"https://doi.org/10.1093/bioinformatics/btae217","title":"Conway\u2013Bromage\u2013Lyndon (CBL): an exact, dynamic representation of <i>k</i>-mer sets","display_name":"Conway\u2013Bromage\u2013Lyndon (CBL): an exact, dynamic representation of <i>k</i>-mer sets","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400140650","doi":"https://doi.org/10.1093/bioinformatics/btae217","pmid":"https://pubmed.ncbi.nlm.nih.gov/38940123"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae217","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae217","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i48/58354678/btae217.pdf","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://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i48/58354678/btae217.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092252951","display_name":"Igor Martayan","orcid":"https://orcid.org/0009-0008-3007-6168"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]},{"id":"https://openalex.org/I7454413","display_name":"\u00c9cole Centrale de Lille","ror":"https://ror.org/01x441g73","country_code":"FR","type":"education","lineage":["https://openalex.org/I7454413"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Igor Martayan","raw_affiliation_strings":["Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France"],"raw_orcid":"https://orcid.org/0009-0008-3007-6168","affiliations":[{"raw_affiliation_string":"Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France","institution_ids":["https://openalex.org/I2279609970","https://openalex.org/I7454413","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063113085","display_name":"Bastien Cazaux","orcid":"https://orcid.org/0000-0002-1761-4354"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]},{"id":"https://openalex.org/I7454413","display_name":"\u00c9cole Centrale de Lille","ror":"https://ror.org/01x441g73","country_code":"FR","type":"education","lineage":["https://openalex.org/I7454413"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Bastien Cazaux","raw_affiliation_strings":["Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France"],"raw_orcid":"https://orcid.org/0000-0002-1761-4354","affiliations":[{"raw_affiliation_string":"Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France","institution_ids":["https://openalex.org/I2279609970","https://openalex.org/I7454413","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001793115","display_name":"Antoine Limasset","orcid":"https://orcid.org/0000-0002-0669-4141"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]},{"id":"https://openalex.org/I7454413","display_name":"\u00c9cole Centrale de Lille","ror":"https://ror.org/01x441g73","country_code":"FR","type":"education","lineage":["https://openalex.org/I7454413"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Antoine Limasset","raw_affiliation_strings":["Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France"],"raw_orcid":"https://orcid.org/0000-0002-0669-4141","affiliations":[{"raw_affiliation_string":"Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France","institution_ids":["https://openalex.org/I2279609970","https://openalex.org/I7454413","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048303382","display_name":"Camille Marchet","orcid":"https://orcid.org/0000-0002-7235-7346"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]},{"id":"https://openalex.org/I7454413","display_name":"\u00c9cole Centrale de Lille","ror":"https://ror.org/01x441g73","country_code":"FR","type":"education","lineage":["https://openalex.org/I7454413"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Camille Marchet","raw_affiliation_strings":["Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France"],"raw_orcid":"https://orcid.org/0000-0002-7235-7346","affiliations":[{"raw_affiliation_string":"Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL , Lille, F-59000, France","institution_ids":["https://openalex.org/I2279609970","https://openalex.org/I7454413","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.4437,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.90264765,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"40","issue":"Supplement_1","first_page":"i48","last_page":"i57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.5317999720573425,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.5317999720573425,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11106","display_name":"Data Management and Algorithms","score":0.09099999815225601,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10317","display_name":"Advanced Database Systems and Queries","score":0.0568000003695488,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lexicographical-order","display_name":"Lexicographical order","score":0.8105918169021606},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6047974228858948},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.544540286064148},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5090000629425049},{"id":"https://openalex.org/keywords/cache","display_name":"Cache","score":0.44818875193595886},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.397803395986557},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37173670530319214},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3643655478954315},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.3618001937866211},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.30703026056289673},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2947338819503784},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19085082411766052},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08538082242012024}],"concepts":[{"id":"https://openalex.org/C159254197","wikidata":"https://www.wikidata.org/wiki/Q1144915","display_name":"Lexicographical order","level":2,"score":0.8105918169021606},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6047974228858948},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.544540286064148},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5090000629425049},{"id":"https://openalex.org/C115537543","wikidata":"https://www.wikidata.org/wiki/Q165596","display_name":"Cache","level":2,"score":0.44818875193595886},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.397803395986557},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37173670530319214},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3643655478954315},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3618001937866211},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.30703026056289673},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2947338819503784},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19085082411766052},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08538082242012024}],"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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae217","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae217","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i48/58354678/btae217.pdf","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:38940123","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38940123","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:11211824","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11211824","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11211824/pdf/btae217.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae217","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae217","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_1/i48/58354678/btae217.pdf","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":[{"id":"https://metadata.un.org/sdg/11","score":0.7099999785423279,"display_name":"Sustainable cities and communities"}],"awards":[{"id":"https://openalex.org/G2249550848","display_name":"Full-length and in-depth analysis of RNA","funder_award_id":"ANR-23-CE45-0003","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G2801727279","display_name":null,"funder_award_id":"ANR-21-CE45-0012","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400140650.pdf","grobid_xml":"https://content.openalex.org/works/W4400140650.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1493802692","https://openalex.org/W2030062409","https://openalex.org/W2105656684","https://openalex.org/W2127901812","https://openalex.org/W2133531097","https://openalex.org/W2138071529","https://openalex.org/W2278452282","https://openalex.org/W2586556622","https://openalex.org/W2809002316","https://openalex.org/W2949074212","https://openalex.org/W2949672921","https://openalex.org/W2957382730","https://openalex.org/W3002913576","https://openalex.org/W3029205155","https://openalex.org/W3043153155","https://openalex.org/W3043768949","https://openalex.org/W3085875665","https://openalex.org/W3134677442","https://openalex.org/W3134947292","https://openalex.org/W3177877512","https://openalex.org/W4220923634","https://openalex.org/W4220999759","https://openalex.org/W4225502295","https://openalex.org/W4226101760","https://openalex.org/W4231199984","https://openalex.org/W4283803941","https://openalex.org/W4295087956","https://openalex.org/W4313226304","https://openalex.org/W4376602515","https://openalex.org/W4382632370","https://openalex.org/W4383749413","https://openalex.org/W4386889019","https://openalex.org/W4389194970","https://openalex.org/W4391099685"],"related_works":["https://openalex.org/W1993634787","https://openalex.org/W3125614403","https://openalex.org/W2476923378","https://openalex.org/W3100240142","https://openalex.org/W2803221307","https://openalex.org/W4211001408","https://openalex.org/W2903963821","https://openalex.org/W2366147410","https://openalex.org/W62366039","https://openalex.org/W239928435"],"abstract_inverted_index":{"SUMMARY:":[0],"In":[1,43],"this":[2,98],"article,":[3],"we":[4,52],"introduce":[5],"the":[6,29,104],"Conway-Bromage-Lyndon":[7],"(CBL)":[8],"structure,":[9],"a":[10,54,61,71,75,121],"compressed,":[11],"dynamic":[12,47,55,92],"and":[13,23,49,83],"exact":[14,107],"method":[15],"for":[16,126],"representing":[17],"k-mer":[18,93,108,127],"sets.":[19],"Originating":[20],"from":[21],"Conway":[22],"Bromage's":[24],"concept,":[25],"CBL":[26,89,100],"innovatively":[27],"employs":[28],"smallest":[30],"cyclic":[31],"rotations":[32],"of":[33,78],"k-mers,":[34],"akin":[35],"to":[36,39,45,97],"Lyndon":[37],"words,":[38],"leverage":[40],"lexicographic":[41],"redundancies.":[42],"order":[44],"support":[46],"operations":[48],"set":[50,94,112,128],"operations,":[51],"propose":[53],"bit":[56],"vector":[57],"structure":[58,67,109,125],"that":[59,88],"draws":[60],"parallel":[62],"with":[63],"Elias-Fano's":[64],"scheme.":[65],"This":[66],"is":[68],"encapsulated":[69],"in":[70],"Rust":[72],"library,":[73],"demonstrating":[74],"balanced":[76],"blend":[77],"construction":[79],"efficiency,":[80],"cache":[81],"locality,":[82],"compression.":[84],"Our":[85],"findings":[86],"suggest":[87],"outperforms":[90],"existing":[91],"methods.":[95],"Unique":[96],"work,":[99],"stands":[101],"out":[102],"as":[103,120],"only":[105],"known":[106],"offering":[110],"in-place":[111],"operations.":[113],"Its":[114],"different":[115],"combined":[116],"abilities":[117],"position":[118],"it":[119],"flexible":[122],"Swiss":[123],"knife":[124],"management.":[129],"AVAILABILITY":[130],"AND":[131],"IMPLEMENTATION:":[132],"https://github.com/imartayan/CBL.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2024-06-29T00:00:00"}