{"id":"https://openalex.org/W7156966170","doi":"https://doi.org/10.1186/s13015-025-00289-3","title":"Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs","display_name":"Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs","publication_year":2026,"publication_date":"2026-04-28","ids":{"openalex":"https://openalex.org/W7156966170","doi":"https://doi.org/10.1186/s13015-025-00289-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/42050549"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-025-00289-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00289-3","pdf_url":null,"source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13015-025-00289-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092574883","display_name":"Rocco Ascone","orcid":"https://orcid.org/0009-0006-1390-4967"},"institutions":[{"id":"https://openalex.org/I142444530","display_name":"University of Trieste","ror":"https://ror.org/02n742c10","country_code":"IT","type":"education","lineage":["https://openalex.org/I142444530"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rocco Ascone","raw_affiliation_strings":["University of Trieste, Trieste , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Trieste, Trieste , Italy","institution_ids":["https://openalex.org/I142444530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134771616","display_name":"Giulia Bernardini","orcid":null},"institutions":[{"id":"https://openalex.org/I142444530","display_name":"University of Trieste","ror":"https://ror.org/02n742c10","country_code":"IT","type":"education","lineage":["https://openalex.org/I142444530"]},{"id":"https://openalex.org/I4210088820","display_name":"International School of Trieste","ror":"https://ror.org/006ffhv52","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210088820"]},{"id":"https://openalex.org/I4210132581","display_name":"Giuliani (Italy)","ror":"https://ror.org/03f9ys929","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210132581"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giulia Bernardini","raw_affiliation_strings":["University of Milan, Milan , Italy. giulia.bernardini@units.it","University of Trieste, Trieste , Italy. giulia.bernardini@units.it"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Milan, Milan , Italy. giulia.bernardini@units.it","institution_ids":["https://openalex.org/I4210132581"]},{"raw_affiliation_string":"University of Trieste, Trieste , Italy. giulia.bernardini@units.it","institution_ids":["https://openalex.org/I142444530","https://openalex.org/I4210088820"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086573637","display_name":"Alessio Conte","orcid":"https://orcid.org/0000-0003-0770-2235"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessio Conte","raw_affiliation_strings":["University of Pisa, Pisa , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pisa, Pisa , Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053359236","display_name":"Massimo Equi","orcid":"https://orcid.org/0000-0001-8609-0040"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Massimo Equi","raw_affiliation_strings":["University of Helsinki, Helsinki , Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Helsinki, Helsinki , Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057312811","display_name":"Est\u00e9ban Gabory","orcid":"https://orcid.org/0000-0002-9897-1512"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]},{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT","NL"],"is_corresponding":false,"raw_author_name":"Esteban Gabory","raw_affiliation_strings":["CWI Amsterdam, Amsterdam, Netherlands","University of Palermo, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CWI Amsterdam, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I1341640284"]},{"raw_affiliation_string":"University of Palermo, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134787972","display_name":"Roberto Grossi","orcid":null},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Roberto Grossi","raw_affiliation_strings":["University of Pisa, Pisa , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pisa, Pisa , Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081785647","display_name":"Nadia Pisanti","orcid":"https://orcid.org/0000-0003-3915-7665"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nadia Pisanti","raw_affiliation_strings":["University of Pisa, Pisa , Italy. nadia.pisanti@unipi.it"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pisa, Pisa , Italy. nadia.pisanti@unipi.it","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5134771616"],"corresponding_institution_ids":["https://openalex.org/I142444530","https://openalex.org/I4210088820","https://openalex.org/I4210132581"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":6.7614,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.96758464,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"21","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.4041000008583069,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T12292","display_name":"Graph Theory and Algorithms","score":0.4041000008583069,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.1582999974489212,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.0697999969124794,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/variable","display_name":"Variable (mathematics)","score":0.6341999769210815},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.545199990272522},{"id":"https://openalex.org/keywords/degenerate-energy-levels","display_name":"Degenerate energy levels","score":0.5422000288963318},{"id":"https://openalex.org/keywords/quadratic-equation","display_name":"Quadratic equation","score":0.5192999839782715},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5024999976158142},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.49720001220703125},{"id":"https://openalex.org/keywords/upper-and-lower-bounds","display_name":"Upper and lower bounds","score":0.4514000117778778}],"concepts":[{"id":"https://openalex.org/C182365436","wikidata":"https://www.wikidata.org/wiki/Q50701","display_name":"Variable (mathematics)","level":2,"score":0.6341999769210815},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5544000267982483},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.545199990272522},{"id":"https://openalex.org/C72319582","wikidata":"https://www.wikidata.org/wiki/Q584304","display_name":"Degenerate energy levels","level":2,"score":0.5422000288963318},{"id":"https://openalex.org/C129844170","wikidata":"https://www.wikidata.org/wiki/Q41299","display_name":"Quadratic equation","level":2,"score":0.5192999839782715},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5024999976158142},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.49720001220703125},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.4514000117778778},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4311999976634979},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.41850000619888306},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.4041000008583069},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3853999972343445},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3815999925136566},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.3700000047683716},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36550000309944153},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3635999858379364},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.362199991941452},{"id":"https://openalex.org/C94624232","wikidata":"https://www.wikidata.org/wiki/Q3150667","display_name":"Indeterminate","level":2,"score":0.3424000144004822},{"id":"https://openalex.org/C136979486","wikidata":"https://www.wikidata.org/wiki/Q773483","display_name":"Existential quantification","level":2,"score":0.334199994802475},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.2939000129699707},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.27790001034736633}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-025-00289-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00289-3","pdf_url":null,"source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:42050549","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42050549","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:air.unimi.it:2434/1254375","is_oa":true,"landing_page_url":"https://hdl.handle.net/2434/1254375","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:bc7a987210d1435b80ce4e6ed456532a","is_oa":true,"landing_page_url":"https://doaj.org/article/bc7a987210d1435b80ce4e6ed456532a","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":"Algorithms for Molecular Biology, Vol 21, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13182080","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13182080/","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-025-00289-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00289-3","pdf_url":null,"source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1115267702","display_name":null,"funder_award_id":"ECS00000017","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1953887145","display_name":null,"funder_award_id":"2014\u20102020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2585677828","display_name":null,"funder_award_id":"872539","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G2758135197","display_name":null,"funder_award_id":"PRIN 2022 YRB97K PINC","funder_id":"https://openalex.org/F4320331528","funder_display_name":"Ministero dell'Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G342311010","display_name":null,"funder_award_id":"MUR - FSE REACT EU - PON R\\&I 2014-2020","funder_id":"https://openalex.org/F4320331528","funder_display_name":"Ministero dell'Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G5245466801","display_name":null,"funder_award_id":"PRIN 2022","funder_id":"https://openalex.org/F4320311030","funder_display_name":"Istituto Nazionale di Alta Matematica \"Francesco Severi\""},{"id":"https://openalex.org/G6253329826","display_name":null,"funder_award_id":"956229","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G6697205189","display_name":"Pan-genome Graph Algorithms and Data Integration","funder_award_id":"872539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7009277087","display_name":null,"funder_award_id":"PNRR ECS00000017","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7440903218","display_name":"ALgorithms for PAngenome Computational Analysis","funder_award_id":"956229","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G792356639","display_name":null,"funder_award_id":"CUPE53C24001950001","funder_id":"https://openalex.org/F4320334079","funder_display_name":"Gruppo Nazionale per il Calcolo Scientifico"},{"id":"https://openalex.org/G972786147","display_name":null,"funder_award_id":"PRIN-2022","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G990108450","display_name":null,"funder_award_id":"CUP - E53C24001950001","funder_id":"https://openalex.org/F4320311030","funder_display_name":"Istituto Nazionale di Alta Matematica \"Francesco Severi\""},{"id":"https://openalex.org/G999758409","display_name":null,"funder_award_id":"ECS00000017","funder_id":"https://openalex.org/F7311471023","funder_display_name":"NextGenerationEU"}],"funders":[{"id":"https://openalex.org/F4320311030","display_name":"Istituto Nazionale di Alta Matematica \"Francesco Severi\"","ror":"https://ror.org/01vx64p53"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320331528","display_name":"Ministero dell'Universit\u00e0 e della Ricerca","ror":null},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334079","display_name":"Gruppo Nazionale per il Calcolo Scientifico","ror":null},{"id":"https://openalex.org/F7311471023","display_name":"NextGenerationEU","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1517097234","https://openalex.org/W1521547794","https://openalex.org/W1830109290","https://openalex.org/W1961096930","https://openalex.org/W1975200441","https://openalex.org/W1977410585","https://openalex.org/W1985108724","https://openalex.org/W1985572324","https://openalex.org/W1987638846","https://openalex.org/W1989204408","https://openalex.org/W1996113955","https://openalex.org/W1997434888","https://openalex.org/W2017919929","https://openalex.org/W2037140152","https://openalex.org/W2047973219","https://openalex.org/W2055119906","https://openalex.org/W2056446691","https://openalex.org/W2066846592","https://openalex.org/W2067386559","https://openalex.org/W2081143975","https://openalex.org/W2084732238","https://openalex.org/W2104067743","https://openalex.org/W2107079154","https://openalex.org/W2110753344","https://openalex.org/W2112777598","https://openalex.org/W2135914634","https://openalex.org/W2149992227","https://openalex.org/W2237665886","https://openalex.org/W2533248932","https://openalex.org/W2583491810","https://openalex.org/W2603734366","https://openalex.org/W2622971911","https://openalex.org/W2743382354","https://openalex.org/W2753393840","https://openalex.org/W2809441573","https://openalex.org/W2888300707","https://openalex.org/W2912383825","https://openalex.org/W2950122868","https://openalex.org/W2964091527","https://openalex.org/W2968539773","https://openalex.org/W3010580865","https://openalex.org/W3043054601","https://openalex.org/W3081483715","https://openalex.org/W3089568060","https://openalex.org/W3091142854","https://openalex.org/W3110971799","https://openalex.org/W3126170517","https://openalex.org/W3131672637","https://openalex.org/W3158236668","https://openalex.org/W4210743444","https://openalex.org/W4220680041","https://openalex.org/W4254652536","https://openalex.org/W4285151990","https://openalex.org/W4307770952","https://openalex.org/W4312491697","https://openalex.org/W4313344207","https://openalex.org/W4323241266","https://openalex.org/W4327590906","https://openalex.org/W4376133202","https://openalex.org/W4376224197","https://openalex.org/W4380363487","https://openalex.org/W4387818211","https://openalex.org/W4390061859","https://openalex.org/W4398163926","https://openalex.org/W4402894605","https://openalex.org/W4406143065","https://openalex.org/W4408473367","https://openalex.org/W4410406894","https://openalex.org/W7156966170"],"related_works":[],"abstract_inverted_index":{"Elastic":[0,5],"Degenerate":[1],"(ED)":[2],"strings":[3,46,84,92,143],"and":[4,41,85,128,135,153,186],"Founder":[6],"(EF)":[7],"graphs,":[8,87],"here":[9],"collectively":[10],"named":[11],"variable":[12,45,91,116,123,142],"strings,":[13],"are":[14,137],"two":[15],"representations":[16],"of":[17,20,27,44,56,90,111,118,125,141,147,191],"acyclic":[18],"components":[19],"pangenomes":[21],"which":[22],"extend":[23],"the":[24,53,94,100,108,145,178],"well-known":[25],"notion":[26],"indeterminate":[28],"string.":[29],"Recent":[30],"studies":[31],"have":[32],"focused":[33],"extensively":[34],"on":[35],"algorithmic":[36],"tasks":[37],"involving":[38],"these":[39],"structures":[40],"other":[42],"forms":[43],"that":[47],"they":[48],"generalize.":[49],"Among":[50],"such":[51],"tasks,":[52],"basic":[54],"operation":[55],"matching":[57,112],"a":[58,61,63,79,113,122,158,169,176],"pattern":[59,117],"into":[60,121],"text,":[62],"fundamental":[64],"toolkit":[65],"for":[66,164,184],"pangenomic":[67],"data":[68],"analysis,":[69],"deserves":[70],"special":[71],"attention.":[72],"In":[73],"this":[74,192],"paper,":[75],"(1)":[76],"we":[77,106,155,167],"establish":[78],"clear":[80],"taxonomy":[81,146],"across":[82],"ED":[83],"EF":[86],"categorizing":[88],"types":[89,140],"from":[93,139],"simplest":[95],"linear":[96],"(solid)":[97],"string":[98],"to":[99],"most":[101],"complex":[102],"general":[103],"cases;":[104],"(2)":[105],"consider":[107],"problem":[109],"MATCH(X,Y)":[110],"solid":[114],"or":[115,166],"type":[119,126],"X":[120,134,152],"text":[124],"Y,":[127,154],"investigate":[129],"its":[130],"time":[131],"complexity":[132],"when":[133],"Y":[136],"chosen":[138],"in":[144,195],"(1).":[148],"For":[149],"all":[150],"possible":[151],"either":[156],"provide":[157],"non-trivial,":[159],"often":[160],"sub-quadratic,":[161],"upper":[162],"bound":[163],"MATCH(X,Y),":[165],"prove":[168],"quadratic":[170,180],"conditional":[171,181],"lower":[172,182],"bound,":[173],"taking":[174],"as":[175],"reference":[177],"existing":[179],"bounds":[183],"MATCH(SOLID,ED)":[185],"MATCH(SOLID,EF).":[187],"A":[188],"preliminary":[189],"version":[190],"work":[193],"appeared":[194],"[Ascone":[196],"et":[197],"al.,":[198],"WABI":[199],"2024].":[200]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2026-04-29T00:00:00"}
