{"id":"https://openalex.org/W4413998513","doi":"https://doi.org/10.3389/fbinf.2025.1577324","title":"A novel linear indexing method for strings under all internal nodes in a suffix tree","display_name":"A novel linear indexing method for strings under all internal nodes in a suffix tree","publication_year":2025,"publication_date":"2025-09-04","ids":{"openalex":"https://openalex.org/W4413998513","doi":"https://doi.org/10.3389/fbinf.2025.1577324","pmid":"https://pubmed.ncbi.nlm.nih.gov/40980691"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1577324","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1577324","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1577324/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1577324/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074178239","display_name":"Anas Al-okaily","orcid":"https://orcid.org/0000-0002-1188-8266"},"institutions":[{"id":"https://openalex.org/I2799468983","display_name":"King Hussein Cancer Center","ror":"https://ror.org/0564xsr50","country_code":"JO","type":"funder","lineage":["https://openalex.org/I2799468983"]}],"countries":["JO"],"is_corresponding":true,"raw_author_name":"Anas Al-okaily","raw_affiliation_strings":["Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan"],"affiliations":[{"raw_affiliation_string":"Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan","institution_ids":["https://openalex.org/I2799468983"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055032061","display_name":"Abdelghani Tbakhi","orcid":null},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Abdelghani Tbakhi","raw_affiliation_strings":["Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada","institution_ids":["https://openalex.org/I98251732"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074178239"],"corresponding_institution_ids":["https://openalex.org/I2799468983"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11853235,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1577324","last_page":"1577324"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":1.0,"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":1.0,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9753000140190125,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.7551438808441162},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.704147219657898},{"id":"https://openalex.org/keywords/generalized-suffix-tree","display_name":"Generalized suffix tree","score":0.6982842683792114},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6494337916374207},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6078284382820129},{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.6061581373214722},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.5934907793998718},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44615793228149414},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33405694365501404},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.27996379137039185},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2689253091812134},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.18774372339248657},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.15942010283470154},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09979629516601562}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7551438808441162},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.704147219657898},{"id":"https://openalex.org/C118146561","wikidata":"https://www.wikidata.org/wiki/Q5532514","display_name":"Generalized suffix tree","level":4,"score":0.6982842683792114},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6494337916374207},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6078284382820129},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.6061581373214722},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.5934907793998718},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44615793228149414},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33405694365501404},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.27996379137039185},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2689253091812134},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.18774372339248657},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.15942010283470154},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09979629516601562},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2025.1577324","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1577324","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1577324/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40980691","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40980691","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:3f8cfd349e2b4fda80ecd8d2d6a0c6f8","is_oa":true,"landing_page_url":"https://doaj.org/article/3f8cfd349e2b4fda80ecd8d2d6a0c6f8","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11253329","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12443692","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12443692","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12443692/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1577324","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1577324","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1577324/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310017","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413998513.pdf","grobid_xml":"https://content.openalex.org/works/W4413998513.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W160808826","https://openalex.org/W2059513841","https://openalex.org/W2094777380","https://openalex.org/W2121252285","https://openalex.org/W2134283755","https://openalex.org/W2158322625","https://openalex.org/W2533248932","https://openalex.org/W3010768629","https://openalex.org/W4296777868","https://openalex.org/W4390988763","https://openalex.org/W4394666350","https://openalex.org/W4395675017","https://openalex.org/W4400390698","https://openalex.org/W4401090344","https://openalex.org/W4401730694","https://openalex.org/W4403312475","https://openalex.org/W4404021861"],"related_works":["https://openalex.org/W96331545","https://openalex.org/W2003608043","https://openalex.org/W1517600056","https://openalex.org/W2405892617","https://openalex.org/W2073921136","https://openalex.org/W4293529780","https://openalex.org/W1575722140","https://openalex.org/W3022556214","https://openalex.org/W2160738675","https://openalex.org/W1548907175"],"abstract_inverted_index":{"Suffix":[0],"trees":[1],"are":[2],"fundamental":[3],"data":[4],"structures":[5],"in":[6,30,71],"stringology":[7],"and":[8,41,78],"have":[9],"wide":[10],"applications":[11],"across":[12,43],"various":[13],"domains.":[14],"In":[15],"this":[16],"work,":[17],"we":[18],"propose":[19],"two":[20],"linear-time":[21],"algorithms":[22],"for":[23],"indexing":[24,63],"strings":[25],"under":[26],"each":[27],"internal":[28,45],"node":[29],"a":[31,51],"suffix":[32,58],"tree":[33,53],"while":[34],"preserving":[35],"the":[36,57],"ability":[37],"to":[38],"track":[39],"similarities":[40],"redundancies":[42],"different":[44],"nodes.":[46],"This":[47],"is":[48],"achieved":[49],"through":[50],"novel":[52],"structure":[54],"derived":[55],"from":[56],"tree,":[59],"along":[60],"with":[61],"new":[62],"concepts.":[64],"The":[65],"resulting":[66],"indexes":[67],"offer":[68],"practical":[69],"solutions":[70],"several":[72],"areas,":[73],"including":[74],"DNA":[75],"sequence":[76],"analysis":[77],"approximate":[79],"pattern":[80],"matching.":[81]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
