{"id":"https://openalex.org/W4206475898","doi":"https://doi.org/10.1093/bioinformatics/btab117","title":"d-PBWT: dynamic positional Burrows\u2013Wheeler transform","display_name":"d-PBWT: dynamic positional Burrows\u2013Wheeler transform","publication_year":2021,"publication_date":"2021-02-23","ids":{"openalex":"https://openalex.org/W4206475898","doi":"https://doi.org/10.1093/bioinformatics/btab117"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab117","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab117","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016396311","display_name":"Ahsan Sanaullah","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ahsan Sanaullah","raw_affiliation_strings":["Department of Computer Science, University of Central Florida , Orlando, FL 32816,","Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida , Orlando, FL 32816,","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012354604","display_name":"Degui Zhi","orcid":"https://orcid.org/0000-0001-7754-1890"},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Degui Zhi","raw_affiliation_strings":["Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030,","Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":"Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030,","institution_ids":["https://openalex.org/I4210159031","https://openalex.org/I919571938"]},{"raw_affiliation_string":"Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100768909","display_name":"Shaojie Zhang","orcid":"https://orcid.org/0000-0002-4051-5549"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shaojie Zhang","raw_affiliation_strings":["Department of Computer Science, University of Central Florida , Orlando, FL 32816,","Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida , Orlando, FL 32816,","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100768909"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2289,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.88729279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"16","first_page":"2390","last_page":"2397"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9979000091552734,"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"}},"topics":[{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9979000091552734,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9969000220298767,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7198679447174072},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.5609540939331055},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.5108570456504822},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4914649724960327},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47661104798316956},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.47213560342788696},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4488877058029175},{"id":"https://openalex.org/keywords/sorting","display_name":"Sorting","score":0.4465062618255615},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4273383617401123},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.16369348764419556},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15191227197647095},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.12429249286651611},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.11303171515464783},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08636748790740967},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08310934901237488}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7198679447174072},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.5609540939331055},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.5108570456504822},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4914649724960327},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47661104798316956},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.47213560342788696},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4488877058029175},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.4465062618255615},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4273383617401123},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.16369348764419556},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15191227197647095},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.12429249286651611},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.11303171515464783},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08636748790740967},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08310934901237488},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btab117","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab117","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G691053835","display_name":null,"funder_award_id":"R01HG010086","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W783262033","https://openalex.org/W2147477044","https://openalex.org/W2413234541","https://openalex.org/W2786984148","https://openalex.org/W2888300707","https://openalex.org/W2888599454","https://openalex.org/W2895486342","https://openalex.org/W2948091620","https://openalex.org/W2959837610","https://openalex.org/W2962871655","https://openalex.org/W2964006510","https://openalex.org/W2966459122"],"related_works":["https://openalex.org/W3146762847","https://openalex.org/W2398263405","https://openalex.org/W2056886854","https://openalex.org/W2025446304","https://openalex.org/W2166354960","https://openalex.org/W2131321814","https://openalex.org/W1888102361","https://openalex.org/W2171251480","https://openalex.org/W1492100763","https://openalex.org/W2912577640"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Durbin\u2019s":[2],"positional":[3],"Burrows\u2013Wheeler":[4],"transform":[5],"(PBWT)":[6],"is":[7,37,67,103,177],"a":[8,34,90],"scalable":[9],"data":[10,71,92,170,184],"structure":[11,72],"for":[12,113],"haplotype":[13,35,59],"matching.":[14],"It":[15],"has":[16],"been":[17],"successfully":[18],"applied":[19],"to":[20,89],"identical":[21],"by":[22],"descent":[23],"(IBD)":[24],"segment":[25],"identification":[26],"and":[27,53,60,73,115,143,166],"genotype":[28],"imputation.":[29],"Once":[30],"the":[31,61,64,80,86,96],"PBWT":[32,66,88],"of":[33,43,79,117,130,139,157],"panel":[36],"constructed,":[38],"it":[39],"supports":[40],"efficient":[41,54,111],"retrieval":[42],"all":[44,49,128,150],"shared":[45],"long":[46,144],"segments":[47],"among":[48],"individuals":[50],"(long":[51],"matches)":[52],"query":[55,146],"between":[56],"an":[57,68],"external":[58],"panel.":[62,81],"However,":[63],"standard":[65],"array-based":[69],"static":[70,87],"does":[74],"not":[75],"support":[76,127],"dynamic":[77,91],"updates":[78],"Results":[82],"Here,":[83],"we":[84,122,135],"generalize":[85],"structure,":[93],"d-PBWT,":[94],"where":[95],"reverse":[97],"prefix":[98],"sorting":[99],"at":[100,179,187],"each":[101],"position":[102],"stored":[104],"with":[105],"linked":[106],"lists.":[107],"We":[108],"also":[109],"developed":[110],"algorithms":[112,129],"insertion":[114],"deletion":[116],"individual":[118],"haplotypes.":[119],"In":[120,132],"addition,":[121],"verified":[123],"that":[124],"d-PBWT":[125],"can":[126],"PBWT.":[131],"doing":[133],"so,":[134],"systematically":[136],"investigated":[137],"variations":[138],"set":[140],"maximal":[141],"match":[142,145],"algorithms:":[147],"while":[148],"they":[149,160],"have":[151,161],"average":[152],"case":[153,164],"time":[154],"complexity":[155],"independent":[156],"database":[158],"size,":[159],"different":[162],"worst":[163],"complexities":[165],"dependencies":[167],"on":[168],"additional":[169],"structures.":[171],"Availabilityand":[172],"implementation":[173],"The":[174],"benchmarking":[175],"code":[176],"available":[178,186],"genome.ucf.edu/d-PBWT.":[180],"Supplementary":[181,183],"information":[182],"are":[185],"Bioinformatics":[188],"online.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}
