{"id":"https://openalex.org/W2786984148","doi":"https://doi.org/10.1186/s13015-017-0109-9","title":"A graph extension of the positional Burrows\u2013Wheeler transform and its applications","display_name":"A graph extension of the positional Burrows\u2013Wheeler transform and its applications","publication_year":2017,"publication_date":"2017-07-11","ids":{"openalex":"https://openalex.org/W2786984148","doi":"https://doi.org/10.1186/s13015-017-0109-9","mag":"2786984148","pmid":"https://pubmed.ncbi.nlm.nih.gov/28702075"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-017-0109-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0109-9","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-017-0109-9","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","license_id":"https://openalex.org/licenses/cc-by","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://almob.biomedcentral.com/counter/pdf/10.1186/s13015-017-0109-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031360521","display_name":"Adam M. Novak","orcid":"https://orcid.org/0000-0001-5828-047X"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam M. Novak","raw_affiliation_strings":["Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA","Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA, 95064, USA"],"raw_orcid":"https://orcid.org/0000-0001-5828-047X","affiliations":[{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA, 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008992371","display_name":"Erik Garrison","orcid":"https://orcid.org/0000-0003-3821-631X"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Erik Garrison","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK","Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061203088","display_name":"Benedict Paten","orcid":"https://orcid.org/0000-0001-8863-3539"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benedict Paten","raw_affiliation_strings":["Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA","Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA, 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA, 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031360521"],"corresponding_institution_ids":["https://openalex.org/I185103710"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":6.7094,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.98134125,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"18","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11245","display_name":"Advanced Numerical Analysis Techniques","score":0.9679999947547913,"subfield":{"id":"https://openalex.org/subfields/2206","display_name":"Computational Mechanics"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11245","display_name":"Advanced Numerical Analysis Techniques","score":0.9679999947547913,"subfield":{"id":"https://openalex.org/subfields/2206","display_name":"Computational Mechanics"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7506080865859985},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.7017244100570679},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5786786079406738},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.43082165718078613},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19733494520187378}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7506080865859985},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.7017244100570679},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5786786079406738},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.43082165718078613},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19733494520187378}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-017-0109-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0109-9","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-017-0109-9","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:28702075","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28702075","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:doaj.org/article:6d3ba5f4d40b4b08b858ad7343bc88c6","is_oa":true,"landing_page_url":"https://doaj.org/article/6d3ba5f4d40b4b08b858ad7343bc88c6","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 12, Iss 1, Pp 1-12 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5505026","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5505026","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-017-0109-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0109-9","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-017-0109-9","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","license_id":"https://openalex.org/licenses/cc-by","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/G2143955549","display_name":null,"funder_award_id":"SFLIFE# 351901","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"},{"id":"https://openalex.org/G514126070","display_name":null,"funder_award_id":"U01HL137183","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G526700612","display_name":null,"funder_award_id":"U54HG007990","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G6663841836","display_name":null,"funder_award_id":"DT06172015","funder_id":"https://openalex.org/F4320306159","funder_display_name":"W. M. Keck Foundation"},{"id":"https://openalex.org/G8236924658","display_name":null,"funder_award_id":"5U54HG007990","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8824438077","display_name":"BD2K Consortium Activities","funder_award_id":"5u54hg007990-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"},{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320310358","display_name":"Achievement Rewards for College Scientists Foundation","ror":"https://ror.org/054awkm93"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2786984148.pdf","grobid_xml":"https://content.openalex.org/works/W2786984148.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W783262033","https://openalex.org/W1544273448","https://openalex.org/W1962019683","https://openalex.org/W1978981589","https://openalex.org/W1989017925","https://openalex.org/W2035596374","https://openalex.org/W2104549677","https://openalex.org/W2134696992","https://openalex.org/W2137351413","https://openalex.org/W2147477044","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2336928501","https://openalex.org/W2344013120","https://openalex.org/W2345970915","https://openalex.org/W2511515754","https://openalex.org/W2529241974","https://openalex.org/W2786984148","https://openalex.org/W2888599454","https://openalex.org/W2952379406","https://openalex.org/W3100935868","https://openalex.org/W4235690512","https://openalex.org/W6679642144"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2075768550","https://openalex.org/W3022218857","https://openalex.org/W2369178846","https://openalex.org/W2390279801","https://openalex.org/W2370289839","https://openalex.org/W2358668433","https://openalex.org/W2082716031","https://openalex.org/W2899850600"],"abstract_inverted_index":{"We":[0,68,122],"present":[1],"a":[2,23,27,33,36,39,43,51,55,79,97,150],"generalization":[3],"of":[4,26,29,46,54,57,90,128,131],"the":[5,17,83,88,102,126,129],"positional":[6],"Burrows-Wheeler":[7],"transform,":[8],"or":[9],"PBWT,":[10],"to":[11,42,85],"genome":[12,20,37,98],"graphs,":[13],"which":[14],"we":[15,81],"call":[16],"gPBWT.":[18],"A":[19],"graph":[21],"is":[22,50],"collapsed":[24],"representation":[25,53],"set":[28,56],"genomes":[30],"described":[31],"as":[32],"graph.":[34],"In":[35],"graph,":[38,99],"haplotype":[40,111,147],"corresponds":[41],"restricted":[44],"form":[45],"walk.":[47],"The":[48],"gPBWT":[49,73,84,127],"compressible":[52],"these":[58],"graph-encoded":[59],"haplotypes":[60,91],"that":[61,110,124],"allows":[62],"for":[63,72,146],"efficient":[64,70],"subhaplotype":[65],"match":[66],"queries.":[67],"give":[69],"algorithms":[71],"construction":[74],"and":[75,100,143],"query":[76],"operations.":[77],"As":[78],"demonstration,":[80],"use":[82],"quickly":[86],"count":[87],"number":[89],"consistent":[92],"with":[93,101,125],"random":[94],"walks":[95],"in":[96],"paths":[103],"taken":[104],"by":[105],"mapped":[106],"reads;":[107],"results":[108],"suggest":[109],"consistency":[112],"information":[113],"can":[114],"be":[115,141],"practically":[116],"incorporated":[117],"into":[118],"graph-based":[119],"read":[120],"mappers.":[121],"estimate":[123],"order":[130],"100,000":[132],"diploid":[133],"genomes,":[134],"including":[135],"all":[136],"forms":[137],"structural":[138],"variation,":[139],"could":[140],"stored":[142],"made":[144],"searchable":[145],"queries":[148],"using":[149],"single":[151],"large":[152],"compute":[153],"node.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":7}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
