{"id":"https://openalex.org/W2802134368","doi":"https://doi.org/10.1093/bioinformatics/btz575","title":"Haplotype-aware graph indexes","display_name":"Haplotype-aware graph indexes","publication_year":2019,"publication_date":"2019-07-24","ids":{"openalex":"https://openalex.org/W2802134368","doi":"https://doi.org/10.1093/bioinformatics/btz575","mag":"2802134368","pmid":"https://pubmed.ncbi.nlm.nih.gov/31406990"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/2/400/48990879/btz575.pdf","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":"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":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/2/400/48990879/btz575.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066730758","display_name":"Jouni Sir\u00e9n","orcid":"https://orcid.org/0000-0001-5828-4139"},"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"]},{"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","US"],"is_corresponding":true,"raw_author_name":"Jouni Sir\u00e9n","raw_affiliation_strings":["UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064, USA","Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK","UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA","Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"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 Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK","Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","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":false,"raw_author_name":"Adam M Novak","raw_affiliation_strings":["UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064, USA","UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","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":["UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064, USA","UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082040351","display_name":"Richard Durbin","orcid":"https://orcid.org/0000-0002-9130-1006"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"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":"Richard Durbin","raw_affiliation_strings":["Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK","Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK","Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066730758"],"corresponding_institution_ids":["https://openalex.org/I185103710","https://openalex.org/I2802476451"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.0027171,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"36","issue":"2","first_page":"400","last_page":"407"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9961000084877014,"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":0.9961000084877014,"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":0.00039999998989515007,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.00039999998989515007,"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/haplotype","display_name":"Haplotype","score":0.8569903373718262},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6651127934455872},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6484569907188416},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5983339548110962},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5261470675468445},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44400274753570557},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.4385153651237488},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2615506052970886},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18479108810424805},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.1814579963684082},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.14221641421318054},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13806486129760742},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10490474104881287},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07123517990112305}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.8569903373718262},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6651127934455872},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6484569907188416},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5983339548110962},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5261470675468445},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44400274753570557},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.4385153651237488},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2615506052970886},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18479108810424805},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.1814579963684082},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.14221641421318054},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13806486129760742},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10490474104881287},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07123517990112305}],"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":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":15,"locations":[{"id":"doi:10.1093/bioinformatics/btz575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/2/400/48990879/btz575.pdf","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":"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":"doi:10.1101/559583","is_oa":true,"landing_page_url":"https://doi.org/10.1101/559583","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/05/29/559583.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:31406990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31406990","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:arXiv.org:1805.03834","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1805.03834","pdf_url":"https://arxiv.org/pdf/1805.03834","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"mag:2802134368","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1805.03834","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:ark:/13030/qt8618b4mb","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:drops-oai.dagstuhl.de:9306","is_oa":true,"landing_page_url":"https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.4","pdf_url":null,"source":{"id":"https://openalex.org/S4377196569","display_name":"DROPS (Schloss Dagstuhl \u2013 Leibniz Center for Informatics)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799853480","host_organization_name":"Schloss Dagstuhl \u2013 Leibniz Center for Informatics","host_organization_lineage":["https://openalex.org/I2799853480"],"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":"","raw_type":"InProceedings"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6008x92m","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6008x92m","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt8618b4mb","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/8618b4mb","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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, vol 36, iss 2","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt8jz1g157","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/8jz1g157","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7223266","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7223266","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/296161","is_oa":false,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/296161","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.48550/arxiv.1805.03834","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1805.03834","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.17863/cam.43167","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.43167","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.4230/lipics.wabi.2018.4","is_oa":true,"landing_page_url":"https://doi.org/10.4230/lipics.wabi.2018.4","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"ConferencePaper"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/2/400/48990879/btz575.pdf","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":"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":[],"awards":[{"id":"https://openalex.org/G1623698995","display_name":null,"funder_award_id":"U41 HG007234","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G1765775889","display_name":"GENCODE: comprehensive reference genome annotation for human and mouse","funder_award_id":"5u24hg007234-10","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3915766360","display_name":null,"funder_award_id":"WT207492","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4097197391","display_name":"Whole genome sequence based analysis of genetic variation and genome evolution","funder_award_id":"207492/Z/17/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4642712072","display_name":null,"funder_award_id":"WT206194","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G499495141","display_name":"Unbiased analysis of genomic correlates of gene expression in health and disease","funder_award_id":"5u01hl137183-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"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/G5705692003","display_name":"Unbiased analysis of genomic correlates of gene expression in health and disease","funder_award_id":"1u01hl137183-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"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"}],"funders":[{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2802134368.pdf","grobid_xml":"https://content.openalex.org/works/W2802134368.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1201605537","https://openalex.org/W1498437305","https://openalex.org/W1962019683","https://openalex.org/W1999058046","https://openalex.org/W2011210839","https://openalex.org/W2051511420","https://openalex.org/W2072021854","https://openalex.org/W2100673218","https://openalex.org/W2104549677","https://openalex.org/W2105708056","https://openalex.org/W2129264270","https://openalex.org/W2137351413","https://openalex.org/W2147477044","https://openalex.org/W2149992227","https://openalex.org/W2159647614","https://openalex.org/W2161488606","https://openalex.org/W2344013120","https://openalex.org/W2547528004","https://openalex.org/W2603734366","https://openalex.org/W2725379159","https://openalex.org/W2759456806","https://openalex.org/W2786984148","https://openalex.org/W2797994607","https://openalex.org/W2888300707","https://openalex.org/W2950122868","https://openalex.org/W2952338502","https://openalex.org/W2952366981","https://openalex.org/W2952379406","https://openalex.org/W2963160145","https://openalex.org/W2963856156","https://openalex.org/W4230945265"],"related_works":["https://openalex.org/W3022795813","https://openalex.org/W2949956533","https://openalex.org/W3011984892","https://openalex.org/W2164971951","https://openalex.org/W2755288336","https://openalex.org/W3012854845","https://openalex.org/W2888763294","https://openalex.org/W3090796548","https://openalex.org/W2142215982","https://openalex.org/W2035345774","https://openalex.org/W1789533689","https://openalex.org/W2291222162","https://openalex.org/W3176168433","https://openalex.org/W2379698163","https://openalex.org/W2767747923","https://openalex.org/W2314976248","https://openalex.org/W2089070048","https://openalex.org/W2383532826","https://openalex.org/W3023601788","https://openalex.org/W2952473885"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"variation":[2,8,113],"graph":[3,17,61],"toolkit":[4],"(VG)":[5],"represents":[6],"genetic":[7],"as":[9],"a":[10,19,56,78],"graph.":[11],"Although":[12],"each":[13],"path":[14],"in":[15,49,122],"the":[16,34,60,64,70,73,82,86,123],"is":[18,130],"potential":[20],"haplotype,":[21],"most":[22],"paths":[23,43],"are":[24,44,141],"non-biological,":[25],"unlikely":[26],"recombinations":[27],"of":[28,59,63,72,81,85,93],"true":[29],"haplotypes.":[30,105,124],"RESULTS:":[31],"We":[32,68,106],"augment":[33],"VG":[35],"model":[36],"with":[37],"haplotype":[38],"information":[39],"to":[40,47],"identify":[41],"which":[42],"more":[45],"likely":[46],"exist":[48],"nature.":[50],"For":[51],"this":[52],"purpose,":[53],"we":[54],"develop":[55,108],"scalable":[57],"implementation":[58,75],"extension":[62],"positional":[65],"Burrows-Wheeler":[66],"transform.":[67],"demonstrate":[69],"scalability":[71],"new":[74],"by":[76],"building":[77],"whole-genome":[79],"index":[80,92],"5008":[83],"haplotypes":[84],"1000":[87],"Genomes":[88],"Project,":[89],"and":[90,135],"an":[91,109],"all":[94],"108":[95],"070":[96],"Trans-Omics":[97],"for":[98,111,115],"Precision":[99],"Medicine":[100],"Freeze":[101],"5":[102],"chromosome":[103],"17":[104],"also":[107],"algorithm":[110],"simplifying":[112],"graphs":[114],"k-mer":[116],"indexing":[117],"without":[118],"losing":[119],"any":[120],"k-mers":[121],"AVAILABILITY":[125],"AND":[126],"IMPLEMENTATION:":[127],"Our":[128],"software":[129],"available":[131,142],"at":[132,143],"https://github.com/vgteam/vg,":[133],"https://github.com/jltsiren/gbwt":[134],"https://github.com/jltsiren/gcsa2.":[136],"SUPPLEMENTARY":[137],"INFORMATION:":[138],"Supplementary":[139],"data":[140],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
