{"id":"https://openalex.org/W3043054601","doi":"https://doi.org/10.1093/bioinformatics/btaa640","title":"Efficient dynamic variation graphs","display_name":"Efficient dynamic variation graphs","publication_year":2020,"publication_date":"2020-07-10","ids":{"openalex":"https://openalex.org/W3043054601","doi":"https://doi.org/10.1093/bioinformatics/btaa640","mag":"3043054601","pmid":"https://pubmed.ncbi.nlm.nih.gov/33040146"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5139/36150450/btaa640.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":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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5139/36150450/btaa640.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054998077","display_name":"Jordan M. Eizenga","orcid":"https://orcid.org/0000-0001-8345-8356"},"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":"Jordan M Eizenga","raw_affiliation_strings":["Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":"https://orcid.org/0000-0001-8345-8356","affiliations":[{"raw_affiliation_string":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]},{"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":["Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":"https://orcid.org/0000-0001-5828-047X","affiliations":[{"raw_affiliation_string":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085452490","display_name":"Emily Kobayashi","orcid":"https://orcid.org/0000-0002-9041-5167"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Kobayashi","raw_affiliation_strings":["Bioinformatics and Systems Biology, University of California San Diego , La Jolla, CA 92093, USA","Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":"https://orcid.org/0000-0002-9041-5167","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, University of California San Diego , La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033476871","display_name":"Flavia Villani","orcid":"https://orcid.org/0000-0003-3633-0610"},"institutions":[{"id":"https://openalex.org/I4210137461","display_name":"Institute of Genetics and Biophysics","ror":"https://ror.org/04hadk112","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210137461","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Flavia Villani","raw_affiliation_strings":["Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli Federico II , Naples 80138, Italy","Institute of Genetics and Biophysics, Consiglio Nazionale di Ricerche , Naples 80131, Italy"],"raw_orcid":"https://orcid.org/0000-0003-3633-0610","affiliations":[{"raw_affiliation_string":"Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli Federico II , Naples 80138, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Institute of Genetics and Biophysics, Consiglio Nazionale di Ricerche , Naples 80131, Italy","institution_ids":["https://openalex.org/I4210137461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072312074","display_name":"Cecilia Cisar","orcid":"https://orcid.org/0000-0001-8487-5936"},"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":"Cecilia Cisar","raw_affiliation_strings":["Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":"https://orcid.org/0000-0001-8487-5936","affiliations":[{"raw_affiliation_string":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040033163","display_name":"Simon Heumos","orcid":"https://orcid.org/0000-0003-3326-817X"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Simon Heumos","raw_affiliation_strings":["Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3326-817X","affiliations":[{"raw_affiliation_string":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077539873","display_name":"Glenn Hickey","orcid":"https://orcid.org/0000-0002-2280-9404"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Glenn Hickey","raw_affiliation_strings":["Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008251529","display_name":"Vincenza Colonna","orcid":"https://orcid.org/0000-0002-3966-0474"},"institutions":[{"id":"https://openalex.org/I4210137461","display_name":"Institute of Genetics and Biophysics","ror":"https://ror.org/04hadk112","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210137461","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Vincenza Colonna","raw_affiliation_strings":["Institute of Genetics and Biophysics, Consiglio Nazionale di Ricerche , Naples 80131, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Genetics and Biophysics, Consiglio Nazionale di Ricerche , Naples 80131, Italy","institution_ids":["https://openalex.org/I4210137461"]}]},{"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":["Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008992371","display_name":"Erik Garrison","orcid":"https://orcid.org/0000-0003-3821-631X"},"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":"Erik Garrison","raw_affiliation_strings":["Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","Genomics Institute , Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Engineering and Bioinformatics, University of California Santa Cruz , Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute , Santa Cruz, CA 95064, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008992371"],"corresponding_institution_ids":["https://openalex.org/I185103710"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9421,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.86887016,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"21","first_page":"5139","last_page":"5144"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7215999960899353,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7215999960899353,"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"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.06989999860525131,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.04560000076889992,"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/mit-license","display_name":"MIT License","score":0.857541561126709},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8281089663505554},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8215464949607849},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.5078971982002258},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.49309632182121277},{"id":"https://openalex.org/keywords/computational-genomics","display_name":"Computational genomics","score":0.4884158968925476},{"id":"https://openalex.org/keywords/call-graph","display_name":"Call graph","score":0.4672159254550934},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4638305902481079},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43308401107788086},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3685770034790039},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3400300443172455},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2905787229537964},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.17462915182113647},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09737241268157959},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09075173735618591}],"concepts":[{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.857541561126709},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8281089663505554},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8215464949607849},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.5078971982002258},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.49309632182121277},{"id":"https://openalex.org/C39238701","wikidata":"https://www.wikidata.org/wiki/Q2091816","display_name":"Computational genomics","level":5,"score":0.4884158968925476},{"id":"https://openalex.org/C102379954","wikidata":"https://www.wikidata.org/wiki/Q2589940","display_name":"Call graph","level":2,"score":0.4672159254550934},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4638305902481079},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43308401107788086},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3685770034790039},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3400300443172455},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2905787229537964},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.17462915182113647},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09737241268157959},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09075173735618591},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D007990","descriptor_name":"Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007990","descriptor_name":"Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007990","descriptor_name":"Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007990","descriptor_name":"Libraries","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaa640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5139/36150450/btaa640.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33040146","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33040146","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:ark:/13030/qt44p9v0nx","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:escholarship.org:ark:/13030/qt44p9v0nx","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/44p9v0nx","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 36, iss 21","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7850124","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7850124","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5139/36150450/btaa640.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"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/G1824916433","display_name":null,"funder_award_id":"T32 HG008345","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3344988642","display_name":null,"funder_award_id":"R01HG010485","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3920667064","display_name":"Enabling Comparative Pangenomics","funder_award_id":"5r01hg010485-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G472851475","display_name":null,"funder_award_id":"U24HG007234","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4810168628","display_name":"UC Santa Cruz Training Program In Genomic Sciences","funder_award_id":"5t32hg008345-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"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/G6281845084","display_name":"The Human Pangenome Reference Consortium Coordination Center","funder_award_id":"2u41hg010972-06","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"},{"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"},{"id":"https://openalex.org/G8969870","display_name":"The construction and utility of reference pan-genome graphs","funder_award_id":"5u01hg010961-03","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/F4320323803","display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie","ror":"https://ror.org/02vgg2808"},{"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/W3043054601.pdf","grobid_xml":"https://content.openalex.org/works/W3043054601.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2547528004","https://openalex.org/W2603734366","https://openalex.org/W2808052219","https://openalex.org/W2888300707","https://openalex.org/W2949062400","https://openalex.org/W2952366981","https://openalex.org/W2966459122","https://openalex.org/W2981050756","https://openalex.org/W2996038910","https://openalex.org/W3007365321","https://openalex.org/W3098689499","https://openalex.org/W4285719527","https://openalex.org/W6769260855"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W2546377002","https://openalex.org/W4221030787","https://openalex.org/W2790811106","https://openalex.org/W4285209474","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4212902261"],"abstract_inverted_index":{"MOTIVATION:":[0],"Pangenomics":[1],"is":[2],"a":[3,56,67,89,93],"growing":[4],"field":[5],"within":[6],"computational":[7],"genomics.":[8],"Many":[9],"pangenomic":[10,36],"analyses":[11],"use":[12,66],"bidirected":[13],"sequence":[14],"graphs":[15,78,113],"as":[16],"their":[17],"core":[18],"data":[19,27],"model.":[20],"However,":[21],"implementing":[22],"and":[23,32,63,108,121,153,163],"correctly":[24],"using":[25,146],"this":[26,50],"model":[28],"can":[29,38],"be":[30,39],"difficult,":[31],"the":[33,119,133,138],"scale":[34],"of":[35,58,76,96,110,129],"datasets":[37],"challenging":[40],"to":[41,72,126,145],"work":[42],"at.":[43],"These":[44],"challenges":[45],"have":[46],"impeded":[47],"progress":[48],"in":[49,137],"field.":[51],"RESULTS:":[52],"Here,":[53],"we":[54,99],"present":[55],"stack":[57],"two":[59],"C++":[60],"libraries,":[61],"libbdsg":[62,154],"libhandlegraph,":[64],"which":[65,141],"simple,":[68],"field-proven":[69],"interface,":[70],"designed":[71],"expose":[73],"elementary":[74],"features":[75],"these":[77,102],"while":[79],"preventing":[80],"common":[81],"graph":[82,135],"manipulation":[83,109],"mistakes.":[84],"The":[85],"libraries":[86],"also":[87],"provide":[88],"Python":[90],"binding.":[91],"Using":[92],"diverse":[94],"collection":[95],"pangenome":[97],"graphs,":[98],"demonstrate":[100],"that":[101],"tools":[103],"allow":[104],"for":[105],"efficient":[106],"construction":[107],"large":[111],"genome":[112],"with":[114],"dense":[115],"variation.":[116],"For":[117],"instance,":[118],"speed":[120],"memory":[122],"usage":[123],"are":[124,155],"up":[125],"an":[127,158],"order":[128],"magnitude":[130],"better":[131],"than":[132],"prior":[134],"implementation":[136],"VG":[139],"toolkit,":[140],"has":[142],"now":[143],"transitioned":[144],"libbdsg's":[147],"implementations.":[148],"AVAILABILITY":[149],"AND":[150],"IMPLEMENTATION:":[151],"libhandlegraph":[152],"available":[156],"under":[157],"MIT":[159],"License":[160],"from":[161],"https://github.com/vgteam/libhandlegraph":[162],"https://github.com/vgteam/libbdsg.":[164]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
