{"id":"https://openalex.org/W1850890413","doi":"https://doi.org/10.1089/cmb.2014.0146","title":"Building a Pan-Genome Reference for a Population","display_name":"Building a Pan-Genome Reference for a Population","publication_year":2015,"publication_date":"2015-01-07","ids":{"openalex":"https://openalex.org/W1850890413","doi":"https://doi.org/10.1089/cmb.2014.0146","mag":"1850890413","pmid":"https://pubmed.ncbi.nlm.nih.gov/25565268"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2014.0146","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2014.0146","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4424974","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108549697","display_name":"Ngan Nguyen","orcid":"https://orcid.org/0009-0006-4738-5632"},"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ngan Nguyen","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077539873","display_name":"Glenn Hickey","orcid":"https://orcid.org/0000-0002-2280-9404"},"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Glenn Hickey","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001128672","display_name":"Daniel R. Zerbino","orcid":"https://orcid.org/0000-0001-5350-3056"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel R. Zerbino","raw_affiliation_strings":["Wellcome Trust Genome Campus","EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Trust Genome Campus","institution_ids":["https://openalex.org/I87048295"]},{"raw_affiliation_string":"EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I87048295","https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063722321","display_name":"Brian J. Raney","orcid":"https://orcid.org/0000-0002-9708-1390"},"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Raney","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053546027","display_name":"Dent Earl","orcid":null},"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dent Earl","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001974568","display_name":"Joel Armstrong","orcid":"https://orcid.org/0000-0003-2077-4671"},"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joel Armstrong","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048922940","display_name":"W. James Kent","orcid":null},"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. James Kent","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090849321","display_name":"David Haussler","orcid":"https://orcid.org/0000-0003-1533-4575"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"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/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Haussler","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","Howard Hughes Medical Institute, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I1344073410"]}]},{"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"]},{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benedict Paten","raw_affiliation_strings":["University of California","Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]},{"raw_affiliation_string":"Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5061203088"],"corresponding_institution_ids":["https://openalex.org/I185103710","https://openalex.org/I2803209242"],"apc_list":null,"apc_paid":null,"fwci":3.5806,"has_fulltext":false,"cited_by_count":55,"citation_normalized_percentile":{"value":0.93547408,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"5","first_page":"387","last_page":"401"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9980999827384949,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8623207807540894},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.7571017742156982},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5006570816040039},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.4471832513809204},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40760210156440735},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39889708161354065},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3937731385231018},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30797457695007324},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1532110869884491}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8623207807540894},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.7571017742156982},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5006570816040039},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4471832513809204},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40760210156440735},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39889708161354065},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3937731385231018},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30797457695007324},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1532110869884491},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","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":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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1089/cmb.2014.0146","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2014.0146","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:25565268","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25565268","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:ark:/13030/qt2hw627nn","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/qt2hw627nn","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/2hw627nn","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":"Journal of Computational Biology, vol 22, iss 5","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4424974","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4424974","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":"J Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4424974","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4424974","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":"J Comput Biol","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1234929443","display_name":null,"funder_award_id":"U41 HG002371","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G1243730289","display_name":"Ensembl","funder_award_id":"095908","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G2119279804","display_name":null,"funder_award_id":"U01HG004695","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3312423975","display_name":null,"funder_award_id":"U54HG004555","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3675087243","display_name":null,"funder_award_id":"P41HG002371","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4802061397","display_name":null,"funder_award_id":"U54 HG007990","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8649922166","display_name":null,"funder_award_id":"U41HG004568","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1544691147","https://openalex.org/W1985514943","https://openalex.org/W1992406580","https://openalex.org/W2029036185","https://openalex.org/W2030191595","https://openalex.org/W2035596374","https://openalex.org/W2036626452","https://openalex.org/W2037219729","https://openalex.org/W2042160423","https://openalex.org/W2044506914","https://openalex.org/W2054334091","https://openalex.org/W2072483773","https://openalex.org/W2093932542","https://openalex.org/W2103441770","https://openalex.org/W2138113165","https://openalex.org/W2159126316","https://openalex.org/W2166825456","https://openalex.org/W2171777347","https://openalex.org/W2885727518","https://openalex.org/W2916083703","https://openalex.org/W4240249796","https://openalex.org/W4256046779"],"related_works":["https://openalex.org/W2279684808","https://openalex.org/W3137911940","https://openalex.org/W3217304749","https://openalex.org/W2894932706","https://openalex.org/W2066142713","https://openalex.org/W2767606877","https://openalex.org/W2773247701","https://openalex.org/W1969895229","https://openalex.org/W1560725704","https://openalex.org/W4232517363"],"abstract_inverted_index":{"A":[0],"reference":[1,66,109,149],"genome":[2,8,112,124],"is":[3,10,72],"a":[4,13,20,29,64,88,107,132,141,148],"high":[5],"quality":[6],"individual":[7],"that":[9,50],"used":[11,120],"as":[12,131,147],"coordinate":[14],"system":[15],"for":[16,110,143,150],"the":[17,41,47,51,57,81,138],"genomes":[18,23,32],"of":[19,24,31,43,83,101,140],"population,":[21],"or":[22],"closely":[25],"related":[26],"subspecies.":[27],"Given":[28],"set":[30],"partitioned":[33],"by":[34],"homology":[35],"into":[36],"alignment":[37],"blocks":[38,48],"we":[39,136],"formalize":[40],"problem":[42,71],"ordering":[44,53,60],"and":[45,61,78,114,146],"orienting":[46],"such":[49],"resulting":[52],"maximally":[54],"agrees":[55],"with":[56],"underlying":[58],"genomes'":[59],"orientation,":[62],"creating":[63],"pan-genome":[65,108,142],"ordering.":[67],"We":[68,97],"show":[69],"this":[70],"NP-hard,":[73],"but":[74],"also":[75],"demonstrate,":[76],"empirically":[77],"within":[79],"simulations,":[80],"performance":[82],"heuristic":[84],"algorithms":[85],"based":[86],"upon":[87],"cactus":[89],"graph":[90],"decomposition":[91],"to":[92,105,121],"find":[93],"locally":[94],"maximal":[95],"solutions.":[96],"describe":[98],"an":[99],"extension":[100],"our":[102],"Cactus":[103],"software":[104],"create":[106,122],"whole":[111],"alignments,":[113],"demonstrate":[115],"how":[116],"it":[117],"can":[118],"be":[119],"novel":[123],"browser":[125],"visualizations":[126],"using":[127],"human":[128],"variation":[129],"data":[130],"test.":[133],"In":[134],"addition,":[135],"test":[137],"use":[139],"describing":[144],"variations":[145],"read":[151],"mapping.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
