{"id":"https://openalex.org/W4400344131","doi":"https://doi.org/10.1093/bioinformatics/btae436","title":"Unravelling reference bias in ancient DNA datasets","display_name":"Unravelling reference bias in ancient DNA datasets","publication_year":2024,"publication_date":"2024-07-01","ids":{"openalex":"https://openalex.org/W4400344131","doi":"https://doi.org/10.1093/bioinformatics/btae436","pmid":"https://pubmed.ncbi.nlm.nih.gov/38960861"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae436","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae436","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae436","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100019452","display_name":"Stephanie Dolenz","orcid":null},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I4210152515","display_name":"Centre for Palaeogenetics","ror":"https://ror.org/04sx39q13","country_code":"SE","type":"facility","lineage":["https://openalex.org/I161593684","https://openalex.org/I2801711128","https://openalex.org/I4210152515"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Stephanie Dolenz","raw_affiliation_strings":["Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","Department of Geological Sciences, Stockholm University , Stockholm, SE-106 91, Sweden","Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden"],"affiliations":[{"raw_affiliation_string":"Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I4210152515"]},{"raw_affiliation_string":"Department of Geological Sciences, Stockholm University , Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034886260","display_name":"Tom van der Valk","orcid":"https://orcid.org/0000-0001-6582-3452"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I2801711128","display_name":"Swedish Museum of Natural History","ror":"https://ror.org/05k323c76","country_code":"SE","type":"archive","lineage":["https://openalex.org/I2801711128"]},{"id":"https://openalex.org/I4210152515","display_name":"Centre for Palaeogenetics","ror":"https://ror.org/04sx39q13","country_code":"SE","type":"facility","lineage":["https://openalex.org/I161593684","https://openalex.org/I2801711128","https://openalex.org/I4210152515"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Tom van der Valk","raw_affiliation_strings":["Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm, SE-114 18, Sweden","Science for Life Laboratory , Stockholm, SE-171 65, Sweden","Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden"],"affiliations":[{"raw_affiliation_string":"Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I4210152515"]},{"raw_affiliation_string":"Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm, SE-114 18, Sweden","institution_ids":["https://openalex.org/I2801711128"]},{"raw_affiliation_string":"Science for Life Laboratory , Stockholm, SE-171 65, Sweden","institution_ids":["https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden","institution_ids":["https://openalex.org/I2801711128"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021868362","display_name":"Chenyu Jin","orcid":"https://orcid.org/0000-0002-2392-7090"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2801711128","display_name":"Swedish Museum of Natural History","ror":"https://ror.org/05k323c76","country_code":"SE","type":"archive","lineage":["https://openalex.org/I2801711128"]},{"id":"https://openalex.org/I4210152515","display_name":"Centre for Palaeogenetics","ror":"https://ror.org/04sx39q13","country_code":"SE","type":"facility","lineage":["https://openalex.org/I161593684","https://openalex.org/I2801711128","https://openalex.org/I4210152515"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Chenyu Jin","raw_affiliation_strings":["Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm, SE-114 18, Sweden","Department of Zoology, Stockholm University , Stockholm, SE-106 91, Sweden","Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden"],"affiliations":[{"raw_affiliation_string":"Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I4210152515"]},{"raw_affiliation_string":"Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm, SE-114 18, Sweden","institution_ids":["https://openalex.org/I2801711128"]},{"raw_affiliation_string":"Department of Zoology, Stockholm University , Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden","institution_ids":["https://openalex.org/I2801711128"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064985686","display_name":"Jonas Oppenheimer","orcid":"https://orcid.org/0000-0001-7973-6173"},"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":"Jonas Oppenheimer","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA, 95064, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA, 95064, United States","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025409086","display_name":"Muhammad Bilal Sharif","orcid":"https://orcid.org/0000-0002-0581-0542"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I4210152515","display_name":"Centre for Palaeogenetics","ror":"https://ror.org/04sx39q13","country_code":"SE","type":"facility","lineage":["https://openalex.org/I161593684","https://openalex.org/I2801711128","https://openalex.org/I4210152515"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Muhammad Bilal Sharif","raw_affiliation_strings":["Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","Department of Zoology, Stockholm University , Stockholm, SE-106 91, Sweden"],"affiliations":[{"raw_affiliation_string":"Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I4210152515"]},{"raw_affiliation_string":"Department of Zoology, Stockholm University , Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046648575","display_name":"Ludovic Orlando","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I4400009051","display_name":"Centre d'Anthropobiologie et de G\u00e9nomique de Toulouse","ror":"https://ror.org/045p8nc06","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4400009051"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ludovic Orlando","raw_affiliation_strings":["Centre for Anthropobiology and Genomics of Toulouse (CAGT, CNRS UMR5288), University Paul Sabatier, Facult\u00e9 de Sant\u00e9, Toulouse, 31000, France"],"affiliations":[{"raw_affiliation_string":"Centre for Anthropobiology and Genomics of Toulouse (CAGT, CNRS UMR5288), University Paul Sabatier, Facult\u00e9 de Sant\u00e9, Toulouse, 31000, France","institution_ids":["https://openalex.org/I134560555","https://openalex.org/I1294671590","https://openalex.org/I4400009051"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039594974","display_name":"Beth Shapiro","orcid":"https://orcid.org/0000-0002-2733-7776"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Beth Shapiro","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, University of California Santa Cruz , Santa Cruz, CA, 95064, United States","Howard Hughes Medical Institute, University of California Santa Cruz , Santa Cruz, CA, 95064, United States"],"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, University of California Santa Cruz , Santa Cruz, CA, 95064, United States","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, University of California Santa Cruz , Santa Cruz, CA, 95064, United States","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038121718","display_name":"Love Dal\u00e9n","orcid":"https://orcid.org/0000-0001-8270-7613"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2801711128","display_name":"Swedish Museum of Natural History","ror":"https://ror.org/05k323c76","country_code":"SE","type":"archive","lineage":["https://openalex.org/I2801711128"]},{"id":"https://openalex.org/I4210152515","display_name":"Centre for Palaeogenetics","ror":"https://ror.org/04sx39q13","country_code":"SE","type":"facility","lineage":["https://openalex.org/I161593684","https://openalex.org/I2801711128","https://openalex.org/I4210152515"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Love Dal\u00e9n","raw_affiliation_strings":["Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm, SE-114 18, Sweden","Department of Zoology, Stockholm University , Stockholm, SE-106 91, Sweden","Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden"],"affiliations":[{"raw_affiliation_string":"Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I4210152515"]},{"raw_affiliation_string":"Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm, SE-114 18, Sweden","institution_ids":["https://openalex.org/I2801711128"]},{"raw_affiliation_string":"Department of Zoology, Stockholm University , Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden","institution_ids":["https://openalex.org/I2801711128"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064259803","display_name":"Peter D. Heintzman","orcid":"https://orcid.org/0000-0002-6449-0219"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I4210152515","display_name":"Centre for Palaeogenetics","ror":"https://ror.org/04sx39q13","country_code":"SE","type":"facility","lineage":["https://openalex.org/I161593684","https://openalex.org/I2801711128","https://openalex.org/I4210152515"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Peter D Heintzman","raw_affiliation_strings":["Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","Department of Geological Sciences, Stockholm University , Stockholm, SE-106 91, Sweden","Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden"],"affiliations":[{"raw_affiliation_string":"Centre for Palaeogenetics, Svante Arrhenius v\u00e4g 20C, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I4210152515"]},{"raw_affiliation_string":"Department of Geological Sciences, Stockholm University , Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden","institution_ids":["https://openalex.org/I161593684"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5100019452"],"corresponding_institution_ids":["https://openalex.org/I161593684","https://openalex.org/I4210152515"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.9818,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.96166942,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"40","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10751","display_name":"Forensic and Genetic Research","score":0.9958999752998352,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.8692495822906494},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.6707070469856262},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6010681390762329},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3962949514389038},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36296966671943665},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3305862247943878},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32599562406539917},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3226395845413208},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.2389925718307495},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17183378338813782},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1276407241821289}],"concepts":[{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.8692495822906494},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.6707070469856262},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6010681390762329},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3962949514389038},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36296966671943665},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3305862247943878},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32599562406539917},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3226395845413208},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2389925718307495},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17183378338813782},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1276407241821289}],"mesh":[{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btae436","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae436","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"pmid:38960861","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38960861","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:HAL:hal-04729870v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04729870","pdf_url":"https://hal.science/hal-04729870/document","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2024, 40 (7), pp.btae436. ⟨10.1093/bioinformatics/btae436⟩","raw_type":"Journal articles"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7mh8h0t9","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7mh8h0t9","pdf_url":"https://escholarship.org/content/qt7mh8h0t9/qt7mh8h0t9.pdf","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 40, iss 7","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11254355","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11254355","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11254355/pdf/btae436.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:ark:/13030/qt7mh8h0t9","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae436","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae436","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G1322033128","display_name":null,"funder_award_id":"KAW 2022.0033","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G1889593718","display_name":"Horse Power: Interactions between China, Mongolia and the steppe 2000-0 BCE","funder_award_id":"101071707","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G247595552","display_name":null,"funder_award_id":"2021-00625","funder_id":"https://openalex.org/F4320336376","funder_display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science"},{"id":"https://openalex.org/G3165808449","display_name":null,"funder_award_id":"022-06725","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G3250127029","display_name":null,"funder_award_id":"2021-00625","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G326506993","display_name":null,"funder_award_id":"KAW 2020.0239","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G4066480865","display_name":null,"funder_award_id":"KAW 2021","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G4353964202","display_name":null,"funder_award_id":"KAW 2021.0048","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G4493597635","display_name":null,"funder_award_id":"NAISS","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G5317956557","display_name":null,"funder_award_id":"2020.","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6832510969","display_name":null,"funder_award_id":"KAW 2022","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G7054268934","display_name":null,"funder_award_id":"101054984","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7230600129","display_name":null,"funder_award_id":"2021.0048","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G8080935424","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8338695050","display_name":null,"funder_award_id":"2022-0672","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8511050629","display_name":null,"funder_award_id":"2020.0239","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G8683756101","display_name":null,"funder_award_id":"support","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G8709696155","display_name":null,"funder_award_id":"KAW 2020.0239","funder_id":"https://openalex.org/F4320325677","funder_display_name":"Science for Life Laboratory"},{"id":"https://openalex.org/G8869864247","display_name":null,"funder_award_id":"2022-06725","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320325677","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22"},{"id":"https://openalex.org/F4320336376","display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1993435119","https://openalex.org/W2011301426","https://openalex.org/W2022327489","https://openalex.org/W2034552366","https://openalex.org/W2091193685","https://openalex.org/W2103163845","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2112954194","https://openalex.org/W2124362779","https://openalex.org/W2150163641","https://openalex.org/W2156330112","https://openalex.org/W2170551349","https://openalex.org/W2544029679","https://openalex.org/W2898389874","https://openalex.org/W2951912016","https://openalex.org/W2964989753","https://openalex.org/W3022542573","https://openalex.org/W3086246013","https://openalex.org/W3109220766","https://openalex.org/W3114070225","https://openalex.org/W3129075539","https://openalex.org/W3130861457","https://openalex.org/W3151257524","https://openalex.org/W3152826503","https://openalex.org/W3201939971","https://openalex.org/W4311546538","https://openalex.org/W4387876540"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W3113091479","https://openalex.org/W2162899405","https://openalex.org/W941090075","https://openalex.org/W2044987316","https://openalex.org/W3134374554","https://openalex.org/W2237480245","https://openalex.org/W2075065631","https://openalex.org/W2519167559","https://openalex.org/W3163755236"],"abstract_inverted_index":{"AMBER":[0],"is":[1],"available":[2,18],"for":[3],"noncommercial":[4],"use":[5],"on":[6,19],"GitHub":[7],"(https://github.com/tvandervalk/AMBER.git).":[8],"Scripts":[9],"used":[10],"to":[11],"generate":[12],"and":[13],"analyse":[14],"simulated":[15],"datasets":[16],"are":[17],"Github":[20],"(https://github.com/sdolenz/refbias_scripts).":[21]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-16T15:07:20.185449","created_date":"2025-10-10T00:00:00"}