{"id":"https://openalex.org/W4415407781","doi":"https://doi.org/10.1093/bib/bbaf550","title":"PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis","display_name":"PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4415407781","doi":"https://doi.org/10.1093/bib/bbaf550","pmid":"https://pubmed.ncbi.nlm.nih.gov/41115209"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf550","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf550/64819766/bbaf550.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf550/64819766/bbaf550.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032318263","display_name":"Zhengfa Xue","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengfa Xue","raw_affiliation_strings":["School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an, Shaanxi 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an 710049 ,","School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28, Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28, Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100445144","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0002-0431-1039"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Wang","raw_affiliation_strings":["The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054657033","display_name":"Xuwen Wang","orcid":"https://orcid.org/0000-0003-3022-6513"},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuwen Wang","raw_affiliation_strings":["Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Beilin District, Xi'an 710003, Shaanxi ,","Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Beilin District, Xi'an 710003, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , No. 157, Xiwu Road, Beilin District, Xi'an 710003, Shaanxi ,","institution_ids":["https://openalex.org/I4210131893"]},{"raw_affiliation_string":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Beilin District, Xi'an 710003, Shaanxi, China","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032316050","display_name":"Jiajing Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiajing Yuan","raw_affiliation_strings":["School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an, Shaanxi 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an 710049 ,","School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28, Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28, Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403149","display_name":"Lin Wang","orcid":"https://orcid.org/0000-0002-1880-1143"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Wang","raw_affiliation_strings":["The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024305174","display_name":"Jingyu Zeng","orcid":"https://orcid.org/0000-0002-9089-3126"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingyu Zeng","raw_affiliation_strings":["The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China"],"raw_orcid":"https://orcid.org/0000-0002-9089-3126","affiliations":[{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083114703","display_name":"Xin Jin","orcid":"https://orcid.org/0000-0001-7554-4975"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Jin","raw_affiliation_strings":["State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China"],"raw_orcid":"https://orcid.org/0000-0001-7554-4975","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research , Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083 ,","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032858241","display_name":"Huanhuan Zhu","orcid":"https://orcid.org/0000-0002-2995-4911"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huanhuan Zhu","raw_affiliation_strings":["Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research , Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research , Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083 ,","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , No. 381, Wushan Road, Tianhe District, Guangzhou 510006 ,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, No. 381, Wushan Road, Tianhe District, Guangzhou 510006, China","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027360778","display_name":"Jiayin Wang","orcid":"https://orcid.org/0000-0002-3862-6557"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayin Wang","raw_affiliation_strings":["School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an, Shaanxi 710049 ,","Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an 710049 ,","School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28, Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":"https://orcid.org/0000-0002-3862-6557","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , No. 28, Xianning West Road, Beilin District, Xi\u2019an 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28, Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.4176,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.63834092,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9805999994277954,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9805999994277954,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9677000045776367,"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":0.9466000199317932,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.7124999761581421},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5218999981880188},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.5099999904632568},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5016999840736389},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4771000146865845},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43299999833106995}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.7124999761581421},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5218999981880188},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.520799994468689},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.5099999904632568},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5016999840736389},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4771000146865845},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43299999833106995},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4212999939918518},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.36550000309944153},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3652999997138977},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.34209999442100525},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32829999923706055},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.29580000042915344},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.2802000045776367},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.2612999975681305}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf550","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf550/64819766/bbaf550.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41115209","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41115209","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11344684","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12536880","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12536880/pdf/bbaf550.pdf","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf550","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf550/64819766/bbaf550.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2715084110","display_name":null,"funder_award_id":"62402376","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3180425335","display_name":null,"funder_award_id":"72293581","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G516663181","display_name":null,"funder_award_id":"72274152","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4415407781.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1848483543","https://openalex.org/W2107126369","https://openalex.org/W2118630694","https://openalex.org/W2124873881","https://openalex.org/W2125359798","https://openalex.org/W2134599124","https://openalex.org/W2140968934","https://openalex.org/W2150506261","https://openalex.org/W2337209831","https://openalex.org/W2400156025","https://openalex.org/W2627277170","https://openalex.org/W2734691271","https://openalex.org/W2759456806","https://openalex.org/W2781895613","https://openalex.org/W2788099780","https://openalex.org/W2920143708","https://openalex.org/W2952366981","https://openalex.org/W2997001777","https://openalex.org/W3092652421","https://openalex.org/W3100651612","https://openalex.org/W3120188855","https://openalex.org/W3159082119","https://openalex.org/W3197410642","https://openalex.org/W4200597270","https://openalex.org/W4224278121","https://openalex.org/W4251751280","https://openalex.org/W4255836900","https://openalex.org/W4294376397","https://openalex.org/W4362660695","https://openalex.org/W4376133202","https://openalex.org/W4380730560","https://openalex.org/W4382139325","https://openalex.org/W4399352524","https://openalex.org/W4399761111","https://openalex.org/W4402459535","https://openalex.org/W4411441131"],"related_works":[],"abstract_inverted_index":{"In":[0,116],"population-scale":[1,78,129],"genomic":[2,79],"variation":[3,30,80],"studies":[4],"based":[5],"on":[6,198],"shallow":[7],"whole":[8],"genome":[9],"sequencing,":[10],"pangenomes":[11],"have":[12],"become":[13],"an":[14],"effective":[15],"tool":[16],"for":[17,100,127,226,235],"identifying":[18],"population-specific":[19,85,114],"single-nucleotide":[20],"polymorphisms":[21,88],"and":[22,103,147,169,183,201,230],"indels.":[23],"Extending":[24],"these":[25],"advantages":[26],"to":[27,36,63,108],"copy":[28,86],"number":[29,56,87],"(CNV),":[31],"however,":[32],"remains":[33],"challenging":[34],"due":[35],"two":[37],"unresolved":[38],"issues.":[39],"First,":[40],"current":[41],"pangenome":[42,61,95,124,145],"frameworks":[43,96],"exhibit":[44],"pronounced":[45],"population-representation":[46,174],"bias":[47],"arising":[48],"from":[49,67,73,112,180,195,211],"uneven":[50],"sampling":[51],"across":[52],"populations.":[53,75],"As":[54],"the":[55,60,144,165,176],"of":[57],"samples":[58,204],"increases,":[59],"tends":[62],"capture":[64],"variations":[65],"primarily":[66],"majority":[68,192],"populations":[69],"while":[70,190],"suppressing":[71],"signals":[72,194],"minority":[74],"Second,":[76],"in":[77],"analyses,":[81],"common":[82,212],"but":[83],"benign":[84],"(CNPs)":[89],"frequently":[90],"obscure":[91],"pathogenic":[92,110,209],"CNVs.":[93],"Existing":[94],"lack":[97],"dedicated":[98],"mechanisms":[99],"representing":[101],"CNPs":[102,139,214],"CNVs,":[104],"limiting":[105],"their":[106],"ability":[107],"distinguish":[109],"CNVs":[111,210],"benign,":[113],"CNPs.":[115],"this":[117],"study,":[118],"we":[119,136],"present":[120],"PangenomeX,":[121],"a":[122,149,155,223,232],"graph-convolutional":[123],"framework":[125],"tailored":[126],"low-coverage,":[128],"CNV":[130,150,168],"analysis.":[131],"To":[132,172],"address":[133],"CNP":[134,170],"representation,":[135],"embed":[137],"known":[138],"as":[140],"prior":[141],"knowledge":[142],"into":[143,239],"graph":[146,159],"construct":[148],"relationship":[151],"network":[152,161],"guided":[153],"by":[154],"phylogenetic":[156],"tree.":[157],"A":[158],"convolutional":[160],"(GCN)":[162],"then":[163],"learns":[164],"interactions":[166],"between":[167],"nodes.":[171],"mitigate":[173],"bias,":[175],"GCN":[177],"aggregates":[178],"information":[179],"only":[181],"one-":[182],"two-hop":[184],"neighborhoods,":[185],"preserving":[186],"local":[187],"population":[188,213],"context":[189],"preventing":[191],"group":[193],"dominating.":[196],"Evaluation":[197],"simulated":[199],"cohorts":[200],"561":[202],"real":[203],"shows":[205],"that":[206],"PangenomeX":[207,221],"distinguishes":[208],"markedly":[215],"better":[216],"than":[217],"existing":[218],"methods.":[219],"Overall,":[220],"offers":[222],"methodological":[224],"blueprint":[225],"large-cohort":[227],"variant":[228],"screening":[229],"provides":[231],"practical":[233],"path":[234],"bringing":[236],"graph-based":[237],"genomics":[238],"clinical":[240],"practice.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-22T00:00:00"}
