{"id":"https://openalex.org/W4408245599","doi":"https://doi.org/10.1093/bib/bbaf076","title":"Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets","display_name":"Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets","publication_year":2025,"publication_date":"2025-02-11","ids":{"openalex":"https://openalex.org/W4408245599","doi":"https://doi.org/10.1093/bib/bbaf076","pmid":"https://pubmed.ncbi.nlm.nih.gov/40037644"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf076","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf076/62262639/bbaf076.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/26/2/bbaf076/62262639/bbaf076.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101657730","display_name":"Minfang Song","orcid":"https://orcid.org/0000-0003-4685-1823"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I4210157781","display_name":"Shanghai Clinical Research Center","ror":"https://ror.org/057tkkm33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157781"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minfang Song","raw_affiliation_strings":["Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China","Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","institution_ids":["https://openalex.org/I4210123185"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115591868","display_name":"Shuai Ma","orcid":"https://orcid.org/0000-0003-3452-1739"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I4210157781","display_name":"Shanghai Clinical Research Center","ror":"https://ror.org/057tkkm33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157781"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuai Ma","raw_affiliation_strings":["School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China","Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","institution_ids":["https://openalex.org/I4210157781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102200047","display_name":"Gong Wang","orcid":"https://orcid.org/0000-0003-0193-5476"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I4210157781","display_name":"Shanghai Clinical Research Center","ror":"https://ror.org/057tkkm33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157781"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gong Wang","raw_affiliation_strings":["School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100416676","display_name":"Yukun Wang","orcid":"https://orcid.org/0000-0003-1574-6254"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I4210157781","display_name":"Shanghai Clinical Research Center","ror":"https://ror.org/057tkkm33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157781"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yukun Wang","raw_affiliation_strings":["School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115594397","display_name":"Zhenzhen Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I112536369","display_name":"Yazd University","ror":"https://ror.org/02x99ac45","country_code":"IR","type":"education","lineage":["https://openalex.org/I112536369"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Zhenzhen Yang","raw_affiliation_strings":["Yazhouwan National Laboratory , Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan Province 572025 ,","Yazhouwan National Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan Province 572025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yazhouwan National Laboratory , Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan Province 572025 ,","institution_ids":["https://openalex.org/I112536369"]},{"raw_affiliation_string":"Yazhouwan National Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan Province 572025, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114125058","display_name":"Bin Xie","orcid":"https://orcid.org/0000-0002-3962-5644"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Xie","raw_affiliation_strings":["Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","institution_ids":["https://openalex.org/I4210123185"]},{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I4210160507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113314298","display_name":"Tongkun Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tongkun Guo","raw_affiliation_strings":["Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","institution_ids":["https://openalex.org/I4210123185"]},{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I4210160507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057361452","display_name":"Xingxu Huang","orcid":"https://orcid.org/0000-0001-8934-1247"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingxu Huang","raw_affiliation_strings":["Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","institution_ids":["https://openalex.org/I4210123185"]},{"raw_affiliation_string":"Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I4210160507"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101768117","display_name":"Liye Zhang","orcid":"https://orcid.org/0000-0003-2104-6828"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I4210157781","display_name":"Shanghai Clinical Research Center","ror":"https://ror.org/057tkkm33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157781"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liye Zhang","raw_affiliation_strings":["School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China"],"raw_orcid":"https://orcid.org/0000-0003-2104-6828","affiliations":[{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center, Keyuan Road, Pudong New District, Shanghai, 201210, China","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5101657730"],"corresponding_institution_ids":["https://openalex.org/I30809798","https://openalex.org/I4210123185","https://openalex.org/I4210157781","https://openalex.org/I4210160507"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.368,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.94174335,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"26","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9882000088691711,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.6884413957595825},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.6183900237083435},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5487030148506165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5455294847488403},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5319863557815552},{"id":"https://openalex.org/keywords/breakpoint","display_name":"Breakpoint","score":0.44988375902175903},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4449910521507263},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3289825916290283},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2961425483226776},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.29365766048431396},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20909550786018372},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1602514088153839},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13293686509132385},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.11494240164756775}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6884413957595825},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.6183900237083435},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5487030148506165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5455294847488403},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5319863557815552},{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.44988375902175903},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4449910521507263},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3289825916290283},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2961425483226776},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29365766048431396},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20909550786018372},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1602514088153839},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13293686509132385},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.11494240164756775},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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":false},{"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},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf076","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf076/62262639/bbaf076.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:40037644","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40037644","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:pubmedcentral.nih.gov:11879432","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11879432","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf076","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf076/62262639/bbaf076.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/G2203038449","display_name":null,"funder_award_id":"No. 31871332","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":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408245599.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W2002739724","https://openalex.org/W2016299037","https://openalex.org/W2105970624","https://openalex.org/W2134672574","https://openalex.org/W2148256570","https://openalex.org/W2171892226","https://openalex.org/W2236083456","https://openalex.org/W2332292689","https://openalex.org/W2406250479","https://openalex.org/W2610509384","https://openalex.org/W2771542157","https://openalex.org/W2952708922","https://openalex.org/W2954610188","https://openalex.org/W2997123690","https://openalex.org/W3093450816","https://openalex.org/W3093924329","https://openalex.org/W3111222208","https://openalex.org/W3118017075","https://openalex.org/W3123988232","https://openalex.org/W3129513070","https://openalex.org/W3131055609","https://openalex.org/W3133005300","https://openalex.org/W3142571537","https://openalex.org/W3146734731","https://openalex.org/W3158873796","https://openalex.org/W3210182159","https://openalex.org/W4210254201","https://openalex.org/W4220837089","https://openalex.org/W4284888900","https://openalex.org/W4291019543","https://openalex.org/W4292122046","https://openalex.org/W4297241645","https://openalex.org/W4306711441","https://openalex.org/W4306929214","https://openalex.org/W4308620781","https://openalex.org/W4313546429","https://openalex.org/W4322008861","https://openalex.org/W4399585236","https://openalex.org/W4401357416","https://openalex.org/W4401388829"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Copy":[0],"number":[1,125],"alterations":[2],"(CNAs)":[3],"are":[4],"an":[5],"important":[6],"type":[7],"of":[8,21,26,137,149],"genomic":[9],"variation":[10],"which":[11],"play":[12],"a":[13,155],"crucial":[14],"role":[15],"in":[16,64,79,96,114,123,160],"the":[17,24,111,147,162],"initiation":[18],"and":[19,76,118,143],"progression":[20],"cancer.":[22],"With":[23],"explosion":[25],"single-cell":[27],"RNA":[28],"sequencing":[29],"(scRNA-seq),":[30],"several":[31],"computational":[32],"methods":[33,59,164],"have":[34,49],"been":[35],"developed":[36],"to":[37,44],"infer":[38],"CNAs":[39,70],"from":[40],"scRNA-seq":[41],"studies.":[42],"However,":[43],"date,":[45],"no":[46],"independent":[47],"studies":[48],"comprehensively":[50],"benchmarked":[51],"their":[52,62,166],"performance.":[53],"Herein,":[54],"we":[55,131],"evaluated":[56],"five":[57],"state-of-the-art":[58],"based":[60],"on":[61],"performance":[63,113,148],"tumor":[65,73,138,141,144],"versus":[66],"normal":[67],"cell":[68],"classification;":[69],"profile":[71],"accuracy,":[72],"subclone":[74],"inference,":[75],"aneuploidy":[77],"identification":[78],"non-malignant":[80],"cells.":[81],"Our":[82],"results":[83],"showed":[84,110,120],"that":[85],"Numbat":[86,119],"outperformed":[87],"others":[88],"across":[89],"most":[90],"evaluation":[91],"criteria,":[92],"while":[93],"CopyKAT":[94],"excelled":[95],"scenarios":[97],"when":[98],"expression":[99],"matrix":[100],"alone":[101],"was":[102],"used":[103],"as":[104],"input.":[105],"In":[106],"specific":[107],"tasks,":[108],"SCEVAN":[109],"best":[112],"clonal":[115],"breakpoint":[116],"detection":[117],"high":[121],"sensitivity":[122],"copy":[124],"neutral":[126],"LOH":[127],"(cnLOH)":[128],"detection.":[129],"Additionally,":[130],"investigated":[132],"how":[133],"referencing":[134],"settings,":[135],"inclusion":[136],"microenvironment":[139],"cells,":[140],"type,":[142],"purity":[145],"impact":[146],"these":[150],"tools.":[151],"This":[152],"study":[153],"provides":[154],"valuable":[156],"guideline":[157],"for":[158,165],"researchers":[159],"selecting":[161],"appropriate":[163],"datasets.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6}],"updated_date":"2026-05-24T08:33:08.758527","created_date":"2025-10-10T00:00:00"}