{"id":"https://openalex.org/W4414818014","doi":"https://doi.org/10.1093/bib/bbaf380","title":"The current landscape and emerging challenges of benchmarking single-cell methods","display_name":"The current landscape and emerging challenges of benchmarking single-cell methods","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414818014","doi":"https://doi.org/10.1093/bib/bbaf380","pmid":"https://pubmed.ncbi.nlm.nih.gov/41045508"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf380","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf380/64495567/bbaf380.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","license_id":"https://openalex.org/licenses/cc-by","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/bbaf380/64495567/bbaf380.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100726809","display_name":"Yue Cao","orcid":"https://orcid.org/0000-0002-2356-4031"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yue Cao","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":"https://orcid.org/0000-0002-2356-4031","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101451530","display_name":"Lijia Yu","orcid":"https://orcid.org/0000-0001-6735-9569"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Lijia Yu","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","Computational Systems Biology Group, Children\u2019s Medical Research Institute, University of Sydney , Westmead ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":"https://orcid.org/0000-0001-6735-9569","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Computational Systems Biology Group, Children\u2019s Medical Research Institute, University of Sydney , Westmead ,","institution_ids":["https://openalex.org/I146584863"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034299568","display_name":"Marni Torkel","orcid":null},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Marni Torkel","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100326309","display_name":"Sanghyun Kim","orcid":"https://orcid.org/0000-0001-8393-7613"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Sanghyun Kim","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033771420","display_name":"Yingxin Lin","orcid":"https://orcid.org/0000-0002-4299-7326"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yingxin Lin","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114375167","display_name":"Pengyi Yang","orcid":"https://orcid.org/0000-0003-1098-3138"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Pengyi Yang","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","Computational Systems Biology Group, Children\u2019s Medical Research Institute, University of Sydney , Westmead ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":"https://orcid.org/0000-0003-1098-3138","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Computational Systems Biology Group, Children\u2019s Medical Research Institute, University of Sydney , Westmead ,","institution_ids":["https://openalex.org/I146584863"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001135422","display_name":"Terence P. Speed","orcid":"https://orcid.org/0000-0002-5403-7998"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Terence P Speed","raw_affiliation_strings":["Walter and Eliza Hall Institute for Medical Research , Parkville, VIC 3052 ,"],"raw_orcid":"https://orcid.org/0000-0002-5403-7998","affiliations":[{"raw_affiliation_string":"Walter and Eliza Hall Institute for Medical Research , Parkville, VIC 3052 ,","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087355766","display_name":"Shila Ghazanfar","orcid":"https://orcid.org/0000-0001-7861-6997"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Shila Ghazanfar","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028524705","display_name":"Jean Yang","orcid":"https://orcid.org/0000-0002-5271-2603"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jean Yee Hwa Yang","raw_affiliation_strings":["Charles Perkins Centre, University of Sydney , Sydney ,","School of Mathematics and Statistics, University of Sydney , Sydney ,","Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,"],"raw_orcid":"https://orcid.org/0000-0002-5271-2603","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney , Sydney ,","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW, 2006 ,","institution_ids":["https://openalex.org/I129604602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"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":1.9472,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.86844833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9922999739646912,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.988099992275238},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5659000277519226},{"id":"https://openalex.org/keywords/best-practice","display_name":"Best practice","score":0.49970000982284546},{"id":"https://openalex.org/keywords/current","display_name":"Current (fluid)","score":0.37770000100135803}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.988099992275238},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6093999743461609},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5659000277519226},{"id":"https://openalex.org/C184356942","wikidata":"https://www.wikidata.org/wiki/Q830382","display_name":"Best practice","level":2,"score":0.49970000982284546},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4805000126361847},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.4230000078678131},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.37770000100135803},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.36800000071525574},{"id":"https://openalex.org/C195094911","wikidata":"https://www.wikidata.org/wiki/Q14167904","display_name":"Process management","level":1,"score":0.35510000586509705},{"id":"https://openalex.org/C2778464652","wikidata":"https://www.wikidata.org/wiki/Q309849","display_name":"Open research","level":2,"score":0.30230000615119934}],"mesh":[{"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":"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":true},{"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":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf380","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf380/64495567/bbaf380.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41045508","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41045508","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:11305638","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12495992","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12495992","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12495992/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf380","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf380/64495567/bbaf380.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","license_id":"https://openalex.org/licenses/cc-by","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/G3100051334","display_name":"Towards machine learning-based precision stem cell therapy","funder_award_id":"1173469","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320320966","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12"},{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414818014.pdf","grobid_xml":"https://content.openalex.org/works/W4414818014.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W2098923148","https://openalex.org/W2130301347","https://openalex.org/W2302501749","https://openalex.org/W2766959028","https://openalex.org/W2922985761","https://openalex.org/W2946232537","https://openalex.org/W2947877009","https://openalex.org/W2951624434","https://openalex.org/W2986518719","https://openalex.org/W3111690181","https://openalex.org/W3146142859","https://openalex.org/W3209238322","https://openalex.org/W3211595762","https://openalex.org/W4200624484","https://openalex.org/W4225598893","https://openalex.org/W4311825323","https://openalex.org/W4328048773","https://openalex.org/W4377010404","https://openalex.org/W4384071683","https://openalex.org/W4399702760","https://openalex.org/W4404764563","https://openalex.org/W4406110856","https://openalex.org/W4406855744","https://openalex.org/W4412353239"],"related_works":[],"abstract_inverted_index":{"With":[0],"the":[1,18,29,33,51,66,72,121,124,133],"rapid":[2],"development":[3,58],"of":[4,20,32,71,75,93,96,135],"computational":[5],"methods":[6,97],"for":[7],"single-cell":[8,76],"sequencing":[9],"data,":[10],"benchmarking":[11,21,77,114,128],"serves":[12],"as":[13,91,106],"a":[14,37,137],"valuable":[15],"resource.":[16],"As":[17],"number":[19],"studies":[22,115],"surges,":[23],"it":[24],"is":[25],"timely":[26],"to":[27,108,141],"assess":[28],"current":[30,73],"state":[31],"field.":[34],"We":[35,79],"conducted":[36],"systematic":[38],"literature":[39],"search":[40,52],"and":[41,53,98,116,126,145],"assessed":[42],"282":[43],"papers,":[44],"including":[45,86],"all":[46],"130":[47],"benchmark-only":[48],"papers":[49,59],"from":[50],"an":[54],"additional":[55],"152":[56],"method":[57],"containing":[60],"benchmarking.":[61],"This":[62,130],"collective":[63],"effort":[64],"provides":[65],"most":[67],"comprehensive":[68],"quantitative":[69],"summary":[70],"landscape":[74],"studies.":[78],"examine":[80],"performances":[81],"across":[82,112],"nine":[83],"broad":[84],"categories,":[85],"often":[87],"ignored":[88],"aspects":[89],"such":[90,105],"role":[92],"datasets,":[94],"robustness":[95],"downstream":[99],"evaluation.":[100],"Our":[101],"analysis":[102],"highlights":[103,132],"challenges":[104,144],"how":[107],"effectively":[109],"combine":[110],"knowledge":[111],"multiple":[113],"in":[117],"what":[118],"ways":[119],"can":[120],"community":[122],"recognize":[123],"risk":[125],"prevent":[127],"fatigue.":[129],"paper":[131],"importance":[134],"adopting":[136],"community-led":[138],"research":[139],"paradigm":[140],"tackle":[142],"these":[143],"establish":[146],"best":[147],"practice":[148],"standards.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
