{"id":"https://openalex.org/W4417498412","doi":"https://doi.org/10.1093/bib/bbaf684","title":"Benchmarking single-sample gene set scoring methods for application in precision medicine","display_name":"Benchmarking single-sample gene set scoring methods for application in precision medicine","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4417498412","doi":"https://doi.org/10.1093/bib/bbaf684","pmid":"https://pubmed.ncbi.nlm.nih.gov/41405962"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf684","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf684","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf684/65943708/bbaf684.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/26/6/bbaf684/65943708/bbaf684.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085159862","display_name":"Daniel Toro\u2010Dom\u00ednguez","orcid":"https://orcid.org/0000-0001-8440-312X"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210137003","display_name":"Bristol-Myers Squibb (Belgium)","ror":"https://ror.org/03c09ma81","country_code":"BE","type":"company","lineage":["https://openalex.org/I4210091812","https://openalex.org/I4210137003"]}],"countries":["BE","SE"],"is_corresponding":false,"raw_author_name":"Daniel Toro-Dom\u00ednguez","raw_affiliation_strings":["Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,","Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute , Nobel v\u00e4g 13, Solna 171 67 ,"],"raw_orcid":"https://orcid.org/0000-0001-8440-312X","affiliations":[{"raw_affiliation_string":"Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,","institution_ids":["https://openalex.org/I4210137003"]},{"raw_affiliation_string":"Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute , Nobel v\u00e4g 13, Solna 171 67 ,","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115694925","display_name":"Chang Wang","orcid":"https://orcid.org/0009-0007-5274-9098"},"institutions":[{"id":"https://openalex.org/I4210137003","display_name":"Bristol-Myers Squibb (Belgium)","ror":"https://ror.org/03c09ma81","country_code":"BE","type":"company","lineage":["https://openalex.org/I4210091812","https://openalex.org/I4210137003"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Chang Wang","raw_affiliation_strings":["Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,","institution_ids":["https://openalex.org/I4210137003"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092135219","display_name":"Iv\u00e1n Ellson Lancho","orcid":"https://orcid.org/0000-0001-6307-3141"},"institutions":[{"id":"https://openalex.org/I4210142177","display_name":"Pfizer-University of Granada-Junta de Andaluc\u00eda Centre for Genomics and Oncological Research","ror":"https://ror.org/04hr99439","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142177"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Iv\u00e1n Ellson-Lancho","raw_affiliation_strings":["GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,"],"raw_orcid":"https://orcid.org/0000-0001-6307-3141","affiliations":[{"raw_affiliation_string":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","institution_ids":["https://openalex.org/I4210142177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018778757","display_name":"Jordi Martorell\u2010Marug\u00e1n","orcid":"https://orcid.org/0000-0002-5186-0735"},"institutions":[{"id":"https://openalex.org/I4210113665","display_name":"Instituto de Investigaci\u00f3n Biosanitaria de Granada","ror":"https://ror.org/026yy9j15","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210113665"]},{"id":"https://openalex.org/I4210142177","display_name":"Pfizer-University of Granada-Junta de Andaluc\u00eda Centre for Genomics and Oncological Research","ror":"https://ror.org/04hr99439","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142177"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jordi Martorell-Marug\u00e1n","raw_affiliation_strings":["Fundaci\u00f3n para la Investigaci\u00f3n Biosanitaria de Andaluc\u00eda Oriental-Alejandro Otero (FIBAO) , Avenida de Madrid 15, Granada 18012 ,","GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,"],"raw_orcid":"https://orcid.org/0000-0002-5186-0735","affiliations":[{"raw_affiliation_string":"Fundaci\u00f3n para la Investigaci\u00f3n Biosanitaria de Andaluc\u00eda Oriental-Alejandro Otero (FIBAO) , Avenida de Madrid 15, Granada 18012 ,","institution_ids":["https://openalex.org/I4210113665"]},{"raw_affiliation_string":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","institution_ids":["https://openalex.org/I4210142177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045696966","display_name":"Ra\u00fal L\u00f3pez-Dom\u00ednguez","orcid":"https://orcid.org/0000-0001-8634-117X"},"institutions":[{"id":"https://openalex.org/I4210142177","display_name":"Pfizer-University of Granada-Junta de Andaluc\u00eda Centre for Genomics and Oncological Research","ror":"https://ror.org/04hr99439","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142177"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Ra\u00fal L\u00f3pez-Dom\u00ednguez","raw_affiliation_strings":["GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,"],"raw_orcid":"https://orcid.org/0000-0001-8634-117X","affiliations":[{"raw_affiliation_string":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","institution_ids":["https://openalex.org/I4210142177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079394518","display_name":"Pedro Carmona\u2010S\u00e1ez","orcid":"https://orcid.org/0000-0002-6173-7255"},"institutions":[{"id":"https://openalex.org/I173304897","display_name":"Universidad de Granada","ror":"https://ror.org/04njjy449","country_code":"ES","type":"education","lineage":["https://openalex.org/I173304897"]},{"id":"https://openalex.org/I4210142177","display_name":"Pfizer-University of Granada-Junta de Andaluc\u00eda Centre for Genomics and Oncological Research","ror":"https://ror.org/04hr99439","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142177"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pedro Carmona-S\u00e1ez","raw_affiliation_strings":["Department of Statistics, University of Granada , Avenida de Fuentenueva s/n, Granada 18071 ,","GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,"],"raw_orcid":"https://orcid.org/0000-0002-6173-7255","affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Granada , Avenida de Fuentenueva s/n, Granada 18071 ,","institution_ids":["https://openalex.org/I173304897"]},{"raw_affiliation_string":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","institution_ids":["https://openalex.org/I4210142177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052973247","display_name":"Marta E. Alarc\u00f3n\u2010Riquelme","orcid":"https://orcid.org/0000-0002-7632-4154"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210142177","display_name":"Pfizer-University of Granada-Junta de Andaluc\u00eda Centre for Genomics and Oncological Research","ror":"https://ror.org/04hr99439","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142177"]}],"countries":["ES","SE"],"is_corresponding":false,"raw_author_name":"Marta E Alarc\u00f3n-Riquelme","raw_affiliation_strings":["GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute , Nobel v\u00e4g 13, Solna 171 67 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","institution_ids":["https://openalex.org/I4210142177"]},{"raw_affiliation_string":"Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute , Nobel v\u00e4g 13, Solna 171 67 ,","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013446926","display_name":"Fr\u00e9d\u00e9ric Baribaud","orcid":"https://orcid.org/0000-0001-9233-1664"},"institutions":[{"id":"https://openalex.org/I4210137003","display_name":"Bristol-Myers Squibb (Belgium)","ror":"https://ror.org/03c09ma81","country_code":"BE","type":"company","lineage":["https://openalex.org/I4210091812","https://openalex.org/I4210137003"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Fr\u00e9d\u00e9ric Baribaud","raw_affiliation_strings":["Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,","institution_ids":["https://openalex.org/I4210137003"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"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":0.576,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.73787968,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"26","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4104999899864197,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4104999899864197,"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":0.39419999718666077,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.14409999549388885,"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":0.7768999934196472},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.7060999870300293},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.43869999051094055},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42809998989105225},{"id":"https://openalex.org/keywords/downstream","display_name":"Downstream (manufacturing)","score":0.3971000015735626},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.3847000002861023},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.3707999885082245}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7768999934196472},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7264000177383423},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.7060999870300293},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5458999872207642},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.531000018119812},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4519999921321869},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.43869999051094055},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42809998989105225},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.3971000015735626},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.3847000002861023},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.3707999885082245},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.31459999084472656},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.288100004196167},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.2863999903202057},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C534262118","wikidata":"https://www.wikidata.org/wiki/Q177719","display_name":"Medical diagnosis","level":2,"score":0.2800999879837036},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.2754000127315521},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.2630000114440918},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.2535000145435333}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":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":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf684","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf684","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf684/65943708/bbaf684.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:41405962","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41405962","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:12710473","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12710473/","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/bbaf684","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf684","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf684/65943708/bbaf684.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/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2309174360","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G2585926585","display_name":null,"funder_award_id":"13039/501100011033/FEDER","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G300979063","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G430777504","display_name":null,"funder_award_id":"10.13039/501100011033/","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G454059402","display_name":null,"funder_award_id":"/10.13039/501100011033/","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5080475149","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5421974903","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G586857820","display_name":null,"funder_award_id":"501100011033/FEDER","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G6071709581","display_name":null,"funder_award_id":"13039/501100011033/","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G6675802839","display_name":null,"funder_award_id":"PP2024.PP-07","funder_id":"https://openalex.org/F4320323834","funder_display_name":"Universidad de Granada"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7391727506","display_name":null,"funder_award_id":"10.13039/501100011033/FEDER","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G7643708868","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8055432103","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320323834","display_name":"Universidad de Granada","ror":"https://ror.org/04njjy449"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417498412.pdf","grobid_xml":"https://content.openalex.org/works/W4417498412.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1831050183","https://openalex.org/W1992045522","https://openalex.org/W2054225389","https://openalex.org/W2115462905","https://openalex.org/W2123879591","https://openalex.org/W2128985829","https://openalex.org/W2156527837","https://openalex.org/W2158384363","https://openalex.org/W2159707944","https://openalex.org/W2321809676","https://openalex.org/W2506941935","https://openalex.org/W2517421365","https://openalex.org/W2616922646","https://openalex.org/W2802773414","https://openalex.org/W2900032527","https://openalex.org/W2943166830","https://openalex.org/W2954876467","https://openalex.org/W3048253480","https://openalex.org/W3099862724","https://openalex.org/W3113299032","https://openalex.org/W3162215872","https://openalex.org/W3173692280","https://openalex.org/W4214876469","https://openalex.org/W4220657516","https://openalex.org/W4280528160","https://openalex.org/W4292599015","https://openalex.org/W4294074103","https://openalex.org/W4296360173","https://openalex.org/W4361204468","https://openalex.org/W4366819509","https://openalex.org/W4388454971","https://openalex.org/W4388706662","https://openalex.org/W4392769383","https://openalex.org/W4399570801","https://openalex.org/W4403107764","https://openalex.org/W4404838998","https://openalex.org/W4411076040","https://openalex.org/W6906614649"],"related_works":[],"abstract_inverted_index":{"Gene":[0],"set-based":[1],"single-sample":[2,61],"scoring":[3,62,111],"methods":[4,63,112],"are":[5],"promising":[6],"to":[7,64],"elucidate":[8],"patient":[9,92],"level":[10],"disease":[11,104],"heterogeneity":[12],"and":[13,35,68,94,123],"enable":[14],"functional":[15],"interpretation":[16],"of":[17,27,56,60,77,103,109,120],"molecular":[18],"data":[19,79,81],"for":[20,36,39,90,116,134],"precision":[21,40],"medicine":[22,41],"approaches.":[23],"Despite":[24],"the":[25,114],"availability":[26],"numerous":[28],"algorithms,":[29],"their":[30,66,88],"performance":[31],"under":[32,71,130],"different":[33,131,135],"scenarios":[34,73,132],"downstream":[37,91],"applications":[38],"approaches":[42],"has":[43],"not":[44],"been":[45],"systematically":[46],"evaluated.":[47],"In":[48],"this":[49],"study,":[50],"we":[51],"conducted":[52],"a":[53,117],"comprehensive":[54],"survey":[55],"an":[57],"exhaustive":[58],"list":[59],"assess":[65],"stability":[67],"reproducibility":[69],"performances":[70,89],"commo":[72],"which":[74],"include":[75],"limitations":[76],"input":[78],"or":[80,133],"integration":[82],"across":[83],"studies.":[84],"We":[85],"also":[86],"evaluated":[87],"stratification":[93],"clinical":[95],"association":[96],"analyses,":[97],"as":[98,100],"well":[99],"predictive":[101],"modeling":[102],"states.":[105],"The":[106],"in-depth":[107],"characterization":[108],"these":[110],"highlights":[113],"importance":[115],"rational":[118],"design":[119],"analysis":[121],"strategies":[122],"provides":[124],"fundamental":[125],"insights":[126],"into":[127],"method":[128],"selection":[129],"applications.":[136]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-12-19T00:00:00"}
