{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T13:27:12Z","timestamp":1780666032656,"version":"3.54.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":46,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006393","name":"Universidad de Granada","doi-asserted-by":"publisher","award":["PP2024.PP-07"],"award-info":[{"award-number":["PP2024.PP-07"]}],"id":[{"id":"10.13039\/501100006393","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Agencia estatal de Investigaci\u00f3n\u2014Ministerio de Ciencia e Innovaci\u00f3n","award":["PTA2021-021013-I"],"award-info":[{"award-number":["PTA2021-021013-I"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Gene set-based single-sample scoring methods are promising to elucidate patient level disease heterogeneity and enable functional interpretation of molecular data for precision medicine approaches. Despite the availability of numerous algorithms, their performance under different scenarios and for downstream applications for precision medicine approaches has not been systematically evaluated. In this study, we conducted a comprehensive survey of an exhaustive list of single-sample scoring methods to assess their stability and reproducibility performances under commo scenarios which include limitations of input data or data integration across studies. We also evaluated their performances for downstream patient stratification and clinical association analyses, as well as predictive modeling of disease states. The in-depth characterization of these scoring methods highlights the importance for a rational design of analysis strategies and provides fundamental insights into method selection under different scenarios or for different applications.<\/jats:p>","DOI":"10.1093\/bib\/bbaf684","type":"journal-article","created":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T13:13:41Z","timestamp":1764767621000},"source":"Crossref","is-referenced-by-count":1,"title":["Benchmarking single-sample gene set scoring methods for application in precision medicine"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8440-312X","authenticated-orcid":false,"given":"Daniel","family":"Toro-Dom\u00ednguez","sequence":"first","affiliation":[{"name":"Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute , Nobel v\u00e4g 13, Solna 171 67 ,","place":["Sweden"]},{"name":"Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang","family":"Wang","sequence":"additional","affiliation":[{"name":"Bristol Myers Squibb Research & Early Development , 3551 Lawrenceville Road, Princeton 08648, New Jersey ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6307-3141","authenticated-orcid":false,"given":"Iv\u00e1n","family":"Ellson-Lancho","sequence":"additional","affiliation":[{"name":"GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada , Andalusian Regional Government, PTS Granada, Avenida de la Ilustraci\u00f3n 114, Granada 18016 ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5186-0735","authenticated-orcid":false,"given":"Jordi","family":"Martorell-Marug\u00e1n","sequence":"additional","affiliation":[{"name":"GENYO. 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