{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T05:43:33Z","timestamp":1775713413241,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T00:00:00Z","timestamp":1735516800000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Stan Perron Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Over the last two decades, transcriptomics has become a standard technique in biomedical research. We now have large databases of RNA-seq data, accompanied by valuable metadata detailing scientific objectives and the experimental procedures used. The metadata is crucial in understanding and replicating published studies, but so far has been underutilized in helping researchers to discover existing datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present SampleExplorer, a tool allowing researchers to search for relevant data using both text and gene set queries. SampleExplorer embeds sample metadata and uses a transformer-based language model to retrieve similar datasets. Extensive benchmarking (see Supplementary Materials and Methods) using the ARCHS4 database demonstrates that SampleExplorer provides an effective approach for retrieving biologically relevant samples from large-scale transcriptomicdata. This tool provides an efficient approach for discovering relevant gene expression datasets in large public repositories. It improves sample and dataset identification across diverse experimental contexts, helping researchers leverage existing transcriptomic data for potential replication or verification studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>\u2002<\/jats:title>\n                  <jats:p>Availability and implementation: SampleExplorer is available as a Python package compatible with versions 3.9 to 3.11, available for installation via the Python Package Index (PyPI). The codebase and documentation are accessible at https:\/\/github.com\/wlchin\/SampleExplorer. Supplementary data (Supplementary Materials and Methods) provides detailed methodological information, including an algorithmic description of the retrieval process and data preparation steps.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae759","type":"journal-article","created":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T15:42:02Z","timestamp":1735573322000},"source":"Crossref","is-referenced-by-count":1,"title":["SampleExplorer: using language models to discover relevant transcriptome data"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2549-3601","authenticated-orcid":false,"given":"Wee Loong","family":"Chin","sequence":"first","affiliation":[{"name":"National Centre for Asbestos Related Diseases , QEII Medical Centre , Nedlands, WA 6009,","place":["Australia"]},{"name":"Department of Medical Oncology, Sir Charles Gairdner Hospital , Hospital Ave , Nedlands, WA 6009,","place":["Australia"]},{"name":"The Kids Research Institute Australia , North Entrance, Perth Children's Hospital, 15 Hospital Ave , Nedlands, WA 6009,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0138-2691","authenticated-orcid":false,"given":"Timo","family":"Lassmann","sequence":"additional","affiliation":[{"name":"The Kids Research Institute Australia , North Entrance, Perth Children's Hospital, 15 Hospital Ave , Nedlands, WA 6009,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,12,30]]},"reference":[{"key":"2025012209310588500_btae759-B1","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/978-1-4939-3578-9_5","article-title":"The gene expression omnibus database","volume":"1418","author":"Clough","year":"2016","journal-title":"Methods Mol Biol"},{"key":"2025012209310588500_btae759-B2","doi-asserted-by":"crossref","first-page":"3445","DOI":"10.1093\/nar\/22.17.3445","article-title":"The European Bioinformatics Institute (EBI) databases","volume":"22","author":"Emmert","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"2025012209310588500_btae759-B3","doi-asserted-by":"publisher","author":"Gao","DOI":"10.48550\/arXiv.2312.10997,"},{"key":"2025012209310588500_btae759-B4","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1745-6150-5-51","article-title":"Measuring gene expression divergence: the distance to keep","volume":"5","author":"Glazko","year":"2010","journal-title":"Biol Direct"},{"key":"2025012209310588500_btae759-B5","doi-asserted-by":"publisher","author":"Harispe","DOI":"10.48550\/arXiv.1704.05295,"},{"key":"2025012209310588500_btae759-B6","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s12859-022-04609-x","article-title":"Distance correlation application to gene co-expression network analysis","volume":"23","author":"Hou","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2025012209310588500_btae759-B7","first-page":"i119","volume-title":"Bioinformatics","author":"Jeong","year":"2024"},{"key":"2025012209310588500_btae759-B8","doi-asserted-by":"crossref","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025012209310588500_btae759-B9","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/s41467-018-03751-6","article-title":"Massive mining of publicly available RNA-seq data from human and mouse","volume":"9","author":"Lachmann","year":"2018","journal-title":"Nat Commun"},{"key":"2025012209310588500_btae759-B10","first-page":"287","author":"Li","year":"2006"},{"key":"2025012209310588500_btae759-B11","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The molecular signatures database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst"},{"key":"2025012209310588500_btae759-B12","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/s12859-021-04130-7","article-title":"Correlation AnalyzeR: functional predictions from gene co-expression correlations","volume":"22","author":"Miller","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2025012209310588500_btae759-B13","doi-asserted-by":"publisher","author":"Naveed","DOI":"10.48550\/arXiv.2307.06435,"},{"key":"2025012209310588500_btae759-B14","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1748-7188-8-23","article-title":"Jaccard index based similarity measure to compare transcription factor binding site models","volume":"8","author":"Vorontsov","year":"2013","journal-title":"Algorithms Mol Biol"},{"key":"2025012209310588500_btae759-B15","volume-title":"NEJM AI","author":"Zakka","year":"2024"},{"key":"2025012209310588500_btae759-B16","doi-asserted-by":"publisher","author":"Zhang","DOI":"10.1101\/2024.01.02.573793,"},{"key":"2025012209310588500_btae759-B17","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12864-020-6490-7","article-title":"Identifying critical state of complex diseases by single-sample Kullback\u2013Leibler divergence","volume":"21","author":"Zhong","year":"2020","journal-title":"BMC Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae759\/61296381\/btae759.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btae759\/61296381\/btae759.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btae759\/61296381\/btae759.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,22]],"date-time":"2025-01-22T09:31:21Z","timestamp":1737538281000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae759\/7934860"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,12,26]]},"references-count":17,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12,26]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae759","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,12,26]]},"article-number":"btae759"}}