{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T14:39:53Z","timestamp":1767969593973,"version":"3.49.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Institut National de la Sant\u00e9 et de la Recherche Biom\u00e9dicale"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>High-throughput multi-omics technologies produce increasingly large and heterogeneous datasets that are difficult to analyze without advanced computational expertise. Existing bioinformatics tools are often fragmented or limited to specific omics types, hindering reproducibility and accessibility. There is a critical need for an integrated, user-friendly, and scalable platform capable of supporting multi-omics analyses across different data modalities.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Profiler, an open-source, modular platform that unifies data import, quality control, preprocessing, statistical testing, machine and deep learning, biomarker discovery, pathway and drug\u2013target enrichment, and survival modeling within a single reproducible environment. Built in Python with Streamlit, Profiler is available as both a web-based platform deployed on high-performance computing and a desktop version for local execution, enabling flexible usage across computational infrastructures. Profiler supports diverse omics modalities, including proteomics, transcriptomics, lipidomics, and electroencephalogram data. Through applications to glioblastoma proteomic, pancancer, and multi-omics datasets, Profiler reproduced known molecular subtypes, revealed potential therapeutic targets, and generated fully traceable analysis reports within minutes. By integrating advanced analytics behind an intuitive interface, Profiler democratizes multi-omics analysis and provides a robust, scalable foundation for systems biology and precision medicine research.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Profiler is open-source and freely available via its web platform (https:\/\/prism-profiler.univ-lille.fr) and GitHub (web version: https:\/\/github.com\/yanisZirem\/Profiler_v1_requests_datatests, desktop version: https:\/\/github.com\/yanisZirem\/prism-profiler), and archived on Zenodo (DOI: https:\/\/doi.org\/10.5281\/zenodo.17478158).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf644","type":"journal-article","created":{"date-parts":[[2025,11,27]],"date-time":"2025-11-27T13:13:35Z","timestamp":1764249215000},"source":"Crossref","is-referenced-by-count":0,"title":["Profiler: an open web platform for multi-omics analysis"],"prefix":"10.1093","volume":"42","author":[{"given":"Yanis","family":"Zirem","sequence":"first","affiliation":[{"name":"Univ. Lille, Inserm, CHU Lille, U1192, Prot\u00e9omique R\u00e9ponse Inflammatoire Spectrom\u00e9trie de Masse, PRISM , Lille F-59000,","place":["France"]}]},{"given":"L\u00e9a","family":"Ledoux","sequence":"additional","affiliation":[{"name":"Univ. Lille, Inserm, CHU Lille, U1192, Prot\u00e9omique R\u00e9ponse Inflammatoire Spectrom\u00e9trie de Masse, PRISM , Lille F-59000,","place":["France"]}]},{"given":"Isabelle","family":"Fournier","sequence":"additional","affiliation":[{"name":"Univ. Lille, Inserm, CHU Lille, U1192, Prot\u00e9omique R\u00e9ponse Inflammatoire Spectrom\u00e9trie de Masse, PRISM , Lille F-59000,","place":["France"]},{"name":"Institut Universitaire de France, minist\u00e8re de l\u2019Enseignement sup\u00e9rieur, de la Recherche et de l\u2019Innovation , Paris Cedex 05 75231,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4318-0817","authenticated-orcid":false,"given":"Michel","family":"Salzet","sequence":"additional","affiliation":[{"name":"Univ. Lille, Inserm, CHU Lille, U1192, Prot\u00e9omique R\u00e9ponse Inflammatoire Spectrom\u00e9trie de Masse, PRISM , Lille F-59000,","place":["France"]},{"name":"Institut Universitaire de France, minist\u00e8re de l\u2019Enseignement sup\u00e9rieur, de la Recherche et de l\u2019Innovation , Paris Cedex 05 75231,","place":["France"]}]}],"member":"286","published-online":{"date-parts":[[2025,12,1]]},"reference":[{"key":"2026010906514712800_btaf644-B1","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026010906514712800_btaf644-B2","doi-asserted-by":"crossref","first-page":"e0295632","DOI":"10.1371\/journal.pone.0295632","article-title":"Improving prediction of cervical cancer using KNN imputer and multi-model ensemble 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