{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T19:39:24Z","timestamp":1754163564852,"version":"3.41.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T00:00:00Z","timestamp":1753142400000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Pathway enrichment analysis is a fundamental technique in bioinformatics for interpreting gene expression data to pinpoint biological pathways associated with specific conditions or diseases. We introduce Pathway Enrichment Analysis through Network UTilization (PEANUT), a web-based tool for pathway enrichment analysis that enhances traditional pipelines by integrating network propagation computations within a network of protein\u2013protein interactions (PPIs). By diffusing gene expression scores through the PPI network, PEANUT amplifies the signals of connected sets of genes, thereby improving the detection of relevant pathways.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The tool is accessible as an open-source web application at https:\/\/peanut.cs.tau.ac.il\/. The source code is available at https:\/\/github.com\/Yapibe\/PEANUT with a permanent identifier (DOI: https:\/\/doi.org\/10.5281\/zenodo.15184862).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf410","type":"journal-article","created":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T04:22:32Z","timestamp":1753158152000},"source":"Crossref","is-referenced-by-count":0,"title":["PEANUT: Pathway Enrichment Analysis through Network UTilization"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-0470-6604","authenticated-orcid":false,"given":"Yair","family":"Pickholz Berliner","sequence":"first","affiliation":[{"name":"School of Computer Science and AI, Tel Aviv University , Tel Aviv, 69978,","place":["Israel"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8363-4882","authenticated-orcid":false,"given":"Roded","family":"Sharan","sequence":"additional","affiliation":[{"name":"School of Computer Science and AI, Tel Aviv 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