{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T12:23:03Z","timestamp":1777119783957,"version":"3.51.4"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T00:00:00Z","timestamp":1747958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and more recent deep learning techniques, the last of which often overlook the underlying gene expression mechanisms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we introduce TRENDY, a novel GRN inference method that integrates transformer models to enhance the mechanism-based WENDY approach. Through testing on both simulated and experimental datasets, TRENDY demonstrates superior performance compared to existing methods. Furthermore, we apply this transformer-based approach to three additional inference methods, showcasing its broad potential to enhance GRN inference.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Code and data files are available at https:\/\/github.com\/YueWangMathbio\/TRENDY, with DOI: 10.6084\/m9.figshare.28236074.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf314","type":"journal-article","created":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T09:10:18Z","timestamp":1747818618000},"source":"Crossref","is-referenced-by-count":6,"title":["TRENDY: gene regulatory network inference enhanced by transformer"],"prefix":"10.1093","volume":"41","author":[{"given":"Xueying","family":"Tian","sequence":"first","affiliation":[{"name":"School of Information, University of California , Berkeley, CA 94720,","place":["United 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