{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T23:41:40Z","timestamp":1761176500700,"version":"build-2065373602"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"PNRR","award":["MCNT2 2023-12377755"],"award-info":[{"award-number":["MCNT2 2023-12377755"]}]},{"name":"Next Generation EU\u2014Italian NRRP"},{"name":"Relatech S.p.A"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The increasing availability of large-scale omics data calls for robust analytical frameworks capable of handling complex gene expression datasets while offering interpretable results. Recent advances in artificial intelligence have enabled the identification of aberrant molecular patterns distinguishing disease states from healthy controls. Coupled with improvements in model interpretability, these tools now support the identification of genes potentially driving disease phenotypes. However, current approaches to gene anomaly detection often remain limited to single datasets and lack accessible graphical interfaces. We introduce E-ABIN, a general-purpose, explainable framework for anomaly detection in biological networks. E-ABIN combines classical machine learning and graph-based deep learning techniques within a unified, user-friendly platform, enabling the detection and interpretation of anomalies from gene expression or methylation-derived networks. By integrating algorithms\u00a0such as support vector machines, random forests, graph autoencoders, and graph adversarial attributed networks, E-ABIN ensures high predictive accuracy while maintaining interpretability. We demonstrate the utility of E-ABIN through case studies of bladder cancer and celiac disease, where it effectively uncovers biologically relevant anomalies and offers insights into disease mechanisms. E-ABIN is freely available on the Zenodo platform at\u00a0https:\/\/doi.org\/10.5281\/zenodo.17062501.<\/jats:p>","DOI":"10.1093\/nargab\/lqaf135","type":"journal-article","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T11:55:51Z","timestamp":1758196551000},"source":"Crossref","is-referenced-by-count":0,"title":["E-ABIN: an explainable module for anomaly detection in biological networks"],"prefix":"10.1093","volume":"7","author":[{"given":"Ugo","family":"Lomoio","sequence":"first","affiliation":[{"name":"Magna Graecia University Department of Surgical and Medical Sciences, , Viale Europa, 88100 Catanzaro ,","place":["Italy"]},{"name":"Relatech , 87036 Rende ,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tommaso","family":"Mazza","sequence":"additional","affiliation":[{"name":"Computational Biology and Bioinformatics Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS , 00168 Roma ,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierangelo","family":"Veltri","sequence":"additional","affiliation":[{"name":"DIMES, University of Calabria , 87036 Rende ,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5542-2997","authenticated-orcid":false,"given":"Pietro\u00a0Hiram","family":"Guzzi","sequence":"additional","affiliation":[{"name":"Magna Graecia University Department of Surgical and Medical Sciences, , Viale Europa, 88100 Catanzaro ,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,10,22]]},"reference":[{"key":"2025102206144057500_B1","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/s41579-023-00984-1","article-title":"Machine learning for microbiologists","volume":"22","author":"Asnicar","year":"2024","journal-title":"Nat Rev 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