{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T05:11:47Z","timestamp":1790053907920,"version":"4.0.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":83,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2025-06236"],"award-info":[{"award-number":["RGPIN-2025-06236"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Algoma University Research Fund","id":[{"id":"https:\/\/ror.org\/0131d6623","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Accurate prioritization of T-cell receptor (TCR)-epitope interactions and identification of tumor-reactive T cells are important but difficult steps in immunotherapy-oriented bioinformatics workflows. Existing methods typically address these tasks separately and either model TCR-epitope pairs as independent observations or rely primarily on transcriptomic signatures. In this study, we present DUET (Dual Unified Evaluation of TCR-Epitopes and Tumor-reactive T cells), a graph-based computational workflow that unifies both applications within a single heterogeneous graph framework. The protocol represents TCRs, epitopes, and T cells as typed nodes connected by similarity and association edges, and combines pretrained sequence embeddings with edge-aware graph attention, Laplacian positional encoding, and bidirectional cross-domain attention. Applied to the IEDB and VDJdb benchmarks, DUET achieved AUROC\/AUPR values of 0.937\/0.922 and 0.992\/0.990, respectively, outperforming five state-of-the-art algorithms under standard evaluation. On a single-cell RNA-seq tumor-reactivity benchmark, the workflow achieved an area under the receiver operating characteristic curve of 0.985 and an area under the precision-recall curve of 0.975, substantially exceeding transcriptomic signature-based baselines. Additional generalization analyses showed that DUET\u2019s clearest graph-specific benefit occurred under epitope-disjoint TCR-epitope prediction. Ablation analysis showed that Laplacian positional encoding provided the largest performance gain, particularly in sparse graph settings. These results suggest that heterogeneous graph modeling can serve as a practical protocol for integrating receptor sequence, antigen context, and cellular phenotype in computational immunology.<\/jats:p>","DOI":"10.1093\/bib\/bbag519","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T11:37:38Z","timestamp":1788521858000},"source":"Crossref","is-referenced-by-count":0,"title":["DUET: a graph-based workflow for TCR-epitope prioritization and tumor-reactive T-cell identification"],"prefix":"10.1093","volume":"27","author":[{"given":"Yunsheng","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Computer Science & Mathematics, Faculty of Computer Science and Technology, Algoma University , 24 Queen St E, Brampton, ON L6V 1A3 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Giuliano","sequence":"additional","affiliation":[{"name":"Department of Computer Science & Mathematics, Faculty of Computer Science and Technology, Algoma University , 24 Queen St E, Brampton, ON L6V 1A3 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Dacillo","sequence":"additional","affiliation":[{"name":"Marshall McLuhan Catholic Secondary School , 1107 Avenue Rd, Toronto, ON M5N 3B1 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjun","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Computer Science & Mathematics, Faculty of Computer Science and Technology, Algoma University , 24 Queen St E, Brampton, ON L6V 1A3 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8380-2863","authenticated-orcid":false,"given":"Yan","family":"Yan","sequence":"additional","affiliation":[{"name":"College of Computational, Mathematical and Physical Sciences, School of Computer Science, University of Guelph , 474 Gordon 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