{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T17:29:42Z","timestamp":1775064582302,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T00:00:00Z","timestamp":1746144000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["IIS 2347592"],"award-info":[{"award-number":["IIS 2347592"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["2348169"],"award-info":[{"award-number":["2348169"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DBI 2405416"],"award-info":[{"award-number":["DBI 2405416"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["CCF 2348306"],"award-info":[{"award-number":["CCF 2348306"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["CNS 2347617"],"award-info":[{"award-number":["CNS 2347617"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"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>Motivation<\/jats:title>\n                  <jats:p>The biosecurity issue arises as the capability of deep-learning-based protein design has rapidly increased in recent years. Current regulation procedures for DNA synthesizing focus on the biosecurity but ignore the data privacy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose a general framework for adding watermarks to protein sequences designed by various autoregressive deep-learning models. Compared to current regulation procedures, watermarks also ensure robust traceability to achieve biosecurity but maintain privacy of designed sequences by local verification. Benchmarked with other watermarking techniques, the watermark detection efficiency of our method is substantially increased to be more practical in real-world scenarios. Moreover, it provides a convenient way for researchers to claim their own intellectual property since the designer\u2019s information could be embedded into the sequence with our framework.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The implementation of the protein watermark framework is freely available to noncommercial users at https:\/\/github.com\/poseidonchan\/ProteinWatermark.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf141","type":"journal-article","created":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T12:43:15Z","timestamp":1746189795000},"source":"Crossref","is-referenced-by-count":1,"title":["Enhancing privacy in biosecurity with watermarked protein design"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6675-2449","authenticated-orcid":false,"given":"Yanshuo","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]},{"name":"Center of Bioinformatics and Computational Biology , College Park, MD 20740,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0316-146X","authenticated-orcid":false,"given":"Zhengmian","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]}]},{"given":"Yihan","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]}]},{"given":"Ruibo","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]}]},{"given":"Yongrui","family":"Jin","sequence":"additional","affiliation":[{"name":"Graduate School of Design, Harvard University , Boston, MA 02138,","place":["United States"]}]},{"given":"Marcus","family":"Zhan","sequence":"additional","affiliation":[{"name":"Sewickley Academy , Sewickley, PA 15143,","place":["United States"]}]},{"given":"Chengjin","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Economics and Management, China Agricultural University , Beijing 100083,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7196-8703","authenticated-orcid":false,"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15261,","place":["United States"]},{"name":"Department of Pediatrics, UPMC Children\u2019s Hospital of Pittsburgh , Pittsburgh, PA 15224,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3483-8333","authenticated-orcid":false,"given":"Heng","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]},{"name":"Center of Bioinformatics and Computational Biology , College Park, MD 20740,","place":["United States"]},{"name":"Institute of Health Computing, University of Maryland , North Bethesda, MD 20852,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,2]]},"reference":[{"key":"2025072116522663300_btaf141-B1","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1126\/science.ado1671","article-title":"Protein design meets biosecurity","volume":"383","author":"Baker","year":"2024","journal-title":"Science"},{"key":"2025072116522663300_btaf141-B2","author":"Baum","year":"2024"},{"key":"2025072116522663300_btaf141-B3","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/d41586-024-00699-0","article-title":"Could AI-designed proteins be weaponized? Scientists lay out safety guidelines","volume":"627","author":"Callaway","year":"2024","journal-title":"Nature"},{"key":"2025072116522663300_btaf141-B4","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1126\/science.add2187","article-title":"Robust deep learning-based protein sequence design using ProteinMPNN","volume":"378","author":"Dauparas","year":"2022","journal-title":"Science"},{"key":"2025072116522663300_btaf141-B5","doi-asserted-by":"crossref","first-page":"4348","DOI":"10.1038\/s41467-022-32007-7","article-title":"Protgpt2 is a deep unsupervised language model for protein design","volume":"13","author":"Ferruz","year":"2022","journal-title":"Nat Commun"},{"key":"2025072116522663300_btaf141-B6","author":"Gretton","year":"2024"},{"key":"2025072116522663300_btaf141-B7"},{"key":"2025072116522663300_btaf141-B8","article-title":"Generative models for graph-based protein design","volume":"32","author":"Ingraham","year":"2019","journal-title":"Adv Neural Inform Process Syst"},{"key":"2025072116522663300_btaf141-B9","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with Alphafold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2025072116522663300_btaf141-B10","author":"Kirchenbauer","year":"2023"},{"key":"2025072116522663300_btaf141-B11","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"key":"2025072116522663300_btaf141-B12","author":"Lisanza","year":"2023"},{"key":"2025072116522663300_btaf141-B13","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1038\/s41587-022-01618-2","article-title":"Large language models generate functional protein sequences across diverse families","volume":"41","author":"Madani","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025072116522663300_btaf141-B14","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/s41587-024-02127-0","article-title":"Machine learning for functional protein design","volume":"42","author":"Notin","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2025072116522663300_btaf141-B15","first-page":"1","article-title":"Neural autoregressive distribution estimation","volume":"17","author":"Uria","year":"2016","journal-title":"J Mach Learn Res"},{"key":"2025072116522663300_btaf141-B16","author":"Wu"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf141\/63045435\/btaf141.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/7\/btaf141\/63045435\/btaf141.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/7\/btaf141\/63045435\/btaf141.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,21]],"date-time":"2025-07-21T20:52:34Z","timestamp":1753131154000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf141\/8124073"}},"subtitle":[],"editor":[{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,5,2]]},"references-count":16,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2025,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf141","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,5,2]]},"article-number":"btaf141"}}