{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T19:35:20Z","timestamp":1781724920684,"version":"3.54.5"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T00:00:00Z","timestamp":1748304000000},"content-version":"vor","delay-in-days":26,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Noncommunicable Chronic: Diseases-National Science and Technology Major Project","award":["2023ZD05 01001"],"award-info":[{"award-number":["2023ZD05 01001"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272399"],"award-info":[{"award-number":["62272399"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Major Science and Technology Project of Fujian Provincial Health Commission","award":["20212ZD01006"],"award-info":[{"award-number":["20212ZD01006"]}]},{"name":"Fundamental Research Funds the Central Universities","award":["20720220006"],"award-info":[{"award-number":["20720220006"]}]},{"name":"Special Funds for Basic Research Operating Costs of Central Universities","award":["20720220005"],"award-info":[{"award-number":["20720220005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Liquid\u2013liquid phase separation plays a critical role in cellular processes, including protein aggregation and RNA metabolism, by forming membraneless subcellular structures. Accurate identification of phase-separated proteins is essential for understanding and controlling these processes. Traditional identification methods are effective but often costly and time-consuming. The recent machine learning methods have reduced these costs, but most models are restricted to classifying scaffold and client proteins with limited experimental conditions. To address this limitation, we developed a Mamba-based encoder using contrastive learning that incorporates separation probability, protein type, and experimental conditions. Our model achieved 95.2% accuracy in predicting phase-separated proteins and an ROCAUC score of 0.87 in classifying scaffold and client proteins. Further validation in the DgHBP-2 drug delivery system demonstrated its potential for condition modulation in drug development. This study provides an effective framework for the accurate identification and control of phase separation, facilitating advancements in biomedical research and therapeutic applications.<\/jats:p>","DOI":"10.1093\/bib\/bbaf230","type":"journal-article","created":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T09:17:57Z","timestamp":1748337477000},"source":"Crossref","is-referenced-by-count":6,"title":["MambaPhase: deep learning for liquid\u2013liquid phase separation protein classification"],"prefix":"10.1093","volume":"26","author":[{"given":"Jianwei","family":"Huang","sequence":"first","affiliation":[{"name":"Institute of Artificial Intelligence , School of Informatics, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases , School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"State Key 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, School of Informatics, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases , School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases , Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoping","family":"Min","sequence":"additional","affiliation":[{"name":"Institute of Artificial Intelligence , School of Informatics, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases , School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases , Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengxiang","family":"Ge","sequence":"additional","affiliation":[{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases , School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases , Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, No. 422 Siming South Rd, 361005, Xiamen, Fujian,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Institute of Diagnostics and Vaccine Development in Infectious 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