{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T07:21:43Z","timestamp":1792135303426,"version":"4.4.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T00:00:00Z","timestamp":1750291200000},"content-version":"vor","delay-in-days":49,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T24250193"],"award-info":[{"award-number":["T24250193"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32341008"],"award-info":[{"award-number":["32341008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62002265"],"award-info":[{"award-number":["62002265"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1201200"],"award-info":[{"award-number":["2021YFF1201200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200900"],"award-info":[{"award-number":["2021YFF1200900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Pilot Program for Basic Research"},{"name":"Shanghai Science and Technology Innovation Action Plan-Key Specialization in Computational Biology"},{"name":"Shanghai Shuguang Scholars Project"},{"name":"Shanghai Excellent Academic Leader Project"},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2021SHZDZX0100"],"award-info":[{"award-number":["2021SHZDZX0100"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Tongji University \u201cMedicine + X\u201d Cross Research Program","award":["2025080107"],"award-info":[{"award-number":["2025080107"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The rapid development of gene editing technology has revolutionized life science research and biotechnology applications. Prime editing, a precise gene editing tool, has shown promise in various applications, including disease research and therapeutic interventions. However, its suboptimal editing efficiency for extensive fragments and lack of predictive models have hindered its widespread adoption. Existing models exhibit low prediction accuracy and limitations, such as neglecting epigenetic factors that impact gene editing effects. To address these challenges, we developed PrimeNet, a novel prediction model that integrates significant epigenetic factors, including chromatin accessibility and DNA methylation. By incorporating data from multiple cell lines and introducing multiscale convolution and attention mechanisms, PrimeNet enhances the accuracy of predictions and generalization performance. Our results show that PrimeNet achieves a Spearman correlation coefficient of 0.94 and 0.82 on two datasets originated from HEK293T and K562 cell lines, respectively, outperforming existing models. This novel model has the potential to guide experimental design, enhance the success rate of gene editing, and reduce unnecessary experimental costs, thereby advancing the application of gene editing technology in genetic disease treatment and related fields.<\/jats:p>","DOI":"10.1093\/bib\/bbaf293","type":"journal-article","created":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T20:18:38Z","timestamp":1751055518000},"source":"Crossref","is-referenced-by-count":11,"title":["PrimeNet: rational design of Prime editing pegRNAs by deep learning"],"prefix":"10.1093","volume":"26","author":[{"given":"Xichen","family":"Liao","sequence":"first","affiliation":[{"name":"Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, No. 1239 Siping Road, Yangpu District , Shanghai 200092 ,","place":["China"]},{"name":"Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , No. 1239 Siping Road, Yangpu District, Shanghai 200092 ,","place":["China"]},{"name":"National Key Laboratory of Autonomous Intelligent Unmanned Systems, Frontiers Science Center for Intelligent Autonomous Systems, Ministry of Education , No. 366 Shangke Road, Pudong New Area, Shanghai 201804 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, No. 1239 Siping Road, Yangpu District , Shanghai 200092 ,","place":["China"]},{"name":"Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , No. 1239 Siping Road, Yangpu District, Shanghai 200092 ,","place":["China"]},{"name":"National Key Laboratory of Autonomous Intelligent Unmanned Systems, Frontiers Science Center for Intelligent Autonomous Systems, Ministry of Education, No. 366 Shangke Road, Pudong New Area , Shanghai 201804 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guohui","family":"Chuai","sequence":"additional","affiliation":[{"name":"Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , No. 1239 Siping Road, Yangpu District, Shanghai 200092 ,","place":["China"]},{"name":"Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University , No. 1239 Siping Road, Yangpu District, Shanghai 200092 ,","place":["China"]},{"name":"National Key Laboratory of Autonomous Intelligent Unmanned Systems, Frontiers Science Center for Intelligent Autonomous Systems, Ministry of Education, No. 366 Shangke Road, Pudong New Area , Shanghai 201804 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