{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T03:02:08Z","timestamp":1769223728750,"version":"3.49.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T00:00:00Z","timestamp":1727395200000},"content-version":"vor","delay-in-days":0,"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":["62273086"],"award-info":[{"award-number":["62273086"]}],"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":["62471123"],"award-info":[{"award-number":["62471123"]}],"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":["62131004"],"award-info":[{"award-number":["62131004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce. In fact, we\u2019ve found a substantial 91\u00a0291 NLRs confirmed via wet experiments and bioinformatics methods but only 387 CNEs are recognized, which greatly restricts the potential application of NLRs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose a deep learning algorithm called ProNEP to identify NLR-effector pairs in a high-throughput manner. Specifically, we conceptualized the CNE prediction task as a protein\u2013protein interaction (PPI) prediction task. Then, ProNEP predicts the interaction between NLRs and effectors by combining the transfer learning with a bilinear attention network. ProNEP achieves superior performance against state-of-the-art models designed for PPI predictions. Based on ProNEP, we conduct extensive identification of potential CNEs for 91\u00a0291 NLRs. With the rapid accumulation of genomic data, we expect that this tool will be widely used to predict CNEs in new species, advancing biology, immunology, and breeding.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The ProNEP is available at http:\/\/nerrd.cn\/#\/prediction. The project code is available at https:\/\/github.com\/QiaoYJYJ\/ProNEP.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae581","type":"journal-article","created":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T17:17:55Z","timestamp":1727457475000},"source":"Crossref","is-referenced-by-count":7,"title":["Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9315-4135","authenticated-orcid":false,"given":"Baixue","family":"Qiao","sequence":"first","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]},{"name":"State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin 150001,","place":["China"]}]},{"given":"Shuda","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]},{"name":"State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin 150001,","place":["China"]}]},{"given":"Mingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]}]},{"given":"Haodi","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]}]},{"given":"Zhengwenyang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0289-7261","authenticated-orcid":false,"given":"Xueying","family":"Xie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]}]},{"given":"Shaozi","family":"Pang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]}]},{"given":"Chunxue","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Landscape Architecture, Northeast Forestry University , Harbin 150001,","place":["China"]}]},{"given":"Fenglong","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University , Fuzhou 350122,","place":["China"]},{"name":"Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University , Fuzhou 350122,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China , Chengdu 611731,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4358-8636","authenticated-orcid":false,"given":"Shanwen","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University) , Harbin 150001,","place":["China"]},{"name":"State Key Laboratory of Tree Genetics and 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