{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T11:05:54Z","timestamp":1777547154561,"version":"3.51.4"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,9,26]],"date-time":"2022-09-26T00:00:00Z","timestamp":1664150400000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["KYCXJC2022003"],"award-info":[{"award-number":["KYCXJC2022003"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["31671323"],"award-info":[{"award-number":["31671323"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Identification of transcription factor binding sites (TFBSs) is essential to understanding of gene regulation. Designing computational models for accurate prediction of TFBSs is crucial because it is not feasible to experimentally assay all transcription factors (TFs) in all sequenced eukaryotic genomes. Although many methods have been proposed for the identification of TFBSs in humans, methods designed for plants are comparatively underdeveloped. Here, we present PlantBind, a method for integrated prediction and interpretation of TFBSs based on DNA sequences and DNA shape profiles. Built on an attention-based multi-label deep learning framework, PlantBind not only simultaneously predicts the potential binding sites of 315 TFs, but also identifies the motifs bound by transcription factors. During the training process, this model revealed a strong similarity among TF family members with respect to target binding sequences. Trans-species prediction performance using four Zea mays TFs demonstrated the suitability of this model for transfer learning. Overall, this study provides an effective solution for identifying plant TFBSs, which will promote greater understanding of transcriptional regulatory mechanisms in plants.<\/jats:p>","DOI":"10.1093\/bib\/bbac425","type":"journal-article","created":{"date-parts":[[2022,9,26]],"date-time":"2022-09-26T08:50:11Z","timestamp":1664182211000},"source":"Crossref","is-referenced-by-count":21,"title":["PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites"],"prefix":"10.1093","volume":"23","author":[{"given":"Wenkai","family":"Yan","sequence":"first","affiliation":[{"name":"Nanjing Agricultural University"}]},{"given":"Zutan","family":"Li","sequence":"additional","affiliation":[{"name":"Nanjing Agricultur al University"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7401-2926","authenticated-orcid":false,"given":"Cong","family":"Pian","sequence":"additional","affiliation":[{"name":"College of Sciences at Nanjing Agricultural University"}]},{"given":"Yufeng","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, College of Agriculture, Academy for Advanced Interdisciplinary Studies at Nanjing Agricultural University"}]}],"member":"286","published-online":{"date-parts":[[2022,9,24]]},"reference":[{"key":"2023092407460194000_ref1","doi-asserted-by":"crossref","first-page":"102136","DOI":"10.1016\/j.pbi.2021.102136","article-title":"Plant transcription factors\u2014being in the right place with the right company","volume":"65","author":"Strader","year":"2022","journal-title":"Curr Opin Plant Biol"},{"key":"2023092407460194000_ref2","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1126\/science.2667136","article-title":"Transcriptional regulation in mammalian cells by sequence-specific DNA binding 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