{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T04:30:01Z","timestamp":1770957001607,"version":"3.50.1"},"reference-count":73,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,6,8]],"date-time":"2023-06-08T00:00:00Z","timestamp":1686182400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62071079"],"award-info":[{"award-number":["62071079"]}],"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":["62202388"],"award-info":[{"award-number":["62202388"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["3132020170"],"award-info":[{"award-number":["3132020170"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["3132019323"],"award-info":[{"award-number":["3132019323"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Major and Seed Inter-Disciplinary Research Projects"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Promoters are DNA regions that initiate the transcription of specific genes near the transcription start sites. In bacteria, promoters are recognized by RNA polymerases and associated sigma factors. Effective promoter recognition is essential for synthesizing the gene-encoded products by bacteria to grow and adapt to different environmental conditions. A variety of machine learning-based predictors for bacterial promoters have been developed; however, most of them were designed specifically for a particular species. To date, only a few predictors are available for identifying general bacterial promoters with limited predictive performance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we developed TIMER, a Siamese neural network-based approach for identifying both general and species-specific bacterial promoters. Specifically, TIMER uses DNA sequences as the input and employs three Siamese neural networks with the attention layers to train and optimize the models for a total of 13 species-specific and general bacterial promoters. Extensive 10-fold cross-validation and independent tests demonstrated that TIMER achieves a competitive performance and outperforms several existing methods on both general and species-specific promoter prediction. As an implementation of the proposed method, the web server of TIMER is publicly accessible at http:\/\/web.unimelb-bioinfortools.cloud.edu.au\/TIMER\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbad209","type":"journal-article","created":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T04:51:25Z","timestamp":1686286285000},"source":"Crossref","is-referenced-by-count":12,"title":["TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8692-0817","authenticated-orcid":false,"given":"Yan","family":"Zhu","sequence":"first","affiliation":[{"name":"School of Science, Dalian Maritime University , Dalian 116026 , China"}]},{"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Yangling 712100 , China"},{"name":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800 , Australia"},{"name":"Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, Victoria , Australia"}]},{"given":"Xudong","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Yangling 712100 , China"}]},{"given":"Xiaoyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800 , Australia"}]},{"given":"Lachlan J M","family":"Coin","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, Victoria , Australia"}]},{"given":"Geoffrey I","family":"Webb","sequence":"additional","affiliation":[{"name":"Monash Data Futures Institute, Monash University , Melbourne, VIC 3800 , Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800 , Australia"},{"name":"Monash Data Futures Institute, Monash University , Melbourne, VIC 3800 , Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4682-2881","authenticated-orcid":false,"given":"Cangzhi","family":"Jia","sequence":"additional","affiliation":[{"name":"School of Science, Dalian Maritime University , Dalian 116026 , China"}]}],"member":"286","published-online":{"date-parts":[[2023,6,8]]},"reference":[{"key":"2023072020155377800_ref1","doi-asserted-by":"crossref","DOI":"10.1038\/s41564-021-00898-9","article-title":"Widespread 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