{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T21:24:17Z","timestamp":1778621057458,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T00:00:00Z","timestamp":1714694400000},"content-version":"vor","delay-in-days":37,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["62372375"],"award-info":[{"award-number":["62372375"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["32270128"],"award-info":[{"award-number":["32270128"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shaanxi Province Key Research and Development Program","award":["2023-YBSF-114"],"award-info":[{"award-number":["2023-YBSF-114"]}]},{"name":"CAAI-Huawei Mind Spore Open Fund","award":["CAAIXSJLJJ-2022-035A"],"award-info":[{"award-number":["CAAIXSJLJJ-2022-035A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>It is a vital step to recognize cyanobacteria promoters on a genome-wide scale. Computational methods are promising to assist in difficult biological identification. When building recognition models, these methods rely on non-promoter generation to cope with the lack of real non-promoters. Nevertheless, the factitious significant difference between promoters and non-promoters causes over-optimistic prediction. Moreover, designed for E. coli or B. subtilis, existing methods cannot uncover novel, distinct motifs among cyanobacterial promoters. To address these issues, this work first proposes a novel non-promoter generation strategy called phantom sampling, which can eliminate the factitious difference between promoters and generated non-promoters. Furthermore, it elaborates a novel promoter prediction model based on the Siamese network (SiamProm), which can amplify the hidden difference between promoters and non-promoters through a joint characterization of global associations, upstream and downstream contexts, and neighboring associations w.r.t. k-mer tokens. The comparison with state-of-the-art methods demonstrates the superiority of our phantom sampling and SiamProm. Both comprehensive ablation studies and feature space illustrations also validate the effectiveness of the Siamese network and its components. More importantly, SiamProm, upon our phantom sampling, finds a novel cyanobacterial promoter motif (\u2018GCGATCGC\u2019), which is palindrome-patterned, content-conserved, but position-shifted.<\/jats:p>","DOI":"10.1093\/bib\/bbae193","type":"journal-article","created":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T10:29:35Z","timestamp":1714732175000},"source":"Crossref","is-referenced-by-count":9,"title":["Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-7409-3435","authenticated-orcid":false,"given":"Guang","family":"Yang","sequence":"first","affiliation":[{"name":"School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-2298-8074","authenticated-orcid":false,"given":"Jianing","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinlu","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2303-273X","authenticated-orcid":false,"given":"Jian-Yu","family":"Shi","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,5,2]]},"reference":[{"issue":"2","key":"2024050310291962200_ref1","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1111\/1751-7915.13526","article-title":"Progress and challenges in engineering cyanobacteria as chassis for light-driven biotechnology","volume":"13","author":"Hitchcock","year":"2020","journal-title":"J Microbial Biotechnol"},{"issue":"5","key":"2024050310291962200_ref2","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1007\/s00253-019-10344-w","article-title":"Regulatory systems for gene expression control in cyanobacteria","volume":"104","author":"Till","year":"2020","journal-title":"Appl Microbiol Biotechnol"},{"issue":"8","key":"2024050310291962200_ref3","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1016\/j.bbagrm.2015.04.003","article-title":"The core promoter: At the heart of gene expression","volume":"1849","author":"Danino","year":"2015","journal-title":"Biochim Biophys Acta"},{"issue":"4","key":"2024050310291962200_ref4","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1016\/j.molcel.2015.05.004","article-title":"High-throughput sequencing technologies","volume":"58","author":"Reuter","year":"2015","journal-title":"Mol Cell"},{"issue":"2","key":"2024050310291962200_ref5","doi-asserted-by":"crossref","first-page":"bbab551","DOI":"10.1093\/bib\/bbab551","article-title":"Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction","volume":"23","author":"Zhang","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024050310291962200_ref6","first-page":"9","volume-title":"Proceedings of the 2006 Workshop on Intelligent Systems for Bioinformatics","author":"Maetschke","year":"2006"},{"key":"2024050310291962200_ref7","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.jtbi.2011.07.017","article-title":"BacPP: bacterial promoter prediction--a tool for accurate sigma-factor specific assignment in enterobacteria","volume":"287","author":"Avila","year":"2011","journal-title":"J Theor Biol"},{"issue":"1","key":"2024050310291962200_ref8","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s12859-018-2049-x","article-title":"G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs","volume":"19","author":"Di Salvo","year":"2018","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"2024050310291962200_ref9","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/bioinformatics\/btw629","article-title":"bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli","volume":"33","author":"Shahmuradov","year":"2017","journal-title":"Bioinformatics"},{"issue":"4","key":"2024050310291962200_ref10","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1109\/TCBB.2017.2666141","article-title":"Identifying Sigma70 promoters with novel pseudo nucleotide composition","volume":"16","author":"Lin","year":"2019","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"2","key":"2024050310291962200_ref11","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1093\/bib\/bbaa049","article-title":"Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework","volume":"22","author":"Li","year":"2021","journal-title":"Brief Bioinform"},{"key":"2024050310291962200_ref12","doi-asserted-by":"crossref","first-page":"286","DOI":"10.3389\/fgene.2019.00286","article-title":"DeePromoter: robust promoter predictor using deep learning","volume":"10","author":"Oubounyt","year":"2019","journal-title":"Front Genet"},{"issue":"18","key":"2024050310291962200_ref13","doi-asserted-by":"crossref","first-page":"10278","DOI":"10.1093\/nar\/gkac824","article-title":"iPro-WAEL: a comprehensive and robust framework for identifying promoters in multiple species","volume":"50","author":"Zhang","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024050310291962200_ref14","doi-asserted-by":"crossref","first-page":"1067562","DOI":"10.3389\/fgene.2022.1067562","article-title":"TSSNote-CyaPromBERT: development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT","volume":"13","author":"Mai","year":"2022","journal-title":"Front Genet"},{"issue":"6","key":"2024050310291962200_ref15","doi-asserted-by":"crossref","first-page":"829","DOI":"10.3390\/cells12060829","article-title":"iProm-Sigma54: a CNN Base prediction tool for \u03c354 promoters","volume":"12","author":"Shujaat","year":"2023","journal-title":"Cells"},{"key":"2024050310291962200_ref16","first-page":"14","article-title":"Predicting Corynebacterium glutamicum promoters based on novel feature descriptor and feature selection technique","volume":"14","author":"Li","year":"2023","journal-title":"Front Microbiol"},{"key":"2024050310291962200_ref17","doi-asserted-by":"crossref","first-page":"66113","DOI":"10.1109\/ACCESS.2023.3285197","article-title":"iPro-TCN: prediction of DNA promoters recognition and their strength using temporal convolutional network","volume":"11","author":"Raza","year":"2023","journal-title":"IEEE Access"},{"issue":"50","key":"2024050310291962200_ref18","doi-asserted-by":"crossref","first-page":"20130","DOI":"10.1073\/pnas.1112724108","article-title":"Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in anabaena sp. PCC7120","volume":"108","author":"Mitschke","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024050310291962200_ref19","first-page":"65","article-title":"Sigma factors for cyanobacterial transcription","volume":"3","author":"Imamura","year":"2009","journal-title":"Gene Regul Syst Biol"},{"issue":"5","key":"2024050310291962200_ref20","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1093\/dnares\/8.5.205","article-title":"Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium anabaena sp. strain PCC 7120","volume":"8","author":"Kaneko","year":"2001","journal-title":"DNA Res"},{"key":"2024050310291962200_ref21","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.ymeth.2022.03.017","article-title":"Promoter prediction in nannochloropsis based on densely connected convolutional neural networks","volume":"204","author":"Wei","year":"2022","journal-title":"Methods"},{"issue":"13","key":"2024050310291962200_ref22","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"issue":"19","key":"2024050310291962200_ref23","doi-asserted-by":"crossref","first-page":"4869","DOI":"10.1093\/bioinformatics\/btaa609","article-title":"iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters","volume":"36","author":"Amin","year":"2020","journal-title":"Bioinformatics"},{"issue":"4","key":"2024050310291962200_ref24","doi-asserted-by":"crossref","first-page":"bbaa299","DOI":"10.1093\/bib\/bbaa299","article-title":"Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks","volume":"22","author":"Zhu","year":"2021","journal-title":"Brief Bioinform"},{"issue":"1","key":"2024050310291962200_ref25","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1080\/10485252.2017.1404598","article-title":"Multiple predicting K-fold cross-validation for model selection","volume":"30","author":"Jung","year":"2018","journal-title":"J Nonparametr Stat"},{"issue":"Database issue","key":"2024050310291962200_ref26","first-page":"D114","article-title":"ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes","volume":"36","author":"Hu","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2024050310291962200_ref27","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"issue":"1","key":"2024050310291962200_ref28","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1146\/annurev-statistics-030718-104938","article-title":"Statistical aspects of Wasserstein distances","volume":"6","author":"Panaretos","year":"2019","journal-title":"Annu Rev Stat Appl"},{"key":"2024050310291962200_ref29","first-page":"4171","volume-title":"Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies","author":"Devlin","year":"2019"},{"issue":"11","key":"2024050310291962200_ref30","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"Van der Maaten","year":"2008","journal-title":"J Mach Learn Res"},{"issue":"20","key":"2024050310291962200_ref31","doi-asserted-by":"crossref","first-page":"6397","DOI":"10.1128\/jb.176.20.6397-6401.1994","article-title":"Analysis of expression of the argC and argD genes in the cyanobacterium Anabaena sp. strain PCC 7120","volume":"176","author":"Floriano","year":"1994","journal-title":"J Bacteriol"},{"issue":"9","key":"2024050310291962200_ref32","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.1016\/j.str.2004.07.014","article-title":"An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site","volume":"12","author":"Xu","year":"2004","journal-title":"Structure"},{"issue":"4","key":"2024050310291962200_ref33","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1515\/bc.2011.042","article-title":"Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes","volume":"392","author":"Al-Attar","year":"2011","journal-title":"Biol Chem"},{"issue":"1","key":"2024050310291962200_ref34","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/bit.26841","article-title":"Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells","volume":"116","author":"Deng","year":"2019","journal-title":"Biotechnol Bioeng"},{"issue":"6","key":"2024050310291962200_ref35","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1093\/nar\/gkab086","article-title":"Mechanism of forkhead transcription factors binding to a novel palindromic DNA site","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2024050310291962200_ref36","first-page":"495","article-title":"Recent advances in computational promoter analysis in understanding the transcriptional regulatory network","volume":"309","author":"Qiu","year":"2003","journal-title":"Mol Cell Biol Res Commun"},{"issue":"19","key":"2024050310291962200_ref37","doi-asserted-by":"crossref","first-page":"4497","DOI":"10.1093\/bioinformatics\/btac575","article-title":"CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types","volume":"38","author":"Zhang","year":"2022","journal-title":"Bioinformatics"},{"issue":"1","key":"2024050310291962200_ref38","first-page":"538","article-title":"Lnclocator-imb: an imbalance-tolerant ensemble deep learning framework for predicting long non-coding RNA subcellular localization","volume":"28","author":"H","year":"2023","journal-title":"IEEE J Biomed Health Inform"},{"issue":"9","key":"2024050310291962200_ref39","doi-asserted-by":"crossref","first-page":"4559","DOI":"10.1109\/JBHI.2023.3292299","article-title":"IChrom-deep: an attention-based deep learning model for identifying chromatin interactions","volume":"27","author":"Zhang","year":"2023","journal-title":"IEEE J Biomed Health Inform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/3\/bbae193\/57390467\/bbae193.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/3\/bbae193\/57390467\/bbae193.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T10:30:01Z","timestamp":1714732201000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae193\/7663433"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,27]]},"references-count":39,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae193","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,5,1]]},"published":{"date-parts":[[2024,3,27]]},"article-number":"bbae193"}}