{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T07:07:33Z","timestamp":1771484853121,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["62301139"],"award-info":[{"award-number":["62301139"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62225109"],"award-info":[{"award-number":["62225109"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Bacteriophages are the viruses that infect bacterial cells. They are the most diverse biological entities on earth and play important roles in microbiome. According to the phage lifestyle, phages can be divided into the virulent phages and the temperate phages. Classifying virulent and temperate phages is crucial for further understanding of the phage\u2013host interactions. Although there are several methods designed for phage lifestyle classification, they merely either consider sequence features or gene features, leading to low accuracy. A new computational method, DeePhafier, is proposed to improve classification performance on phage lifestyle. Built by several multilayer self-attention neural networks, a global self-attention neural network, and being combined by protein features of the Position Specific Scoring Matrix matrix, DeePhafier improves the classification accuracy and outperforms two benchmark methods. The accuracy of DeePhafier on five-fold cross-validation is as high as 87.54% for sequences with length &amp;gt;2000bp.<\/jats:p>","DOI":"10.1093\/bib\/bbae377","type":"journal-article","created":{"date-parts":[[2024,8,8]],"date-time":"2024-08-08T00:19:55Z","timestamp":1723076395000},"source":"Crossref","is-referenced-by-count":3,"title":["DeePhafier: a phage lifestyle classifier using a multilayer self-attention neural network combining protein information"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7719-426X","authenticated-orcid":false,"given":"Yan","family":"Miao","sequence":"first","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7993-0194","authenticated-orcid":false,"given":"Zhenyuan","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Lin","sequence":"additional","affiliation":[{"name":"National Institute for Data Science in Health and Medicine, Xiamen University , No. 4221 Xiangannan Road, Xiamen, 361102, Fujian, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoran","family":"Gu","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenjing","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingjian","family":"Liang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Hepatosplenic Surgery , Ministry of Education, Department of General Surgery, , No. 23 Postal Street, Harbin, 150007, Heilongjiang, China"},{"name":"the First Affiliated Hospital of Harbin Medical University , Ministry of Education, Department of General Surgery, , No. 23 Postal Street, Harbin, 150007, Heilongjiang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7381-2374","authenticated-orcid":false,"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,8,7]]},"reference":[{"key":"2024080720373469600_ref1","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1007\/s40484-019-0187-4","article-title":"Identifying viruses from metagenomic data using deep learning","volume":"8","author":"Ren","year":"2020","journal-title":"Quant Biol"},{"key":"2024080720373469600_ref2","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/nrmicro.2017.30","article-title":"M\u00e9nage \u00e0 trois in the human gut: interactions between host, bacteria and phages","volume":"15","author":"Mirzaei","year":"2017","journal-title":"Nat Rev Microbiol"},{"key":"2024080720373469600_ref3","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1128\/br.40.4.869-907.1976","article-title":"Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli","volume":"40","author":"Witkin","year":"1976","journal-title":"Bacteriol Rev"},{"key":"2024080720373469600_ref4","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/0168-1656(86)90009-X","article-title":"Effects of growth medium on phage production and induction in Escherichia coli K-12 lambda lysogens","volume":"3","author":"Clark","year":"1986","journal-title":"J Biotechnol"},{"key":"2024080720373469600_ref5","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1111\/j.1574-6968.1998.tb13887.x","article-title":"Virus particle production in lysogenic bacteria exposed to protozoan grazing","volume":"166","author":"Clarke","year":"1998","journal-title":"FEMS Microbiol Lett"},{"key":"2024080720373469600_ref6","doi-asserted-by":"crossref","first-page":"427","DOI":"10.4056\/sigs.2945050","article-title":"VIROME: a standard operating procedure for analysis of viral metagenome sequences","volume":"6","author":"Wommack","year":"2012","journal-title":"Stand Genomic Sci"},{"key":"2024080720373469600_ref7","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/bts014","article-title":"PHACTS, a computational approach to classifying the lifestyle of phages","volume":"28","author":"McNair","year":"2012","journal-title":"Bioinformatics"},{"key":"2024080720373469600_ref8","doi-asserted-by":"crossref","first-page":"1964","DOI":"10.3390\/v13101964","article-title":"Novel virulent bacteriophage $\\varPhi $SG005, which infects Streptococcus gordonii, forms a distinct clade among streptococcus viruses","volume":"13","author":"Fujiki","year":"2021","journal-title":"Viruses"},{"key":"2024080720373469600_ref9","doi-asserted-by":"crossref","first-page":"6309","DOI":"10.1128\/AEM.01212-12","article-title":"Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly","volume":"78","author":"Emerson","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"2024080720373469600_ref10","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1038\/ismej.2013.124","article-title":"Shotgun metagenomics indicates novel family a DNA polymerases predominate within marine virioplankton","volume":"8","author":"Schmidt","year":"2014","journal-title":"ISME J"},{"key":"2024080720373469600_ref11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nmicrobiol.2017.112","article-title":"Bacteriophage evolution differs by host, lifestyle and genome","volume":"2","author":"Mavrich","year":"2017","journal-title":"Nat Microbiol"},{"key":"2024080720373469600_ref12","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1093\/bioinformatics\/btab845","article-title":"Virtifier: a deep learning-based identifier for viral sequences from metagenomes","volume":"38","author":"Miao","year":"2022","journal-title":"Bioinformatics"},{"key":"2024080720373469600_ref13","first-page":"1","article-title":"RNN-VirSeeker: a deep learning method for identification of short viral sequences from metagenomes","volume":"19","author":"Liu","year":"2020","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2024080720373469600_ref14","doi-asserted-by":"crossref","first-page":"1169791","DOI":"10.3389\/fmicb.2023.1169791","article-title":"DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes","volume":"14","author":"Miao","year":"2023","journal-title":"Front Microbiol"},{"key":"2024080720373469600_ref15","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1093\/bioinformatics\/btx383","article-title":"WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs","volume":"33","author":"Galiez","year":"2017","journal-title":"Bioinformatics"},{"key":"2024080720373469600_ref16","doi-asserted-by":"crossref","first-page":"giab056","DOI":"10.1093\/gigascience\/giab056","article-title":"DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach","volume":"10","author":"Wu","year":"2021","journal-title":"GigaScience"},{"key":"2024080720373469600_ref17","article-title":"Poolingformer: long document modeling with pooling attention","author":"Zhang","year":"2021"},{"key":"2024080720373469600_ref18","doi-asserted-by":"crossref","first-page":"292","DOI":"10.3390\/electronics8030292","article-title":"A state-of-the-art survey on deep learning theory and architectures","volume":"8","author":"Alom","year":"2019","journal-title":"electronics"},{"key":"2024080720373469600_ref19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/3530811","article-title":"Efficient transformers: a survey","volume":"55","author":"Tay","year":"2020","journal-title":"ACM Comput Surv"},{"key":"2024080720373469600_ref20","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1109\/TCBB.2022.3199758","article-title":"Predicting TF proteins by incorporating evolution information through PSSM","volume":"20","author":"Du","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2024080720373469600_ref21","doi-asserted-by":"crossref","first-page":"bbad299","DOI":"10.1093\/bib\/bbad299","article-title":"PredLLPS_PSSM: a novel predictor for liquid\u2013liquid protein separation identification based on evolutionary information and a deep neural network","volume":"24","author":"Zhou","year":"2023","journal-title":"Brief Bioinform"},{"key":"2024080720373469600_ref22","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1089\/cmb.2020.0417","article-title":"EPTool: a new enhancing PSSM tool for protein secondary structure prediction","volume":"28","author":"Guo","year":"2021","journal-title":"J Comput Biol"},{"key":"2024080720373469600_ref23","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btq302","article-title":"Applying the Na\u00efve bayes classifier with kernel density estimation to the prediction of protein\u2013protein interaction sites","volume":"26","author":"Murakami","year":"2010","journal-title":"Bioinformatics"},{"key":"2024080720373469600_ref24","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1093\/bioinformatics\/btt709","article-title":"Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection","volume":"30","author":"Liu","year":"2014","journal-title":"Bioinformatics"},{"key":"2024080720373469600_ref25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-8-337","article-title":"Support vector machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs","volume":"8","author":"Rashid","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2024080720373469600_ref26","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2024080720373469600_ref27","doi-asserted-by":"crossref","first-page":"e191","DOI":"10.1093\/nar\/gkq747","article-title":"FragGeneScan: predicting genes in short and error-prone reads","volume":"38","author":"Rho","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024080720373469600_ref28","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2024080720373469600_ref29","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1080\/01621459.1937.10503522","article-title":"The use of ranks to avoid the assumption of normality implicit in the analysis of variance","volume":"32","author":"Friedman","year":"1937","journal-title":"J Am Stat Assoc"},{"key":"2024080720373469600_ref30","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1214\/aoms\/1177731944","article-title":"A comparison of alternative tests of significance for the problem of m rankings","volume":"11","author":"Friedman","year":"1940","journal-title":"Ann Math Stat"},{"key":"2024080720373469600_ref31","article-title":"Distribution-free multiple comparisons","volume-title":"Princeton University","author":"Nemenyi","year":"1963"},{"key":"2024080720373469600_ref32","doi-asserted-by":"crossref","first-page":"116916","DOI":"10.1016\/j.enconman.2023.116916","article-title":"Short-term multi-step wind power forecasting based on spatio-temporal correlations and transformer neural networks","volume":"283","author":"Sun","year":"2023","journal-title":"Energ Conver Manage"},{"key":"2024080720373469600_ref33","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.isprsjprs.2022.06.008","article-title":"UNetFormer: a UNet-like transformer for efficient semantic segmentation of remote sensing urban scene imagery","volume":"190","author":"Wang","year":"2022","journal-title":"ISPRS J Photogramm Remote Sens"},{"key":"2024080720373469600_ref34","doi-asserted-by":"crossref","first-page":"8972","DOI":"10.3390\/app12188972","article-title":"Deep residual learning for image recognition: a survey","volume":"12","author":"Shafiq","year":"2022","journal-title":"Appl Sci"},{"key":"2024080720373469600_ref35","first-page":"1","article-title":"Design of max pooling operation circuit for binarized neural networks using single-flux-quantum circuit","volume":"33","author":"Han","year":"2023","journal-title":"IEEE Trans Appl Supercond"},{"key":"2024080720373469600_ref36","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.ymeth.2020.05.018","article-title":"CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning","volume":"189","author":"Shang","year":"2021","journal-title":"Methods"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/5\/bbae377\/58756246\/bbae377.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/5\/bbae377\/58756246\/bbae377.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,8]],"date-time":"2024-08-08T00:20:23Z","timestamp":1723076423000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae377\/7728939"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,25]]},"references-count":36,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2024,7,25]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae377","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,9]]},"published":{"date-parts":[[2024,7,25]]},"article-number":"bbae377"}}