{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T07:17:35Z","timestamp":1789802255270,"version":"4.0.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":51,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wilhelm Schuler Stiftung"},{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Research Technology and Space","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Excellence Strategy of the German Federal and State Governments"},{"DOI":"10.13039\/501100002345","name":"University of T\u00fcbingen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002345","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Time-resolved transcriptomic profiling has been used to study phage\u2013host interactions for more than a decade. However, the resulting datasets are not readily accessible for custom re-analysis, and resources are lacking that provide standardized processing, storage, and analysis of transcriptomes from phage infections. Here, we present the PhageExpressionAtlas, the first bioinformatics resource for storing time-resolved dual RNA-sequencing data from phage infections. This data was processed uniformly using a custom analysis pipeline and is presented for interactive exploration through visualization. The PhageExpressionAtlas currently hosts 42 datasets from 23 studies. Using the PhageExpressionAtlas, we replicate key findings from original publications and extend hypothesis testing across multiple phage\u2013host systems. By systematically querying and analyzing the underlying database, we evaluate approaches to phage gene classification and find that uncharacterized phage genes dominate all infection phases, with their distribution depending strongly on the classification strategy. Moreover, we provide a comprehensive view of the expression dynamics of anti-phage defenses as well as host- and phage-encoded anti-defense systems in the infection context, indicating unique and conserved patterns of transcriptional regulation underlying bacterial anti-phage immunity and phage counter-strategies. Together, the PhageExpressionAtlas is a unifying resource that democratizes transcriptomics-driven analyses of phage\u2013host interactions and supports integrative cross-study assessment.<\/jats:p>","DOI":"10.1093\/nargab\/lqag097","type":"journal-article","created":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T11:53:41Z","timestamp":1786190021000},"source":"Crossref","is-referenced-by-count":1,"title":["The PhageExpressionAtlas reveals shared and unique transcriptional patterns across phage\u2013host interactions"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6988-2775","authenticated-orcid":false,"given":"Maik","family":"Wolfram-Schauerte","sequence":"first","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , Sand 14, D-72076 Baden-W\u00fcrttemberg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0840-1537","authenticated-orcid":false,"given":"Caroline","family":"Trust","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , Sand 14, D-72076 Baden-W\u00fcrttemberg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nils","family":"Waffenschmidt","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , Sand 14, D-72076 Baden-W\u00fcrttemberg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1283-7065","authenticated-orcid":false,"given":"Kay","family":"Nieselt","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , Sand 14, D-72076 Baden-W\u00fcrttemberg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"2026081705073562200_B1","doi-asserted-by":"publisher","first-page":"2782","DOI":"10.12688\/f1000research.9705.1","article-title":"Bacteriophage-based tools: recent advances and novel applications","volume":"5","author":"O\u201dSullivan","year":"2016","journal-title":"F1000Res"},{"key":"2026081705073562200_B2","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat Commun"},{"key":"2026081705073562200_B3","doi-asserted-by":"publisher","first-page":"eadd8643","DOI":"10.1126\/science.add8643","article-title":"CRISPR technology: A decade of genome editing is only the beginning","volume":"379","author":"Wang","year":"2023","journal-title":"Science"},{"key":"2026081705073562200_B4","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.1016\/j.tim.2024.05.005","article-title":"The growing repertoire of phage anti-defence systems","volume":"32","author":"Murtazalieva","year":"2024","journal-title":"Trends Microbiol"},{"key":"2026081705073562200_B5","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/s41564-024-01616-x","article-title":"Phage proteins target and co-opt host ribosomes immediately upon infection","volume":"9","author":"Gerovac","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026081705073562200_B6","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1038\/s41586-023-06429-2","article-title":"A viral ADP-ribosyltransferase attaches RNA chains to host proteins","volume":"620","author":"Wolfram-Schauerte","year":"2023","journal-title":"Nature"},{"key":"2026081705073562200_B7","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s43586-024-00377-5","article-title":"Phage therapy","volume":"5","author":"Skurnik","year":"2025","journal-title":"Nat Rev Methods Primers"},{"key":"2026081705073562200_B8","doi-asserted-by":"publisher","first-page":"102419","DOI":"10.1016\/j.mib.2023.102419","article-title":"Exploring the transcriptional landscape of phage\u2013host interactions using novel high-throughput approaches","volume":"77","author":"Putzeys","year":"2024","journal-title":"Curr Opin Microbiol"},{"key":"2026081705073562200_B9","doi-asserted-by":"publisher","first-page":"1778","DOI":"10.1080\/15476286.2020.1870844","article-title":"Differential transcription profiling of the phage LUZ19 infection process in different growth media","volume":"18","author":"Brandao","year":"2021","journal-title":"RNA Biol"},{"key":"2026081705073562200_B10","doi-asserted-by":"publisher","first-page":"2502","DOI":"10.3390\/v14112502","article-title":"Integrated omics reveal time-resolved insights into T4 phage infection of E. coli on proteome and transcriptome levels","volume":"14","author":"Wolfram-Schauerte","year":"2022","journal-title":"Viruses"},{"key":"2026081705073562200_B11","doi-asserted-by":"publisher","first-page":"2361","DOI":"10.1016\/j.molcel.2021.03.027","article-title":"Shutoff of host transcription triggers a toxin\u2013antitoxin system to cleave phage RNA and abort infection","volume":"81","author":"Guegler","year":"2021","journal-title":"Mol Cell"},{"key":"2026081705073562200_B12","doi-asserted-by":"publisher","first-page":"2165","DOI":"10.1111\/1462-2920.14979","article-title":"Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages","volume":"22","author":"Lood","year":"2020","journal-title":"Environ Microbiol"},{"key":"2026081705073562200_B13","doi-asserted-by":"publisher","first-page":"e0012322","DOI":"10.1128\/spectrum.00123-22","article-title":"Global transcriptomic analysis of bacteriophage\u2013host interactions between a kayvirus therapeutic phage and Staphylococcus aureus","volume":"10","author":"Finstrlova","year":"2022","journal-title":"Microbiol Spectr"},{"key":"2026081705073562200_B14","doi-asserted-by":"publisher","first-page":"D756","DOI":"10.1093\/nar\/gkad979","article-title":"PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations","volume":"52","author":"Wang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026081705073562200_B15","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1093\/bioinformatics\/btw711","article-title":"PhagesDB: the actinobacteriophage database","volume":"33","author":"Russell","year":"2017","journal-title":"Bioinformatics"},{"key":"2026081705073562200_B16","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di\u00a0Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026081705073562200_B17","article-title":"FastQC: A quality control tool for high throughput sequence data","author":"Andrews","year":"2010","journal-title":"Babraham Bioinformatics"},{"key":"2026081705073562200_B18","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J"},{"key":"2026081705073562200_B19","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026081705073562200_B20","doi-asserted-by":"publisher","first-page":"btac776","DOI":"10.1093\/bioinformatics\/btac776","article-title":"Pharokka: a fast scalable bacteriophage annotation tool","volume":"39","author":"Bouras","year":"2023","journal-title":"Bioinformatics"},{"key":"2026081705073562200_B21","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1128\/MMBR.67.1.86-156.2003","article-title":"Bacteriophage T4 genome","volume":"67","author":"Miller","year":"2003","journal-title":"Microbiol Mol Biol Rev"},{"key":"2026081705073562200_B22","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1006\/viro.2002.1409","article-title":"Microarray analysis of gene expression during bacteriophage T4 infection","volume":"299","author":"Luke","year":"2002","journal-title":"Virology"},{"key":"2026081705073562200_B23","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2026081705073562200_B24","doi-asserted-by":"publisher","first-page":"e27041","DOI":"10.7554\/eLife.27041","article-title":"The Human Cell Atlas","volume":"6","author":"Regev","year":"2017","journal-title":"elife"},{"key":"2026081705073562200_B25","doi-asserted-by":"publisher","first-page":"17365","DOI":"10.1073\/pnas.0408028101","article-title":"The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase","volume":"101","author":"Nechaev","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026081705073562200_B26","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/0022-2836(84)90073-1","article-title":"Gene 68, a new bacteriophage T4 gene which codes for the 17K prohead core protein is involved in head size determination","volume":"179","author":"Keller","year":"1984","journal-title":"J Mol Biol"},{"key":"2026081705073562200_B27","doi-asserted-by":"publisher","first-page":"6323","DOI":"10.1128\/jb.172.11.6323-6332.1990","article-title":"Bacteriophage T4 nrdA and nrdB genes, encoding ribonucleotide reductase, are expressed both separately and coordinately: characterization of the nrdB promoter","volume":"172","author":"Tseng","year":"1990","journal-title":"J Bacteriol"},{"key":"2026081705073562200_B28","doi-asserted-by":"publisher","first-page":"5740","DOI":"10.1128\/jb.174.17.5740-5744.1992","article-title":"Tandem cloning of bacteriophage T4 nrdA and nrdB genes and overproduction of ribonucleoside diphosphate reductase (alpha 2 beta 2) and a mutationally altered form (alpha 2 beta 2(93))","volume":"174","author":"Tseng","year":"1992","journal-title":"J Bacteriol"},{"key":"2026081705073562200_B29","doi-asserted-by":"publisher","first-page":"2382","DOI":"10.1074\/jbc.M110.178871","article-title":"Biochemical characterization of bacteriophage T4 Mre11\u2013Rad50 complex","volume":"286","author":"Herdendorf","year":"2011","journal-title":"J Biol Chem"},{"key":"2026081705073562200_B30","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1128\/JVI.23.3.645-658.1977","article-title":"Bacteriophage T4 virion dihydrofolate reductase: approaches to quantitation and assessment of function","volume":"23","author":"Mosher","year":"1977","journal-title":"J Virol"},{"key":"2026081705073562200_B31","doi-asserted-by":"publisher","first-page":"7548","DOI":"10.1038\/ncomms8548","article-title":"Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution","volume":"6","author":"Sun","year":"2015","journal-title":"Nat Commun"},{"key":"2026081705073562200_B32","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/S0079-6603(08)00802-7","article-title":"RNA processing and decay in bacteriophage T4","volume":"85","author":"Uzan","year":"2009","journal-title":"Prog Mol Biol Transl Sci"},{"key":"2026081705073562200_B33","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1186\/1743-422X-7-360","article-title":"Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation","volume":"7","author":"Uzan","year":"2010","journal-title":"Virol J"},{"key":"2026081705073562200_B34","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1038\/s41586-022-04716-y","article-title":"Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity","volume":"605","author":"Hobbs","year":"2022","journal-title":"Nature"},{"key":"2026081705073562200_B35","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/s41586-019-1605-5","article-title":"Cyclic GMP-AMP signalling protects bacteria against viral infection","volume":"574","author":"Cohen","year":"2019","journal-title":"Nature"},{"key":"2026081705073562200_B36","doi-asserted-by":"publisher","first-page":"gkaf1448","DOI":"10.1093\/nar\/gkaf1448","article-title":"Protein structure-informed bacteriophage genome annotation with Phold","volume":"54","author":"Bouras","year":"2026","journal-title":"Nucleic Acids Res"},{"key":"2026081705073562200_B37","doi-asserted-by":"publisher","first-page":"e00068","DOI":"10.1128\/mSystems.00068-19","article-title":"Global transcriptomic analysis of the interactions between phage phiAbp1 and extensively drug-resistant Acinetobacter baumannii","volume":"4","author":"Yang","year":"2019","journal-title":"mSystems"},{"key":"2026081705073562200_B38","doi-asserted-by":"crossref","article-title":"Environment and physiology shape antiphage system expression","author":"Paoli","DOI":"10.64898\/2025.12.14.694197"},{"key":"2026081705073562200_B39","doi-asserted-by":"publisher","first-page":"4035","DOI":"10.1038\/s41467-026-70381-8","article-title":"Dynamics of phage\u2013host interactions in Bacteroides fragilis resolved by single-cell transcriptomics","volume":"17","author":"Gupta","year":"2026","journal-title":"Nat Commun"},{"key":"2026081705073562200_B40","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1080\/15476286.2020.1827785","article-title":"Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage \u03a6KZ","volume":"18","author":"Wicke","year":"2021","journal-title":"RNA Biol"},{"key":"2026081705073562200_B41","doi-asserted-by":"publisher","article-title":"T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme","author":"Wolfram-Schauerte","DOI":"10.1101\/2024.04.04.588121"},{"key":"2026081705073562200_B42","doi-asserted-by":"publisher","first-page":"2624","DOI":"10.1016\/j.csbj.2022.05.034","article-title":"Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages","volume":"20","author":"Putzeys","year":"2022","journal-title":"Comput Struct Biotechnol J"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag097\/70661100\/lqag097.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag097\/70661100\/lqag097.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T09:07:43Z","timestamp":1786957663000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag097\/8762130"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,27]]},"references-count":42,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,6,27]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag097","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,6,27]]},"article-number":"lqag097"}}