{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T19:15:02Z","timestamp":1790709302307,"version":"4.1.0"},"reference-count":90,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T00:00:00Z","timestamp":1765843200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004622","name":"KWF Kankerbestrijding","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004622","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","award":["HHSN272201400008C"],"award-info":[{"award-number":["HHSN272201400008C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021821","name":"Oncode Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100021821","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["101102733"],"award-info":[{"award-number":["101102733"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Systems"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1016\/j.cels.2025.101489","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T16:20:56Z","timestamp":1770826856000},"page":"101489","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"title":["Live-cell single-vRNP imaging identifies viral gene expression signatures that shape influenza infection heterogeneity"],"prefix":"10.1016","volume":"17","author":[{"given":"Huib H.","family":"Rabouw","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janin","family":"Schokolowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Micha","family":"M\u00fcller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthijs J.D.","family":"Baars","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonella F.M.","family":"Dost","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theo M.","family":"Bestebroer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob","family":"P\u00fcschel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans","family":"Clevers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ron A.M.","family":"Fouchier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8762-0090","authenticated-orcid":false,"given":"Marvin E.","family":"Tanenbaum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cels.2025.101489_bib1","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1056\/NEJMp0904819","article-title":"The persistent legacy of the 1918 influenza virus","volume":"361","author":"Morens","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.cels.2025.101489_bib2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.3201\/eid1209.05-0979","article-title":"1918 Influenza: the mother of all pandemics","volume":"12","author":"Taubenberger","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.cels.2025.101489_bib3","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1093\/infdis\/jis467","article-title":"Seasonality, timing, and climate drivers of influenza activity worldwide","volume":"206","author":"Azziz Baumgartner","year":"2012","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.cels.2025.101489_bib4","doi-asserted-by":"crossref","first-page":"1916","DOI":"10.1080\/15548627.2022.2162798","article-title":"The nucleoprotein of influenza A virus inhibits the innate immune response by inducing mitophagy","volume":"19","author":"Zhang","year":"2023","journal-title":"Autophagy"},{"key":"10.1016\/j.cels.2025.101489_bib5","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1002\/rmv.666","article-title":"Structure of influenza virus ribonucleoprotein complexes and their packaging into virions","volume":"20","author":"Noda","year":"2010","journal-title":"Rev. Med. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib6","doi-asserted-by":"crossref","first-page":"11525","DOI":"10.1073\/pnas.1001984107","article-title":"Influenza A virus-generated small RNAs regulate the switch from transcription to replication","volume":"107","author":"Perez","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib7","doi-asserted-by":"crossref","first-page":"9568","DOI":"10.1128\/JVI.78.17.9568-9572.2004","article-title":"Model suggesting that replication of influenza virus is regulated by stabilization of replicative intermediates","volume":"78","author":"Vreede","year":"2004","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib8","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/s41586-020-2927-z","article-title":"Host ANP32A mediates the assembly of the influenza virus replicase","volume":"587","author":"Carrique","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.cels.2025.101489_bib9","doi-asserted-by":"crossref","first-page":"4708","DOI":"10.1038\/s44319-024-00208-4","article-title":"NS2 induces an influenza A RNA polymerase hexamer and acts as a transcription to replication switch","volume":"25","author":"Sun","year":"2024","journal-title":"EMBO Rep."},{"key":"10.1016\/j.cels.2025.101489_bib10","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.virol.2009.10.003","article-title":"Mechanisms and functional implications of the degradation of host RNA polymerase II in influenza virus infected cells","volume":"396","author":"Vreede","year":"2010","journal-title":"Virology"},{"key":"10.1016\/j.cels.2025.101489_bib11","doi-asserted-by":"crossref","first-page":"e00500-19","DOI":"10.1128\/JVI.00500-19","article-title":"Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity","volume":"93","author":"Russell","year":"2019","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1012257","article-title":"Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR)","volume":"20","author":"Zath","year":"2024","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cels.2025.101489_bib13","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.32303","article-title":"Extreme heterogeneity of influenza virus infection in single cells","volume":"7","author":"Russell","year":"2018","journal-title":"eLife"},{"key":"10.1016\/j.cels.2025.101489_bib14","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.978824","article-title":"Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis","volume":"13","author":"Kelly","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.cels.2025.101489_bib15","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1128\/JVI.02284-12","article-title":"Most influenza a virions fail to express at least one essential viral protein","volume":"87","author":"Brooke","year":"2013","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib16","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1016\/j.cell.2020.10.019","article-title":"Translation and Replication Dynamics of Single RNA Viruses","volume":"183","author":"Boersma","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.cels.2025.101489_bib17","doi-asserted-by":"crossref","DOI":"10.1038\/nmicrobiol.2016.80","article-title":"Phenotypic lentivirus screens to identify functional single domain antibodies","volume":"1","author":"Schmidt","year":"2016","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cels.2025.101489_bib18","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/0166-3542(95)00040-S","article-title":"Inhibitory effect of bafilomycin A1, a specific inhibitor of vacuolar-type proton pump, on the growth of influenza A and B viruses in MDCK cells","volume":"27","author":"Ochiai","year":"1995","journal-title":"Antivir. Res."},{"key":"10.1016\/j.cels.2025.101489_bib19","doi-asserted-by":"crossref","first-page":"e01569-16","DOI":"10.1128\/mBio.01569-16","article-title":"The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment","volume":"7","author":"Hanke","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.cels.2025.101489_bib20","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1073\/pnas.77.1.215","article-title":"Influenza defective interfering viral RNA is formed by internal deletion of genomic RNA","volume":"77","author":"Davis","year":"1980","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib21","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1080\/22221751.2019.1611346","article-title":"SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection","volume":"8","author":"Lui","year":"2019","journal-title":"Emerg. Microbes Infect."},{"key":"10.1016\/j.cels.2025.101489_bib22","doi-asserted-by":"crossref","first-page":"8064","DOI":"10.1128\/JVI.00240-13","article-title":"Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus","volume":"87","author":"Saira","year":"2013","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib23","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0164296","article-title":"Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning","volume":"11","author":"Gaiotto","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.cels.2025.101489_bib24","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2021.777095","article-title":"pH-Dependent Mechanisms of Influenza Infection Mediated by Hemagglutinin","volume":"8","author":"Caffrey","year":"2021","journal-title":"Front. Mol. Biosci."},{"key":"10.1016\/j.cels.2025.101489_bib25","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1073\/pnas.1812632116","article-title":"Real-time dissection of dynamic uncoating of individual influenza viruses","volume":"116","author":"Qin","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib26","doi-asserted-by":"crossref","DOI":"10.1371\/annotation\/8f53e7f2-2348-436f-b37e-a883a01e9bbd","article-title":"Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis","volume":"9","author":"Chou","year":"2013","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cels.2025.101489_bib27","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms9938","article-title":"Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection","volume":"6","author":"Heldt","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2025.101489_bib28","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2018100300","article-title":"Long-term expanding human airway organoids for disease modeling","volume":"38","author":"Sachs","year":"2019","journal-title":"EMBO J."},{"key":"10.1016\/j.cels.2025.101489_bib29","doi-asserted-by":"crossref","first-page":"E4238","DOI":"10.1073\/pnas.1315068110","article-title":"Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus","volume":"110","author":"York","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib30","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/s41586-019-1530-7","article-title":"Structures of influenza A virus RNA polymerase offer insight into viral genome replication","volume":"573","author":"Fan","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.cels.2025.101489_bib31","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1099\/vir.0.009639-0","article-title":"NS2\/NEP protein regulates transcription and replication of the influenza virus RNA genome","volume":"90","author":"Robb","year":"2009","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib32","doi-asserted-by":"crossref","first-page":"20067","DOI":"10.1074\/jbc.M114.569178","article-title":"The nuclear export protein of H5N1 influenza A viruses recruits Matrix 1 (M1) protein to the viral ribonucleoprotein to mediate nuclear export","volume":"289","author":"Brunotte","year":"2014","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cels.2025.101489_bib33","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1128\/JVI.74.4.1781-1786.2000","article-title":"Role of the influenza virus M1 protein in nuclear export of viral ribonucleoproteins","volume":"74","author":"Bui","year":"2000","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib34","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/emboj\/17.1.288","article-title":"The influenza virus NEP (NS2 protein) mediates the nuclear export of viral ribonucleoproteins","volume":"17","author":"O\u2019Neill","year":"1998","journal-title":"EMBO J."},{"key":"10.1016\/j.cels.2025.101489_bib35","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/0092-8674(91)90576-K","article-title":"Nuclear transport of influenza virus ribonucleoproteins: the viral matrix protein (M1) promotes export and inhibits import","volume":"67","author":"Martin","year":"1991","journal-title":"Cell"},{"key":"10.1016\/j.cels.2025.101489_bib36","doi-asserted-by":"crossref","first-page":"16707","DOI":"10.1074\/jbc.M510233200","article-title":"Membrane Accumulation of Influenza A Virus Hemagglutinin Triggers Nuclear Export of the Viral Genome via Protein Kinase C\u03b1-mediated Activation of ERK Signaling","volume":"281","author":"Marjuki","year":"2006","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cels.2025.101489_bib37","doi-asserted-by":"crossref","first-page":"e01248-16","DOI":"10.1128\/mBio.01248-16","article-title":"Complete and Incomplete Genome Packaging of Influenza A and B Viruses","volume":"7","author":"Nakatsu","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.cels.2025.101489_bib38","doi-asserted-by":"crossref","first-page":"9101","DOI":"10.1073\/pnas.1206069109","article-title":"One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis","volume":"109","author":"Chou","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib39","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005075","article-title":"Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency","volume":"12","author":"Schelker","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.cels.2025.101489_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107823","article-title":"Mapping of Influenza Virus RNA-RNA Interactions Reveals a Flexible Network","volume":"31","author":"Le Sage","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.cels.2025.101489_bib41","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms1647","article-title":"Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus","volume":"3","author":"Noda","year":"2012","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2025.101489_bib42","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008671","article-title":"Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection","volume":"16","author":"Sun","year":"2020","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cels.2025.101489_bib43","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1099\/jgv.0.000687","article-title":"Single-cell studies of IFN-beta promoter activation by wild-type and NS1-defective influenza A viruses","volume":"98","author":"Killip","year":"2017","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib44","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1010943","article-title":"Maximal interferon induction by influenza lacking NS1 is infrequent owing to requirements for replication and export","volume":"19","author":"Vicary","year":"2023","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cels.2025.101489_bib45","doi-asserted-by":"crossref","first-page":"e00559-19","DOI":"10.1128\/JVI.00559-19","article-title":"Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1","volume":"93","author":"Ramos","year":"2019","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib46","article-title":"Interferon lambda in respiratory viral infection: immunomodulatory functions and antiviral effects in epithelium","volume":"15","author":"Liu","year":"2024","journal-title":"Front. Immunol."},{"key":"10.1016\/j.cels.2025.101489_bib47","article-title":"The influenza virus PB2 protein evades antiviral innate immunity by inhibiting JAK1\/STAT signalling","volume":"13","author":"Yang","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2025.101489_bib48","doi-asserted-by":"crossref","first-page":"8433","DOI":"10.1128\/JVI.00879-10","article-title":"The PB2 subunit of the influenza virus RNA polymerase affects virulence by interacting with the mitochondrial antiviral signaling protein and inhibiting expression of beta interferon","volume":"84","author":"Graef","year":"2010","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib49","doi-asserted-by":"crossref","first-page":"32064","DOI":"10.1074\/jbc.M110.112458","article-title":"Influenza A virus polymerase inhibits type I interferon induction by binding to interferon beta promoter stimulator 1","volume":"285","author":"Iwai","year":"2010","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cels.2025.101489_bib50","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/BF01315172","article-title":"Incomplete avian influenza virus contains a defective non-interfering component","volume":"71","author":"Carter","year":"1982","journal-title":"Arch. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib51","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/0042-6822(73)90063-9","article-title":"Mechanism of influenza recombination. II. Virus aggregation and its effect on plaque formation by so-called noninfective virus","volume":"56","author":"Hirst","year":"1973","journal-title":"Virology"},{"key":"10.1016\/j.cels.2025.101489_bib52","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-017-02517-w","article-title":"Importance of the 1+7 configuration of ribonucleoprotein complexes for influenza A virus genome packaging","volume":"9","author":"Noda","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2025.101489_bib53","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-11428-x","article-title":"Incomplete influenza A virus genomes occur frequently but are readily complemented during localized viral spread","volume":"10","author":"Jacobs","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2025.101489_bib54","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1183\/09031936.93.01010058","article-title":"Proliferation and differentiation in mammalian airway epithelium","volume":"1","author":"Ayers","year":"1988","journal-title":"Eur. Respir. J."},{"key":"10.1016\/j.cels.2025.101489_bib55","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1165\/rcmb.2012-0146OC","article-title":"Ciliated cells of pseudostratified airway epithelium do not become mucous cells after ovalbumin challenge","volume":"48","author":"Pardo-Saganta","year":"2013","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"10.1016\/j.cels.2025.101489_bib56","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1016\/j.cell.2011.10.001","article-title":"Distal airway stem cells yield alveoli in vitro and during lung regeneration following H1N1 influenza infection","volume":"147","author":"Kumar","year":"2011","journal-title":"Cell"},{"key":"10.1016\/j.cels.2025.101489_bib57","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0013927","article-title":"Influenza virus non-structural protein 1 (NS1) disrupts interferon signaling","volume":"5","author":"Jia","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.cels.2025.101489_bib58","doi-asserted-by":"crossref","first-page":"7011","DOI":"10.1128\/JVI.02581-06","article-title":"Multiple anti-interferon actions of the influenza A virus NS1 protein","volume":"81","author":"Kochs","year":"2007","journal-title":"J. Virol."},{"key":"10.1016\/j.cels.2025.101489_bib59","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-025-10071-5","article-title":"Pre-assembly of biomolecular condensate seeds drives RSV replication","author":"Ratnayake","year":"2026","journal-title":"Nature"},{"key":"10.1016\/j.cels.2025.101489_bib79","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2420595121","article-title":"Integrin-activating Yersinia protein Invasin sustains long-term expansion of primary epithelial cells as 2D organoid sheets","volume":"122","author":"Wijnakker","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib60","series-title":"A Language and Environment for Statistical Computing","year":"2022"},{"key":"10.1016\/j.cels.2025.101489_bib61","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"10.1016\/j.cels.2025.101489_bib62","author":"Wickham"},{"key":"10.1016\/j.cels.2025.101489_bib63","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-04567-y","article-title":"MIST: Accurate and Scalable Microscopy Image Stitching Tool with Stage Modeling and Error Minimization","volume":"7","author":"Chalfoun","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.cels.2025.101489_bib64","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.cell.2015.05.047","article-title":"Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis","volume":"162","author":"Levine","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.cels.2025.101489_bib65","article-title":"UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction","author":"McInnes","year":"2020","journal-title":"arXiv"},{"key":"10.1016\/j.cels.2025.101489_bib66","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1093\/bioinformatics\/btv715","article-title":"destiny: diffusion maps for large-scale single-cell data in R","volume":"32","author":"Angerer","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cels.2025.101489_bib67","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1186\/s12864-018-4772-0","article-title":"Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics","volume":"19","author":"Street","year":"2018","journal-title":"BMC Genomics"},{"key":"10.1016\/j.cels.2025.101489_bib68","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.1038\/s41592-022-01663-4","article-title":"Cellpose 2.0: how to train your own model","volume":"19","author":"Pachitariu","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cels.2025.101489_bib69","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/s41592-022-01507-1","article-title":"TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines","volume":"19","author":"Ershov","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cels.2025.101489_bib70","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.453","article-title":"scikit-image: image processing in Python","volume":"2","author":"van der Walt","year":"2014","journal-title":"PeerJ"},{"key":"10.1016\/j.cels.2025.101489_bib71","doi-asserted-by":"crossref","first-page":"7292","DOI":"10.1093\/nar\/gkab546","article-title":"deepBlink: threshold-independent detection and localization of diffraction-limited spots","volume":"49","author":"Eichenberger","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cels.2025.101489_bib72","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14836","article-title":"A BaSiC tool for background and shading correction of optical microscopy images","volume":"8","author":"Peng","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cels.2025.101489_bib73","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1109\/83.650848","article-title":"A pyramid approach to subpixel registration based on intensity","volume":"7","author":"Th\u00e9venaz","year":"1998","journal-title":"IEEE Trans. Image Process."},{"key":"10.1016\/j.cels.2025.101489_bib74","author":"Sofroniew"},{"key":"10.1016\/j.cels.2025.101489_bib75","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1261\/rna.079073.121","article-title":"FISH-quant v2: a scalable and modular tool for smFISH image analysis","volume":"28","author":"Imbert","year":"2022","journal-title":"RNA"},{"key":"10.1016\/j.cels.2025.101489_bib76","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.virusres.2004.02.028","article-title":"Efficient generation and growth of influenza virus A\/PR\/8\/34 from eight cDNA fragments","volume":"103","author":"de Wit","year":"2004","journal-title":"Virus Res."},{"key":"10.1016\/j.cels.2025.101489_bib77","doi-asserted-by":"crossref","first-page":"2083","DOI":"10.1016\/j.ccell.2023.11.007","article-title":"Druggable growth dependencies and tumor evolution analysis in patient-derived organoids of neuroendocrine neoplasms from multiple body sites","volume":"41","author":"Dayton","year":"2023","journal-title":"Cancer Cell"},{"key":"10.1016\/j.cels.2025.101489_bib78","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1164\/rccm.202310-1831LE","article-title":"Human Airway and Alveolar Organoids from BAL Fluid","volume":"209","author":"Liu","year":"2024","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.cels.2025.101489_bib80","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000936","article-title":"Aequorea\u2019s secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing","volume":"18","author":"Lambert","year":"2020","journal-title":"PLoS Biol."},{"key":"10.1016\/j.cels.2025.101489_bib81","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.1038\/s41587-023-02018-w","article-title":"A monomeric StayGold fluorescent protein","volume":"42","author":"Ivorra-Molla","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cels.2025.101489_bib82","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0103294","article-title":"The breadth of cross sub-type neutralisation activity of a single domain antibody to influenza hemagglutinin can be increased by antibody valency","volume":"9","author":"Hufton","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.cels.2025.101489_bib83","doi-asserted-by":"crossref","first-page":"9065","DOI":"10.1073\/pnas.0800502105","article-title":"Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution","volume":"105","author":"Zeng","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2025.101489_bib84","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s12250-020-00230-5","article-title":"On the Calculation of TCID50 for Quantitation of Virus Infectivity","volume":"36","author":"Lei","year":"2021","journal-title":"Virol. Sin."},{"key":"10.1016\/j.cels.2025.101489_bib85","doi-asserted-by":"crossref","first-page":"4096","DOI":"10.1128\/JCM.38.11.4096-4101.2000","article-title":"Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene","volume":"38","author":"Fouchier","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.cels.2025.101489_bib86","doi-asserted-by":"crossref","DOI":"10.21769\/BioProtoc.2750","article-title":"Terminal Deoxynucleotidyl Transferase Mediated Production of Labeled Probes for Single-molecule FISH or RNA Capture","volume":"8","author":"Gaspar","year":"2018","journal-title":"Bio Protoc."},{"key":"10.1016\/j.cels.2025.101489_bib87","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1038\/nprot.2013.109","article-title":"Single-molecule mRNA detection and counting in mammalian tissue","volume":"8","author":"Lyubimova","year":"2013","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cels.2025.101489_bib88","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1126\/science.1205669","article-title":"A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins","volume":"333","author":"Corti","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.cels.2025.101489_bib89","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cels.2025.101489_bib90","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","article-title":"Cellpose: a generalist algorithm for cellular segmentation","volume":"18","author":"Stringer","year":"2021","journal-title":"Nat. Methods"}],"container-title":["Cell Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2405471225003229?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2405471225003229?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T20:13:14Z","timestamp":1782418394000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2405471225003229"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":90,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["S2405471225003229"],"URL":"https:\/\/doi.org\/10.1016\/j.cels.2025.101489","relation":{},"ISSN":["2405-4712"],"issn-type":[{"value":"2405-4712","type":"print"}],"subject":[],"published":{"date-parts":[[2026,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Live-cell single-vRNP imaging identifies viral gene expression signatures that shape influenza infection heterogeneity","name":"articletitle","label":"Article Title"},{"value":"Cell Systems","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cels.2025.101489","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"101489"}}