{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:58:52Z","timestamp":1790859532842,"version":"4.1.0"},"reference-count":40,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS\u20102151959"],"award-info":[{"award-number":["DMS\u20102151959"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB\u20102029281"],"award-info":[{"award-number":["MCB\u20102029281"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CBET\u20102030750"],"award-info":[{"award-number":["CBET\u20102030750"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["OT2OD030524"],"award-info":[{"award-number":["OT2OD030524"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DK133605"],"award-info":[{"award-number":["R01DK133605"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Cytometry Pt A"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>When infection spreads from an initially infected cell through a cell monolayer, the resulting plaque records successive rounds of virus\u2013cell interaction. Fluorescent reporter viruses permit this process to be followed at single\u2010cell resolution, but whether secondary infected cells retain detectable signatures associated with their plaque of origin remains unclear. Here, we tracked enhanced green fluorescent protein expression in 154 cells from eight rhinovirus plaques and systematically compared feature\u2010based, clustering, dimensionality\u2010reduction, and sequence\u2010alignment methods. Primary and secondary infected cells were distinguished mainly by the time of first detectable fluorescence; no consistent differences were detected in reporter\u2010trajectory kinetics or amplitude. Among secondary cells, most methods detected no plaque\u2010associated structure beyond chance. Affinity propagation detected a small plaque\u2010label association that persisted after removal of the first detection time, although its biological interpretation was limited by session\u2010associated intensity differences. Thus, by the secondary round, cell\u2010to\u2010cell heterogeneity largely exceeded any plaque\u2010associated signature detectable under the present conditions. This work provides a framework for comparing single\u2010cell trajectories across early rounds of plaque growth and for designing studies to resolve subtle lineage\u2010associated effects.<\/jats:p>","DOI":"10.1002\/cyto.a.70069","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:28:34Z","timestamp":1790857714000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single\u2010Cell Reporter Dynamics During the First Two Rounds of Rhinovirus Plaque Growth"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2668-1938","authenticated-orcid":false,"given":"Rahul","family":"Ramachandran","sequence":"first","affiliation":[{"name":"Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin\u2013Madison  Madison Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huicheng","family":"Shi","sequence":"additional","affiliation":[{"name":"Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin\u2013Madison  Madison Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6146-0594","authenticated-orcid":false,"given":"John","family":"Yin","sequence":"additional","affiliation":[{"name":"Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin\u2013Madison  Madison Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"e_1_2_10_2_1","first-page":"373","article-title":"Sur Un Microbe Invisible Antagoniste Des Bacilles Dysenteriques","volume":"165","author":"Herelle F.","year":"1917","journal-title":"Comptes Rendus. Acad\u00e9mie des Sciences"},{"key":"e_1_2_10_3_1","first-page":"319","volume-title":"Advances in Virus Research","author":"Cooper P. D.","year":"1961"},{"key":"e_1_2_10_4_1","volume-title":"Principles of Virology, Volume 1","author":"Flint J.","year":"2020"},{"key":"e_1_2_10_5_1","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1016\/0006-291X(91)91519-I","article-title":"A Quantifiable Phenotype of Viral Propagation","volume":"174","author":"Yin J.","year":"1991","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1016\/S0006-3495(92)81958-6","article-title":"Replication of Viruses in a Growing Plaque: A Reaction\u2010Diffusion Model","volume":"61","author":"Yin J.","year":"1992","journal-title":"Biophysical Journal"},{"key":"e_1_2_10_7_1","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1006\/jtbi.1999.1001","article-title":"Amplification and Spread of Viruses in a Growing Plaque","volume":"200","author":"You L.","year":"1999","journal-title":"Journal of Theoretical Biology"},{"key":"e_1_2_10_8_1","doi-asserted-by":"crossref","first-page":"3727","DOI":"10.1039\/C3AN02323K","article-title":"Viral Plaque Analysis on a Wide Field\u2010of\u2010View, Time\u2010Lapse, On\u2010Chip Imaging Platform","volume":"139","author":"Han C.","year":"2014","journal-title":"Analyst"},{"key":"e_1_2_10_9_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.virol.2025.110408","article-title":"Serum Starvation Impacts Rhinovirus Spread From Cell to Cell","volume":"604","author":"Shi H.","year":"2025","journal-title":"Virology"},{"key":"e_1_2_10_10_1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.virol.2008.10.031","article-title":"Growth of an RNA Virus in Single Cells Reveals a Broad Fitness Distribution","volume":"385","author":"Zhu Y.","year":"2009","journal-title":"Virology"},{"key":"e_1_2_10_11_1","doi-asserted-by":"crossref","first-page":"1599","DOI":"10.1128\/JVI.02190-15","article-title":"High\u2010Throughput Single\u2010Cell Kinetics of Virus Infections in the Presence of Defective Interfering Particles","volume":"90","author":"Akpinar F.","year":"2015","journal-title":"Journal of Virology"},{"key":"e_1_2_10_12_1","doi-asserted-by":"crossref","first-page":"6205","DOI":"10.1128\/JVI.03539-13","article-title":"Single\u2010Cell Analysis Uncovers Extensive Biological Noise in Poliovirus Replication","volume":"88","author":"Schulte M. B.","year":"2014","journal-title":"Journal of Virology"},{"key":"e_1_2_10_13_1","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms9938","article-title":"Single\u2010Cell Analysis and Stochastic Modelling Unveil Large Cell\u2010to\u2010Cell Variability in Influenza A Virus Infection","volume":"6","author":"Heldt F. S.","year":"2015","journal-title":"Nature Communications"},{"key":"e_1_2_10_14_1","doi-asserted-by":"crossref","first-page":"1692","DOI":"10.1016\/j.celrep.2017.10.051","article-title":"Single\u2010Cell Virology: On\u2010Chip Investigation of Viral Infection Dynamics","volume":"21","author":"Guo F.","year":"2017","journal-title":"Cell Reports"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.3390\/v16111659"},{"key":"e_1_2_10_16_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.micinf.2023.105268","article-title":"Dissecting Viral Infections, One Cell at a Time, by Single\u2010Cell Technologies","volume":"26","author":"Bost P.","year":"2024","journal-title":"Microbes and Infection"},{"key":"e_1_2_10_17_1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.virol.2011.12.005","article-title":"Kinetics of Virus Production From Single Cells","volume":"424","author":"Timm A.","year":"2012","journal-title":"Virology"},{"key":"e_1_2_10_18_1","unstructured":"J.WarrickandE.Berthier \u201cJe'Xperiment (JEX) \u201d2015 https:\/\/github.com\/jaywarrick\/jex."},{"key":"e_1_2_10_19_1","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1080\/14786440109462720","article-title":"LIII. On Lines and Planes of Closest Fit to Systems of Points in Space","volume":"2","author":"Pearson K.","year":"1901","journal-title":"London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43586\u2010022\u201000184\u2010w"},{"key":"e_1_2_10_21_1","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1086\/668105","article-title":"Principal Component Analysis With Noisy and\/or Missing Data","volume":"124","author":"Bailey S.","year":"2012","journal-title":"Publications of the Astronomical Society of the Pacific"},{"key":"e_1_2_10_22_1","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1007\/BF02288916","article-title":"Multidimensional Scaling: I. Theory and Method","volume":"17","author":"Torgerson W. S.","year":"1952","journal-title":"Psychometrika"},{"key":"e_1_2_10_23_1","first-page":"93","article-title":"Multidimensional Scaling","volume":"4","author":"Hout M. C.","year":"2013","journal-title":"Wiley Interdisciplinary Reviews: Cognitive Science"},{"key":"e_1_2_10_24_1","first-page":"2579","article-title":"Visualizing Data Using t\u2010SNE","volume":"9","author":"Maaten L.","year":"2008","journal-title":"Journal of Machine Learning Research"},{"key":"e_1_2_10_25_1","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-13056-x","article-title":"The Art of Using t\u2010SNE for Single\u2010Cell Transcriptomics","volume":"10","author":"Kobak D.","year":"2019","journal-title":"Nature Communications"},{"key":"e_1_2_10_26_1","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1126\/science.1136800","article-title":"Clustering by Passing Messages Between Data Points","volume":"315","author":"Frey B. J.","year":"2007","journal-title":"Science"},{"key":"e_1_2_10_27_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.eswa.2021.115506","article-title":"A Cluster\u2010Based Approach to Predict Serious Adverse Events in Surgery","volume":"184","author":"Perez B.","year":"2021","journal-title":"Expert Systems With Applications"},{"key":"e_1_2_10_28_1","first-page":"49","volume-title":"Proceedings of the ACM SIGMOD International Conference on Management of Data","author":"Ankerst M.","year":"1999"},{"key":"e_1_2_10_29_1","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-540-74048-3","volume-title":"Information Retrieval for Music and Motion","author":"Muller M.","year":"2007"},{"key":"e_1_2_10_30_1","doi-asserted-by":"crossref","first-page":"149764","DOI":"10.1109\/ACCESS.2020.3016529","article-title":"Time Adaptive Optimal Transport: A Framework of Time Series Similarity Measure","volume":"8","author":"Zhang Z.","year":"2020","journal-title":"IEEE Access"},{"key":"e_1_2_10_31_1","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.patcog.2017.09.020","article-title":"ShapeDTW: Shape Dynamic Time Warping","volume":"74","author":"Zhao J.","year":"2018","journal-title":"Pattern Recognition"},{"key":"e_1_2_10_32_1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.ins.2020.04.009","article-title":"Adaptively Constrained Dynamic Time Warping for Time Series Classification and Clustering","volume":"534","author":"Li H.","year":"2020","journal-title":"Information Sciences"},{"key":"e_1_2_10_33_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.eswa.2023.122432","article-title":"ESDTW: Extrema\u2010Based Shape Dynamic Time Warping","volume":"239","author":"Qiu L.","year":"2024","journal-title":"Expert Systems With Applications"},{"key":"e_1_2_10_34_1","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/BF01908075","article-title":"Comparing Partitions","volume":"2","author":"Hubert L.","year":"1985","journal-title":"Journal of Classification"},{"key":"e_1_2_10_35_1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: A Graphical Aid to the Interpretation and Validation of Cluster Analysis","volume":"20","author":"Rousseeuw P. J.","year":"1987","journal-title":"Journal of Computational and Applied Mathematics"},{"key":"e_1_2_10_36_1","doi-asserted-by":"crossref","DOI":"10.1186\/s13040-025-00465-6","article-title":"A Simple Guide to the Use of Student's t\u2010Test, Mann\u2013Whitney U Test, Chi\u2010Squared Test, and Kruskal\u2013Wallis Test in Biostatistics","volume":"18","author":"Chicco D.","year":"2025","journal-title":"Biodata Mining"},{"key":"e_1_2_10_37_1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1111\/j.1365-2818.1995.tb03665.x","article-title":"Quantitative Imaging of Green Fluorescent Protein in Cultured Cells: Comparison of Microscopic Techniques, Use in Fusion Proteins and Detection Limits","volume":"180","author":"Niswender K. D.","year":"1995","journal-title":"Journal of Microscopy"},{"key":"e_1_2_10_38_1","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/S0003-2697(02)00281-6","article-title":"Measurement of Green Fluorescent Protein Concentration in Single Cells by Image Analysis","volume":"310","author":"Furtado A.","year":"2002","journal-title":"Analytical Biochemistry"},{"key":"e_1_2_10_39_1","doi-asserted-by":"crossref","first-page":"29361","DOI":"10.1074\/jbc.M101935200","article-title":"Individual Rotavirus\u2010Like Particles Containing 120 Molecules of Fluorescent Protein Are Visible in Living Cells","volume":"276","author":"Charpilienne A.","year":"2001","journal-title":"Journal of Biological Chemistry"},{"key":"e_1_2_10_40_1","doi-asserted-by":"crossref","DOI":"10.1038\/s42003-019-0415-5","article-title":"Diffcyt: Differential Discovery in High\u2010Dimensional Cytometry via High\u2010Resolution Clustering","volume":"2","author":"Weber L. M.","year":"2019","journal-title":"Communications Biology"},{"key":"e_1_2_10_41_1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nmeth.4220","article-title":"Power Analysis of Single\u2010Cell RNA\u2010Sequencing Experiments","volume":"14","author":"Svensson V.","year":"2017","journal-title":"Nature Methods"}],"container-title":["Cytometry Part A"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cyto.a.70069","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/cyto.a.70069","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cyto.a.70069","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:28:40Z","timestamp":1790857720000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/cyto.a.70069"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":40,"alternative-id":["10.1002\/cyto.a.70069"],"URL":"https:\/\/doi.org\/10.1002\/cyto.a.70069","archive":["Portico"],"relation":{},"ISSN":["1552-4922","1552-4930"],"issn-type":[{"value":"1552-4922","type":"print"},{"value":"1552-4930","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,1]]},"assertion":[{"value":"2025-10-14","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-15","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-01","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"cyto.a.70069"}}