{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T10:00:21Z","timestamp":1784973621010,"version":"3.55.0"},"posted":{"date-parts":[[2026,6,9]]},"group-title":"Immunology","reference-count":75,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T00:00:00Z","timestamp":1780963200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["DP2AI171139"],"award-info":[{"award-number":["DP2AI171139"]}]},{"name":"Gilead","award":["Research Scholars Program in Hematologic Malignancies"],"award-info":[{"award-number":["Research Scholars Program in Hematologic Malignancies"]}]},{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"crossref","award":["INV-002704"],"award-info":[{"award-number":["INV-002704"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100013114","name":"Broad Institute","doi-asserted-by":"crossref","award":["Next Generation Award"],"award-info":[{"award-number":["Next Generation Award"]}],"id":[{"id":"10.13039\/100013114","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Dye Family Foundation","award":["\/"],"award-info":[{"award-number":["\/"]}]},{"DOI":"10.13039\/100007130","name":"University of Texas System","doi-asserted-by":"crossref","award":["Rising STARs award"],"award-info":[{"award-number":["Rising STARs award"]}],"id":[{"id":"10.13039\/100007130","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,6,9]]},"abstract":"<jats:p>\n                  Epithelial remodeling is a hallmark of host antiviral responses that strengthen barrier defenses against infection. Our current understanding of viral pathophysiology within the nasal epithelium, the initial site of most respiratory viral infections, remains incomplete due to limited understanding of the native tissue architecture and protective epithelial remodeling during immune events. Leveraging coronavirus disease 2019 (COVID-19) as a model, we applied spatial multi-omics on nasal cross-sectional tissues to characterize the immune\u2013epithelial landscape during infection, identifying a coordinated increase in goblet cells and suppressive macrophages associated with elevated IL13 in the immune compartment. Our results further reveal that goblet cell and suppressive macrophage enrichment are spatially linked in proximity to IL13\u2013expressing CD4 T cells, consistent with IL13-driven remodeling\n                  <jats:italic>in situ<\/jats:italic>\n                  . Using a primary human nasal air\u2013liquid interface model, we demonstrate that IL13 alone is sufficient to remodel epithelial composition and morphology, subsequently restricting viral infection by reshaping the apical mucus barrier of the nasal epithelium. Our findings uncover a spatially organized, IL13\u2013driven circuit for immune-epithelial remodeling as a protective barrier against respiratory viral infections.\n                <\/jats:p>","DOI":"10.64898\/2026.06.08.726938","type":"posted-content","created":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T03:40:18Z","timestamp":1781062818000},"source":"Crossref","is-referenced-by-count":0,"title":["Coordinated immune-epithelial dynamics in the nasal epithelium protect against respiratory virus infection"],"prefix":"10.64898","author":[{"given":"Yao Yu","family":"Yeo","sequence":"first","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"},{"name":"Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsin-Yi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bokai","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Pathology, Stanford University, Stanford, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan T","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsuguhisa","family":"Nakayama","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuchen","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaying","family":"Qiu","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate B","family":"Juergens","sequence":"additional","affiliation":[{"name":"Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sei","family":"Chung","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, UT Southwestern Medical Center, Dallas TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carol H","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, University of California San Diego School of Medicine, San Diego, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara S","family":"Kummerer","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendrik A","family":"Michel","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"},{"name":"Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew Z","family":"Ma","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenrui","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayakar V","family":"Nayak","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garry P","family":"Nolan","sequence":"additional","affiliation":[{"name":"Department of Pathology, Stanford University, Stanford, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R","family":"McIlwain","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Nevada Reno School of Medicine, Reno, NV, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1100-3819","authenticated-orcid":false,"given":"Alexandar","family":"Tzankov","sequence":"additional","affiliation":[{"name":"Institute of Pathology, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2005-5266","authenticated-orcid":false,"given":"Matthias S","family":"Matter","sequence":"additional","affiliation":[{"name":"Institute of Pathology, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chien-Ting","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6149-3142","authenticated-orcid":false,"given":"Sizun","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States"},{"name":"Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, United States"},{"name":"Department of Pathology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA, United States"},{"name":"Broad Institute of Harvard and MIT, Cambridge, MA, United States"},{"name":"Department of Pathology, Dana Farber Cancer Institute, Boston, MA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072502000641000_2026.06.08.726938v1.1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-101721-062818"},{"key":"2026072502000641000_2026.06.08.726938v1.2","doi-asserted-by":"crossref","unstructured":"Daniel Rosenblum and Shruti Naik . Epithelial\u2013immune crosstalk in health and disease. Current opinion in genetics & development, 74:101910, 2022.","DOI":"10.1016\/j.gde.2022.101910"},{"key":"2026072502000641000_2026.06.08.726938v1.3","doi-asserted-by":"crossref","unstructured":"Guanrui Liao , Tsuguhisa Nakayama , Bokai Zhu , Ivan T Lee , Jason Yeung , Yao Yu Yeo , Yuzhou Chang , Cankun Wang , Steven Chun-Kang Liao , Dingani Nkosi , et al. Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation. Immunity, 2025.","DOI":"10.1016\/j.immuni.2025.08.009"},{"key":"2026072502000641000_2026.06.08.726938v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-022-00713-0"},{"key":"2026072502000641000_2026.06.08.726938v1.5","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00014-10"},{"key":"2026072502000641000_2026.06.08.726938v1.6","doi-asserted-by":"crossref","unstructured":"Ellen F Foxman . Layers of defense: protection from respiratory viruses by epithelial-intrinsic immunity. Current Opinion in Immunology, 97:102677, 2025.","DOI":"10.1016\/j.coi.2025.102677"},{"key":"2026072502000641000_2026.06.08.726938v1.7","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-1"},{"key":"2026072502000641000_2026.06.08.726938v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.05.042"},{"issue":"1","key":"2026072502000641000_2026.06.08.726938v1.9","doi-asserted-by":"crossref","first-page":"5453","DOI":"10.1038\/s41467-020-19145-6","article-title":"Ace2 localizes to the respiratory cilia and is not increased by ace inhibitors or arbs","volume":"11","year":"2020","journal-title":"Nature communications"},{"key":"2026072502000641000_2026.06.08.726938v1.10","doi-asserted-by":"crossref","unstructured":"Tsuguhisa Nakayama , Ivan T Lee , Sizun Jiang , Matthias S Matter , Carol H Yan , Jonathan B Overdevest , Chien-Ting Wu , Yury Goltsev , Liang-Chun Shih , Chun-Kang Liao , et al. Determinants of sars-cov-2 entry and replication in airway mucosal tissue and susceptibility in smokers. Cell Reports Medicine, 2(10), 2021.","DOI":"10.1016\/j.xcrm.2021.100421"},{"key":"2026072502000641000_2026.06.08.726938v1.11","doi-asserted-by":"crossref","unstructured":"Hannah D Stacey , Lucas Garin-Ortega , Paul G Lopez , Parham Ramezani-Rad , Sydney I Ramirez , Farhoud Faraji , Disha Bhavsar , Gina Levi , Florian Krammer , and Shane Crotty . Local b-cell immunity and durable memory following live-attenuated influenza intranasal vaccination of humans. bioRxiv, pages 2025\u201307, 2025.","DOI":"10.1101\/2025.07.14.664794"},{"key":"2026072502000641000_2026.06.08.726938v1.12","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2001017"},{"issue":"12","key":"2026072502000641000_2026.06.08.726938v1.13","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1038\/s41562-022-01450-3","article-title":"Life expectancy changes since covid-19","volume":"6","year":"2022","journal-title":"Nature human behaviour"},{"key":"2026072502000641000_2026.06.08.726938v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-024-03173-6"},{"key":"2026072502000641000_2026.06.08.726938v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2021.07.023"},{"key":"2026072502000641000_2026.06.08.726938v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07575-x"},{"issue":"2","key":"2026072502000641000_2026.06.08.726938v1.17","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1111\/his.14134","article-title":"Postmortem examination of covid-19 patients reveals diffuse alveolar damage with severe capillary congestion and variegated findings in lungs and other organs suggesting vascular dysfunction","volume":"77","year":"2020","journal-title":"Histopathology"},{"key":"2026072502000641000_2026.06.08.726938v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0472-9"},{"key":"2026072502000641000_2026.06.08.726938v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.07.010"},{"key":"2026072502000641000_2026.06.08.726938v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/75556"},{"key":"2026072502000641000_2026.06.08.726938v1.21","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-128"},{"key":"2026072502000641000_2026.06.08.726938v1.22","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw377"},{"issue":"6","key":"2026072502000641000_2026.06.08.726938v1.23","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The molecular signatures database hallmark gene set collection","volume":"1","year":"2015","journal-title":"Cell systems"},{"issue":"7","key":"2026072502000641000_2026.06.08.726938v1.24","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/s42255-020-0237-2","article-title":"A metabolic handbook for the covid-19 pandemic","volume":"2","year":"2020","journal-title":"Nature metabolism"},{"issue":"4","key":"2026072502000641000_2026.06.08.726938v1.25","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1038\/mi.2015.32","article-title":"New developments in goblet cell mucus secretion and function","volume":"8","author":"GC4631840 Hansson","year":"2015","journal-title":"Mucosal immunology"},{"issue":"1","key":"2026072502000641000_2026.06.08.726938v1.26","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/s41392-023-01452-1","article-title":"Macrophages in immunoregulation and therapeutics","volume":"8","year":"2023","journal-title":"Signal transduction and targeted therapy"},{"key":"2026072502000641000_2026.06.08.726938v1.27","doi-asserted-by":"crossref","unstructured":"Alexandra N Donlan , Tara E Sutherland , Chelsea Marie , Saskia Preissner , Ben T Bradley , Rebecca M Carpenter , Jeffrey M Sturek , Jennie Z Ma , G Brett Moreau , Jeffrey R Donowitz , et al. Il-13 is a driver of covid-19 severity. MedRxiv, pages 2020\u201306, 2021.","DOI":"10.1172\/jci.insight.150107"},{"key":"2026072502000641000_2026.06.08.726938v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2022.03.020"},{"issue":"3","key":"2026072502000641000_2026.06.08.726938v1.29","doi-asserted-by":"crossref","first-page":"101663","DOI":"10.1016\/j.xpro.2022.101663","article-title":"Combined protein and nucleic acid staining in tissues with panini","volume":"3","year":"2022","journal-title":"STAR protocols"},{"key":"2026072502000641000_2026.06.08.726938v1.30","doi-asserted-by":"publisher","DOI":"10.1002\/j.1538-7305.1948.tb01338.x"},{"key":"2026072502000641000_2026.06.08.726938v1.31","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1977.tb01615.x"},{"key":"2026072502000641000_2026.06.08.726938v1.32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.11.030"},{"key":"2026072502000641000_2026.06.08.726938v1.33","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA117.001068"},{"key":"2026072502000641000_2026.06.08.726938v1.34","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.200811-1744OC"},{"key":"2026072502000641000_2026.06.08.726938v1.35","doi-asserted-by":"publisher","DOI":"10.1172\/JCI200113557"},{"key":"2026072502000641000_2026.06.08.726938v1.36","doi-asserted-by":"publisher","DOI":"10.1111\/all.13489"},{"key":"2026072502000641000_2026.06.08.726938v1.37","doi-asserted-by":"crossref","unstructured":"N Zhong , H Ai , W Zhong , X Huang , K Wang , Q Luo , and J Yu . Effects of pendrin protein in nasal epithelial cells on mucin production in the context of type 2 inflammation. Journal of personalized medicine, 13(3), 2023.","DOI":"10.3390\/jpm13030502"},{"key":"2026072502000641000_2026.06.08.726938v1.38","doi-asserted-by":"publisher","DOI":"10.1172\/JCI84910"},{"key":"2026072502000641000_2026.06.08.726938v1.39","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.pupt.2016.05.005","article-title":"Azithromycin differentially affects the il-13-induced expression profile in human bronchial epithelial cells","volume":"39","year":"2016","journal-title":"Pulmonary pharmacology & therapeutics"},{"key":"2026072502000641000_2026.06.08.726938v1.40","doi-asserted-by":"publisher","DOI":"10.1165\/rcmb.2019-0266OC"},{"key":"2026072502000641000_2026.06.08.726938v1.41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2218083120"},{"key":"2026072502000641000_2026.06.08.726938v1.42","doi-asserted-by":"crossref","unstructured":"S Ghimire , B Xue , K Li , RM Gannon , CL Wohlford-Lenane , AL Thurman, H Gong , GC Necker , J Zheng , and DK Meyerholz . Il-13 decreases susceptibility to airway epithelial sars-cov-2 infection but increases disease severity in vivo via eicosanoid signalling. EBioMedicine, 120:105920, 2025.","DOI":"10.1016\/j.ebiom.2025.105920"},{"issue":"4","key":"2026072502000641000_2026.06.08.726938v1.43","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1165\/rcmb.2021-0364OC","article-title":"The type 2 asthma mediator il-13 inhibits severe acute respiratory syndrome coronavirus 2 infection of bronchial epithelium","volume":"66","year":"2022","journal-title":"American journal of respiratory cell and molecular biology"},{"key":"2026072502000641000_2026.06.08.726938v1.44","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2119680119"},{"key":"2026072502000641000_2026.06.08.726938v1.45","doi-asserted-by":"crossref","unstructured":"MA Liegeois , M Braunreuther , AR Charbit , WW Raymond , M Tang , PG Woodruff , SA Christenson , M Castro , SC Erzurum , and E Israel . Peroxidase-mediated mucin cross-linking drives pathologic mucus gel formation in il-13-stimulated airway epithelial cells. JCI insight, 9, 2024.","DOI":"10.1172\/jci.insight.181024"},{"key":"2026072502000641000_2026.06.08.726938v1.46","doi-asserted-by":"crossref","unstructured":"GS Romano Ibarra , L Lei , W Yu , AL Thurman , ND Gansemer , DK Meyerholz , AA Pezzulo , PB McCray , IM Thornell , and DA Stoltz . Il-13 induces loss of cftr in ionocytes and reduces airway epithelial fluid absorption. Journal of clinical investigation, 134, 2024.","DOI":"10.1172\/JCI181995"},{"key":"2026072502000641000_2026.06.08.726938v1.47","doi-asserted-by":"publisher","DOI":"10.1111\/febs.15731"},{"issue":"9","key":"2026072502000641000_2026.06.08.726938v1.48","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1177\/0145561320920762","article-title":"Clinical presentation of covid-19: a systematic review focusing on upper airway symptoms","volume":"99","year":"2020","journal-title":"Ear, Nose & Throat Journal"},{"issue":"1","key":"2026072502000641000_2026.06.08.726938v1.49","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1093\/cid\/ciac745","article-title":"Dupilumab use is associated with protection from coronavirus disease 2019 mortality: a retrospective analysis","volume":"76","year":"2023","journal-title":"Clinical Infectious Diseases"},{"issue":"3","key":"2026072502000641000_2026.06.08.726938v1.50","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.3390\/cimb45030128","article-title":"Biomarker profiles associated with covid-19 severity and mortality","volume":"45","year":"2023","journal-title":"Current issues in molecular biology"},{"issue":"22","key":"2026072502000641000_2026.06.08.726938v1.51","doi-asserted-by":"crossref","first-page":"e152288","DOI":"10.1172\/jci.insight.152288","article-title":"Human nasal wash rna-seq reveals distinct cell-specific innate immune responses in influenza versus sars-cov-2","volume":"6","year":"2021","journal-title":"JCI insight"},{"issue":"1","key":"2026072502000641000_2026.06.08.726938v1.52","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/s41421-021-00294-x","article-title":"Scrna-seq revealed the kinetic of nasopharyngeal immune responses in asymptomatic covid-19 carriers","volume":"7","year":"2021","journal-title":"Cell Discovery"},{"issue":"4","key":"2026072502000641000_2026.06.08.726938v1.53","doi-asserted-by":"crossref","first-page":"567","DOI":"10.3390\/covid3040041","article-title":"Macrophage-induced exacerbation of nasopharyngeal inflammatory lymphocytes in covid-19 disease","volume":"3","year":"2023","journal-title":"COVID"},{"issue":"48","key":"2026072502000641000_2026.06.08.726938v1.54","doi-asserted-by":"crossref","first-page":"eabd2071","DOI":"10.1126\/sciimmunol.abd2071","article-title":"Phenotype and kinetics of sars-cov-2\u2013specific t cells in covid-19 patients with acute respiratory distress syndrome","volume":"5","year":"2020","journal-title":"Science immunology"},{"key":"2026072502000641000_2026.06.08.726938v1.55","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201142227"},{"issue":"7","key":"2026072502000641000_2026.06.08.726938v1.56","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1002\/eji.201747463","article-title":"Unexpected involvement of il-13 signalling via a stat6 independent mechanism during murine igg2a development following viral vaccination","volume":"48","year":"2018","journal-title":"European journal of immunology"},{"key":"2026072502000641000_2026.06.08.726938v1.57","unstructured":"Yao Yu Yeo , Huaying Qiu , Yunhao Bai , Bokai Zhu , Yuzhou Chang , Jason Yeung , Hendrik A Michel , Kyle Wright , Muhammad Shaban , Sam Sadigh , et al. Epstein-barr virus orchestrates spatial reorganization and immunomodulation within the classic hodgkin lymphoma tumor microenvironment. bioRxiv, pages 2024\u201303, 2024."},{"key":"2026072502000641000_2026.06.08.726938v1.58","unstructured":"Yao Yu Yeo , Yuzhou Chang , Huaying Qiu , Stephanie Pei Tung Yiu , Hendrik A Michel , Wenrui Wu , Xiaojie Jin , Shoko Kure , Lindsay Parmelee , Shuli Luo , et al. Same-slide spatial multi-omics integration reveals tumor virus-linked spatial reorganization of the tumor microenvironment. bioRxiv, 2024."},{"key":"2026072502000641000_2026.06.08.726938v1.59","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506580102"},{"key":"2026072502000641000_2026.06.08.726938v1.60","doi-asserted-by":"crossref","unstructured":"Oscar Franz\u00e9n , Li-Ming Gan , and Johan LM Bj\u00f6rkegren. Panglaodb: a web server for exploration of mouse and human single-cell rna sequencing data. Database, 2019:baz046, 2019.","DOI":"10.1093\/database\/baz046"},{"key":"2026072502000641000_2026.06.08.726938v1.61","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"issue":"5","key":"2026072502000641000_2026.06.08.726938v1.62","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","year":"2015","journal-title":"Nature methods"},{"issue":"8","key":"2026072502000641000_2026.06.08.726938v1.63","doi-asserted-by":"crossref","first-page":"3802","DOI":"10.1038\/s41596-021-00556-8","article-title":"Codex multiplexed tissue imaging with dna-conjugated antibodies","volume":"16","year":"2021","journal-title":"Nature protocols"},{"key":"2026072502000641000_2026.06.08.726938v1.64","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01316-y"},{"key":"2026072502000641000_2026.06.08.726938v1.65","doi-asserted-by":"publisher","DOI":"10.1038\/s41374-022-00778-8"},{"key":"2026072502000641000_2026.06.08.726938v1.66","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/bs.mcb.2024.02.018","article-title":"A hitchhiker\u2019s guide to high-dimensional tissue imaging with multiplexed ion beam imaging","volume":"186","year":"2024","journal-title":"Methods in Cell Biology"},{"issue":"1","key":"2026072502000641000_2026.06.08.726938v1.67","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.jmoldx.2011.08.002","article-title":"Rnascope: a novel in situ rna analysis platform for formalin-fixed, paraffin-embedded tissues","volume":"14","year":"2012","journal-title":"The Journal of molecular diagnostics"},{"key":"2026072502000641000_2026.06.08.726938v1.68","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005177"},{"key":"2026072502000641000_2026.06.08.726938v1.69","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01094-0"},{"key":"2026072502000641000_2026.06.08.726938v1.70","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.05.047"},{"key":"2026072502000641000_2026.06.08.726938v1.71","doi-asserted-by":"publisher","DOI":"10.1101\/2023.06.25.546474"},{"key":"2026072502000641000_2026.06.08.726938v1.72","unstructured":"R Schiemann , PF Gherardini , R Kageyama , M Travers , and L Kitch . Mantis viewer (v1.2.0-beta.1), 2020."},{"key":"2026072502000641000_2026.06.08.726938v1.73","unstructured":"Zijian Niu , Aoife O\u2019Farrell , Jingxin Li , Sam Reffsin , Naveen Jain , Ian Dardani , Yogesh Goyal , and Arjun Raj . Piscis: a novel loss estimator of the f1 score enables accurate spot detection in fluorescence microscopy images via deep learning. bioRxiv, 2024."},{"key":"2026072502000641000_2026.06.08.726938v1.74","first-page":"793","article-title":"Sur la sph\u00e8re vide","volume":"6","year":"1934","journal-title":"a la m\u00e9moire de georges vorono\u00ef"},{"key":"2026072502000641000_2026.06.08.726938v1.75","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1142"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.06.08.726938","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T09:00:21Z","timestamp":1784970021000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.06.08.726938"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,9]]},"references-count":75,"URL":"https:\/\/doi.org\/10.64898\/2026.06.08.726938","relation":{},"subject":[],"published":{"date-parts":[[2026,6,9]]},"subtype":"preprint"}}