{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T11:58:18Z","timestamp":1789646298679,"version":"4.0.0"},"reference-count":148,"publisher":"MDPI AG","issue":"24","license":[{"start":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T00:00:00Z","timestamp":1766016000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Post-translational modifications (PTMs) are crucial chemical alterations occurring on proteins post-synthesis, impacting various cellular processes. During viral infections, PTMs are shown to play a multitude of roles in viral replication, host interaction, and immune evasion. Thus, these modifications can influence infectivity, with direct impact on the anti-viral host immune responses and potentially viral adaptation across species. This field is still scarcely explored, whilst understanding PTMs is not only important to advance the knowledge of virus pathology but also potentially to provide insights for vaccine development. In this review, we attempt to summarize the latest findings mainly published over the last 10 years, focusing on the roles of PTMs involved in virus infection and anti-viral immune responses, in the context of relevant human respiratory infections: influenza A virus (IAV), respiratory syncytial virus (RSV), and SARS-CoV-2. We decided to concentrate on these three viruses because they currently represent a global health problem due to recurrent outbreaks and pandemic potential. A deeper characterization of the PTMs may help in understanding virus\u2013host interaction with possible implications on curative strategies. Further, we will report on cutting-edge technologies to study in vitro virus infection in different cellular-based systems. In particular, we describe and discuss the application of 2D and 3D lung organoid cell-culture systems as in vitro models to mimic respiratory environments and to study the PTMs in a controlled setting. Finally, we will discuss the importance of PTMs in the context of next-generation vaccine design, especially for their potential role to offer effective protection against respiratory viruses.<\/jats:p>","DOI":"10.3390\/ijms262412174","type":"journal-article","created":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T13:45:07Z","timestamp":1766065507000},"page":"12174","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Post-Translational Modifications in Respiratory Virus Infection: Recent Insights into the Development of In Vitro Models"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3562-6401","authenticated-orcid":false,"given":"Emna","family":"Ben Khlifa","sequence":"first","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7023-8183","authenticated-orcid":false,"given":"Alessia","family":"Campese","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7482-3251","authenticated-orcid":false,"given":"Andrea","family":"Corsi","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0295-5938","authenticated-orcid":false,"given":"Cristina","family":"Bombieri","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7360-1195","authenticated-orcid":false,"given":"Maria Grazia","family":"Romanelli","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1166-8033","authenticated-orcid":false,"given":"Maria Teresa","family":"Valenti","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2168-4144","authenticated-orcid":false,"given":"Donato","family":"Zipeto","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matteo","family":"Castelli","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4439-1106","authenticated-orcid":false,"given":"Patricia Marie-Jeanne","family":"Lievens","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1041-7489","authenticated-orcid":false,"given":"Alessandra","family":"Ruggiero","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Biomedicine, and Movement Sciences, School of Medicine, University of Verona, Strada le Grazie 8, 37134 Verona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,18]]},"reference":[{"key":"ref_1","unstructured":"Preedy, V.R. (2017). Chapter 13\u2014Cocaine and Posttranslational Modifications of Neuronal Proteins. The Neuroscience of Cocaine, Academic Press."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e261","DOI":"10.1002\/mco2.261","article-title":"Protein Posttranslational Modifications in Health and Diseases: Functions, Regulatory Mechanisms, and Therapeutic Implications","volume":"4","author":"Zhong","year":"2023","journal-title":"MedComm"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1016\/j.tibs.2024.12.012","article-title":"Protein N-Terminal Modifications: Molecular Machineries and Biological Implications","volume":"50","author":"Lundekvam","year":"2025","journal-title":"Trends Biochem. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"102352","DOI":"10.1016\/j.sbi.2022.102352","article-title":"Uncovering Post-Translational Modification-Associated Protein\u2013Protein Interactions","volume":"74","author":"Wang","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1038\/s41589-024-01805-z","article-title":"Mechanisms of Metabolism-Coupled Protein Modifications","volume":"21","author":"Zhang","year":"2025","journal-title":"Nat. Chem. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/nsmb.1842","article-title":"Post-Translational Modifications in Signal Integration","volume":"17","author":"Deribe","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1038\/s41418-025-01473-z","article-title":"Crosstalk between O-GlcNAcylation and Phosphorylation in Metabolism: Regulation and Mechanism","volume":"32","author":"Zhao","year":"2025","journal-title":"Cell Death Differ."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Kumar, R., Mehta, D., Mishra, N., Nayak, D., and Sunil, S. (2021). Role of Host-Mediated Post-Translational Modifications (PTMs) in RNA Virus Pathogenesis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22010323"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1038\/s41392-024-01886-1","article-title":"Glycosylation: Mechanisms, Biological Functions and Clinical Implications","volume":"9","author":"He","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/s41467-023-35795-8","article-title":"Control of Protein Stability by Post-Translational Modifications","volume":"14","author":"Lee","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1038\/s41580-020-00294-x","article-title":"Global View of Human Protein Glycosylation Pathways and Functions","volume":"21","author":"Schjoldager","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3803","DOI":"10.1158\/0008-5472.CAN-07-6389","article-title":"Inhibition of N-Linked Glycosylation Disrupts Receptor Tyrosine Kinase Signaling in Tumor Cells","volume":"68","author":"Contessa","year":"2008","journal-title":"Cancer Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1074\/jbc.M510893200","article-title":"Core Fucosylation Regulates Epidermal Growth Factor Receptor-Mediated Intracellular Signaling","volume":"281","author":"Wang","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5083","DOI":"10.1021\/acs.analchem.8b05372","article-title":"Remarkable Structural Diversity of N-Glycan Sulfation on Influenza Vaccines","volume":"91","author":"She","year":"2019","journal-title":"Anal. Chem."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1038\/nbt1252","article-title":"Post-Translational Modifications in the Context of Therapeutic Proteins","volume":"24","author":"Walsh","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"baab012","DOI":"10.1093\/database\/baab012","article-title":"Post-Translational Modifications in Proteins: Resources, Tools and Prediction Methods","volume":"2021","author":"Ramazi","year":"2021","journal-title":"Database"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/S0968-0004(01)01958-2","article-title":"Ten Years of Protein Kinase B Signalling: A Hard Akt to Follow","volume":"26","author":"Brazil","year":"2001","journal-title":"Trends Biochem. Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"27462","DOI":"10.1074\/jbc.M102940200","article-title":"Regulation of Protein Kinase B\/Akt-Serine 473 Phosphorylation by Integrin-Linked Kinase: CRITICAL ROLES FOR KINASE ACTIVITY AND AMINO ACIDS ARGININE 211 AND SERINE 343","volume":"276","author":"Persad","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"a020644","DOI":"10.1101\/cshperspect.a020644","article-title":"The Genesis of Tyrosine Phosphorylation","volume":"6","author":"Hunter","year":"2014","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.conb.2021.03.003","article-title":"A Current View on Tau Protein Phosphorylation in Alzheimer\u2019s Disease","volume":"69","author":"Wegmann","year":"2021","journal-title":"Curr. Opin. Neurobiol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Sharma, C., Hamza, A., Boyle, E., Donu, D., and Cen, Y. (2024). Post-Translational Modifications and Diabetes. Biomolecules, 14.","DOI":"10.3390\/biom14030310"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.biocel.2017.12.008","article-title":"Mutant FGFR3 Associated with SADDAN Disease Causes Cytoskeleton Disorganization through PLC\u03b31\/Src-Mediated Paxillin Hyperphosphorylation","volume":"95","author":"Montone","year":"2017","journal-title":"Int. J. Biochem. Amp Cell Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10930-017-9696-z","article-title":"Phosphorylation: Implications in Cancer","volume":"36","author":"Singh","year":"2017","journal-title":"Protein J."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1007\/s12272-020-01281-8","article-title":"Ubiquitin-Proteasome System (UPS) as a Target for Anticancer Treatment","volume":"43","author":"Park","year":"2020","journal-title":"Arch. Pharm. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s12929-024-01003-y","article-title":"Mechanisms and Functions of SUMOylation in Health and Disease: A Review Focusing on Immune Cells","volume":"31","author":"Huang","year":"2024","journal-title":"J. Biomed. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Emenike, B., Nwajiobi, O., and Raj, M. (2022). Covalent Chemical Tools for Profiling Post-Translational Modifications. Front. Chem., 10.","DOI":"10.3389\/fchem.2022.868773"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/nrc3409","article-title":"Protein Arginine Methyltransferases and Cancer","volume":"13","author":"Yang","year":"2013","journal-title":"Nat. Rev. Cancer"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1016\/j.bbapap.2016.06.007","article-title":"The World of Protein Acetylation","volume":"1864","author":"Drazic","year":"2016","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.semcancer.2021.03.001","article-title":"Targeting the Acetylation Signaling Pathway in Cancer Therapy","volume":"85","author":"Dang","year":"2022","journal-title":"Semin. Cancer Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/j.chembiol.2018.05.003","article-title":"Protein Lipidation in Cell Signaling and Diseases: Function, Regulation, and Therapeutic Opportunities","volume":"25","author":"Chen","year":"2018","journal-title":"Cell Chem. Biol."},{"key":"ref_31","first-page":"1","article-title":"Protein Lipidation in Health and Disease: Molecular Basis, Physiological Function and Pathological Implication","volume":"9","author":"Yuan","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.plipres.2009.02.001","article-title":"Dynamic Protein Palmitoylation in Cellular Signaling","volume":"48","author":"Iwanaga","year":"2009","journal-title":"Prog. Lipid Res."},{"key":"ref_33","first-page":"e03861","article-title":"Palmitoyl Transferase FonPAT2-Catalyzed Palmitoylation of the FonAP-2 Complex Is Essential for Growth, Development, Stress Response, and Virulence in Fusarium oxysporum f. sp. niveum","volume":"11","author":"Xiong","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/s41580-024-00700-8","article-title":"Mechanisms and Functions of Protein S-Acylation","volume":"25","author":"Mesquita","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2208","DOI":"10.1128\/MCB.00144-16","article-title":"ZDHHC3 Tyrosine Phosphorylation Regulates Neural Cell Adhesion Molecule Palmitoylation","volume":"36","author":"Lievens","year":"2016","journal-title":"Mol. Cell. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Busquets-Hern\u00e1ndez, C., and Triola, G. (2021). Palmitoylation as a Key Regulator of Ras Localization and Function. Front. Mol. Biosci., 8.","DOI":"10.3389\/fmolb.2021.659861"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"405","DOI":"10.2217\/fvl-2018-0008","article-title":"Post-Translational Modifications of Coronavirus Proteins: Roles and Function","volume":"13","author":"Fung","year":"2018","journal-title":"Future Virol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"8020","DOI":"10.1002\/jcp.30483","article-title":"Cognizance of Posttranslational Modifications in Vaccines: A Way to Enhanced Immunogenicity","volume":"236","author":"Ojha","year":"2021","journal-title":"J. Cell. Physiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"14889","DOI":"10.1073\/pnas.0604045103","article-title":"Identification of Class I MHC-Associated Phosphopeptides as Targets for Cancer Immunotherapy","volume":"103","author":"Zarling","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1080\/1040841X.2024.2339259","article-title":"The Crosstalk between SUMOylation and Immune System in Host-Pathogen Interactions","volume":"51","author":"Zhu","year":"2025","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_41","first-page":"314","article-title":"Manipulation of the Host Protein Acetylation Network by Human Immunodeficiency Virus Type 1","volume":"50","author":"Jeng","year":"2015","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Manzoor, R., Igarashi, M., and Takada, A. (2017). Influenza A Virus M2 Protein: Roles from Ingress to Egress. Int. J. Mol. Sci., 18.","DOI":"10.3390\/ijms18122649"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Ohol, Y.M., Wang, Z., Kemble, G., and Duke, G. (2015). Direct Inhibition of Cellular Fatty Acid Synthase Impairs Replication of Respiratory Syncytial Virus and Other Respiratory Viruses. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0144648"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"101112","DOI":"10.1016\/j.jbc.2021.101112","article-title":"S-Acylation of SARS-CoV-2 Spike Protein: Mechanistic Dissection, in Vitro Reconstitution and Role in Viral Infectivity","volume":"297","author":"Puthenveetil","year":"2021","journal-title":"J. Biol. Chem."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Li, X., Shen, L., Xu, Z., Liu, W., Li, A., and Xu, J. (2022). Protein Palmitoylation Modification During Viral Infection and Detection Methods of Palmitoylated Proteins. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.821596"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e00658-23","DOI":"10.1128\/jvi.00658-23","article-title":"Virus Hijacking of Host Epigenetic Machinery to Impair Immune Response","volume":"97","author":"Locatelli","year":"2023","journal-title":"J. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Hu, J., Zhang, L., and Liu, X. (2020). Role of Post-Translational Modifications in Influenza A Virus Life Cycle and Host Innate Immune Response. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.517461"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Dou, D., Revol, R., \u00d6stbye, H., Wang, H., and Daniels, R. (2018). Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement. Front. Immunol., 9.","DOI":"10.3389\/fimmu.2018.01581"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/s41467-020-14626-0","article-title":"Influenza A Viruses Are Transmitted via the Air from the Nasal Respiratory Epithelium of Ferrets","volume":"11","author":"Richard","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_50","unstructured":"(2025, June 26). CDC About Common Cold, Available online: https:\/\/www.cdc.gov\/common-cold\/about\/index.html."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Hook, J.L., and Bhattacharya, J. (2024). The Pathogenesis of Influenza in Intact Alveoli: Virion Endocytosis and Its Effects on the Lung\u2019s Air-Blood Barrier. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1328453"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.jdsr.2023.12.006","article-title":"Respiratory Tract Barrier Dysfunction in Viral-Bacterial Co-Infection Cases","volume":"60","author":"Sumitomo","year":"2024","journal-title":"Jpn. Dent. Sci. Rev."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"BSR20171505","DOI":"10.1042\/BSR20171505","article-title":"Influenza Virus N-Linked Glycosylation and Innate Immunity","volume":"39","author":"York","year":"2019","journal-title":"Biosci. Rep."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"112035","DOI":"10.1016\/j.cellsig.2025.112035","article-title":"Ubiquitin E3 Ligase MARCH10 Targets Influenza Hemagglutinin for Ubiquitination","volume":"135","author":"Tsai","year":"2025","journal-title":"Cell. Signal."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Park, E.-S., Dezhbord, M., Lee, A.R., and Kim, K.-H. (2022). The Roles of Ubiquitination in Pathogenesis of Influenza Virus Infection. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23094593"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"6618","DOI":"10.1128\/JVI.02401-10","article-title":"The SUMOylation of Matrix Protein M1 Modulates the Assembly and Morphogenesis of Influenza A Virus","volume":"85","author":"Wu","year":"2011","journal-title":"J. Virol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Cong, J., Wang, T., Hahm, B., and Xia, C. (2025). Positive Regulation of Cellular Proteins by Influenza Virus for Productive Infection. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26083584"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Bergeron, H.C., and Tripp, R.A. (2022). RSV Replication, Transmission, and Disease Are Influenced by the RSV G Protein. Viruses, 14.","DOI":"10.3390\/v14112396"},{"key":"ref_59","unstructured":"Jain, H., Schweitzer, J.W., and Justice, N.A. (2024). Respiratory Syncytial Virus Infection in Children. StatPearls, StatPearls Publishing."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1128\/CMR.00010-16","article-title":"Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment","volume":"30","author":"Griffiths","year":"2017","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"6442","DOI":"10.1128\/JVI.74.14.6442-6447.2000","article-title":"The Fusion Glycoprotein of Human Respiratory Syncytial Virus Facilitates Virus Attachment and Infectivity via an Interaction with Cellular Heparan Sulfate","volume":"74","author":"Feldman","year":"2000","journal-title":"J. Virol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"King, T., Mejias, A., Ramilo, O., and Peeples, M.E. (2021). The Larger Attachment Glycoprotein of Respiratory Syncytial Virus Produced in Primary Human Bronchial Epithelial Cultures Reduces Infectivity for Cell Lines. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009469"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Okura, T., Takahashi, T., Kameya, T., Mizukoshi, F., Nakai, Y., Kakizaki, M., Nishi, M., Otsuki, N., Kimura, H., and Miyakawa, K. (2024). MARCH8 Restricts RSV Replication by Promoting Cellular Apoptosis Through Ubiquitin-Mediated Proteolysis of Viral SH Protein. Viruses, 16.","DOI":"10.3390\/v16121935"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"108256","DOI":"10.1016\/j.jbc.2025.108256","article-title":"Regulation of Respiratory Syncytial Virus Nucleoprotein Oligomerization by Phosphorylation","volume":"301","author":"Basse","year":"2025","journal-title":"J. Biol. Chem."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Cheng, N., Liu, M., Li, W., Sun, B., Liu, D., Wang, G., Shi, J., and Li, L. (2023). Protein Post-Translational Modification in SARS-CoV-2 and Host Interaction. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.1068449"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e02202-24","DOI":"10.1128\/jvi.02202-24","article-title":"Role of N-Linked Glycosylation Sites in Human ACE2 in SARS-CoV-2 and hCoV-NL63 Infection","volume":"99","author":"Noettger","year":"2025","journal-title":"J. Virol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e29304","DOI":"10.1002\/jmv.29304","article-title":"Posttranslational Modifications of ACE2 Protein: Implications for SARS-CoV-2 Infection and Beyond","volume":"95","author":"Xiao","year":"2023","journal-title":"J. Med. Virol."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Lauster, D., Osterrieder, K., Haag, R., Ballauff, M., and Herrmann, A. (2023). Respiratory Viruses Interacting with Cells: The Importance of Electrostatics. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1169547"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Trypsteen, W., Van Cleemput, J., van Snippenberg, W., Gerlo, S., and Vandekerckhove, L. (2020). On the Whereabouts of SARS-CoV-2 in the Human Body: A Systematic Review. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1009037"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"6283","DOI":"10.1007\/s12010-025-05333-x","article-title":"Mechanisms and Research Methods of Protein Modification in Virus Entry","volume":"197","author":"Xiao","year":"2025","journal-title":"Appl. Biochem. Biotechnol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/s41385-020-00359-2","article-title":"The Central Role of the Nasal Microenvironment in the Transmission, Modulation, and Clinical Progression of SARS-CoV-2 Infection","volume":"14","author":"Gallo","year":"2021","journal-title":"Mucosal Immunol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1038\/s41422-021-00519-4","article-title":"SARS-CoV-2 Envelope Protein Causes Acute Respiratory Distress Syndrome (ARDS)-like Pathological Damages and Constitutes an Antiviral Target","volume":"31","author":"Xia","year":"2021","journal-title":"Cell Res."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"10438","DOI":"10.1038\/s41467-024-54762-5","article-title":"TRIM7 Ubiquitinates SARS-CoV-2 Membrane Protein to Limit Apoptosis and Viral Replication","volume":"15","author":"Tseng","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"e01072-24","DOI":"10.1128\/jvi.01072-24","article-title":"Palmitoylation of SARS-CoV-2 Envelope Protein Is Central to Virus Particle Formation","volume":"98","author":"Wang","year":"2024","journal-title":"J. Virol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"e0312923","DOI":"10.1128\/mbio.03129-23","article-title":"Comparison of SARS-CoV-2 Variants of Concern in Primary Human Nasal Cultures Demonstrates Delta as Most Cytopathic and Omicron as Fastest Replicating","volume":"15","author":"Tanneti","year":"2024","journal-title":"mBio"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Ramadan, A.A., Mayilsamy, K., McGill, A.R., Ghosh, A., Giulianotti, M.A., Donow, H.M., Mohapatra, S.S., Mohapatra, S., Chandran, B., and Deschenes, R.J. (2022). Identification of SARS-CoV-2 Spike Palmitoylation Inhibitors That Results in Release of Attenuated Virus with Reduced Infectivity. Viruses, 14.","DOI":"10.3390\/v14030531"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"7666","DOI":"10.1038\/s41598-022-11816-2","article-title":"Virus Particle Propagation and Infectivity along the Respiratory Tract and a Case Study for SARS-CoV-2","volume":"12","author":"Vimalajeewa","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Zhu, J., Li, Y., Bradley, K.C., Cao, J., Chen, H., Jin, M., and Zhou, H. (2013). Glycosylation on Hemagglutinin Affects the Virulence and Pathogenicity of Pandemic H1N1\/2009 Influenza A Virus in Mice. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061397"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Valerdi, K.M., Hage, A., van Tol, S., Rajsbaum, R., and Giraldo, M.I. (2021). The Role of the Host Ubiquitin System in Promoting Replication of Emergent Viruses. Viruses, 13.","DOI":"10.3390\/v13030369"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s10020-023-00719-1","article-title":"The Emerging Roles of SUMOylation in Pulmonary Diseases","volume":"29","author":"Zheng","year":"2023","journal-title":"Mol. Med."},{"key":"ref_81","first-page":"20","article-title":"Different Cell Lines for SARS-CoV-2","volume":"2","author":"Bajaj","year":"2021","journal-title":"Coronavirus Disease-19 (COVID-19): A Perspective of New Scenario"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"20417314241232502","DOI":"10.1177\/20417314241232502","article-title":"Advanced Lung Organoids for Respiratory System and Pulmonary Disease Modeling","volume":"15","author":"Joo","year":"2024","journal-title":"J. Tissue Eng."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"L1063","DOI":"10.1152\/ajplung.00190.2019","article-title":"Structural and Functional Variations in Human Bronchial Epithelial Cells Cultured in Air-Liquid Interface Using Different Growth Media","volume":"318","author":"Leung","year":"2020","journal-title":"Am. J. Physiol. Lung Cell. Mol. Physiol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2000624","DOI":"10.1002\/adbi.202000624","article-title":"In Vitro Models for Studying Respiratory Host\u2013Pathogen Interactions","volume":"5","author":"Barron","year":"2021","journal-title":"Adv. Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"106305","DOI":"10.1016\/j.jinf.2024.106305","article-title":"Infant-Derived Human Nasal Organoids Exhibit Relatively Increased Susceptibility, Epithelial Responses, and Cytotoxicity during RSV Infection","volume":"89","author":"Aloisio","year":"2024","journal-title":"J. Infect."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"122208","DOI":"10.1016\/j.lfs.2023.122208","article-title":"Development of Lung Tissue Models and Their Applications","volume":"334","author":"Petpiroon","year":"2023","journal-title":"Life Sci."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Bombieri, C., Corsi, A., Trabetti, E., Ruggiero, A., Marchetto, G., Vattemi, G., Valenti, M.T., Zipeto, D., and Romanelli, M.G. (2024). Advanced Cellular Models for Rare Disease Study: Exploring Neural, Muscle and Skeletal Organoids. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25021014"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1247125","DOI":"10.1126\/science.1247125","article-title":"Organogenesis in a Dish: Modeling Development and Disease Using Organoid Technologies","volume":"345","author":"Lancaster","year":"2014","journal-title":"Science"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s41232-017-0034-9","article-title":"Epithelial Stem Cell Culture: Modeling Human Disease and Applications for Regenerative Medicine","volume":"37","author":"Yamamoto","year":"2017","journal-title":"Inflamm. Regen."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"EMBJ2018100300","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":"ref_91","doi-asserted-by":"crossref","first-page":"e05098","DOI":"10.7554\/eLife.05098","article-title":"In Vitro Generation of Human Pluripotent Stem Cell Derived Lung Organoids","volume":"4","author":"Dye","year":"2015","journal-title":"eLife"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"8398","DOI":"10.1038\/s41467-023-44134-w","article-title":"Intranasal mask for protecting the respiratory tract against viral aerosols","volume":"14","author":"Hu","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"6822","DOI":"10.1073\/pnas.1806308115","article-title":"Differentiated Human Airway Organoids to Assess Infectivity of Emerging Influenza Virus","volume":"115","author":"Zhou","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"2211685","DOI":"10.1080\/22221751.2023.2211685","article-title":"Reciprocal enhancement of SARS-CoV-2 and influenza virus replication in human pluripotent stem cell-derived lung organoids","volume":"12","author":"Kim","year":"2023","journal-title":"Emerg. Microbes Infect."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Zhao, L., Yan, Y., Dai, Q., Li, X., Xu, K., Zou, G., Yang, K., Li, W., Guo, X., and Yang, J. (2020). Development of Novel Anti-influenza Thiazolides with Relatively Broad-Spectrum Antiviral Potentials. Antimicrob. Agents Chemother., 64.","DOI":"10.1128\/AAC.00222-20"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1016\/S2213-2600(18)30236-4","article-title":"Tropism, Replication Competence, and Innate Immune Responses of Influenza Virus: An Analysis of Human Airway Organoids and Ex-Vivo Bronchus Cultures","volume":"6","author":"Hui","year":"2018","journal-title":"Lancet Respir. Med."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"e03511-21","DOI":"10.1128\/mbio.03511-21","article-title":"The Human Nose Organoid Respiratory Virus Model: An Ex Vivo Human Challenge Model to Study Respiratory Syncytial Virus (RSV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pathogenesis and Evaluate Therapeutics","volume":"13","author":"Rajan","year":"2021","journal-title":"mBio"},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Harford, T.J., Rezaee, F., Dye, B.R., Fan, J., Spence, J.R., and Piedimonte, G. (2022). RSV-Induced Changes in a 3-Dimensional Organoid Model of Human Fetal Lungs. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0265094"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/ncb3510","article-title":"A Three-Dimensional Model of Human Lung Development and Disease from Pluripotent Stem Cells","volume":"19","author":"Chen","year":"2017","journal-title":"Nat. Cell Biol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"120439","DOI":"10.1016\/j.envpol.2022.120439","article-title":"Particulate matter exposure exacerbates cellular damage by increasing stress granule formation in respiratory syncytial virus-infected human lung organoids","volume":"315","author":"Choi","year":"2022","journal-title":"Environ. Pollut."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1016\/j.stem.2020.11.009","article-title":"Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men","volume":"27","author":"Samuel","year":"2020","journal-title":"Cell Stem Cell"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2901-9","article-title":"Identification of SARS-CoV-2 inhibitors using lung and colonic organoids","volume":"589","author":"Han","year":"2021","journal-title":"Nature"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41420-021-00439-7","article-title":"Human pluripotent stem cell-derived alveolar organoids for modeling pulmonary fibrosis and drug testing","volume":"7","author":"Kim","year":"2021","journal-title":"Cell Death Discov."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.cell.2022.11.030","article-title":"SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming","volume":"186","author":"Wu","year":"2022","journal-title":"Cell"},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Ekanger, C.T., Zhou, F., Bohan, D., Lotsberg, M.L., Ramnefjell, M., Hoareau, L., R\u00f8sland, G.V., Lu, N., Aanerud, M., and G\u00e4rtner, F. (2022). Human Organotypic Airway and Lung Organoid Cells of Bronchiolar and Alveolar Differentiation Are Permissive to Infection by Influenza and SARS-CoV-2 Respiratory Virus. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.841447"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"e105912","DOI":"10.15252\/embj.2020105912","article-title":"An organoid-derived bronchioalveolar model for SARS-CoV-2 infection of human alveolar type II-like cells","volume":"40","author":"Lamers","year":"2021","journal-title":"EMBO J."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/s42003-022-03499-2","article-title":"Cell response analysis in SARS-CoV-2 infected bronchial organoids","volume":"5","author":"Sano","year":"2022","journal-title":"Commun. Biol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"109920","DOI":"10.1016\/j.celrep.2021.109920","article-title":"An Airway Organoid-Based Screen Identifies a Role for the HIF1\u03b1-Glycolysis Axis in SARS-CoV-2 Infection","volume":"37","author":"Duan","year":"2021","journal-title":"Cell Rep."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"100140","DOI":"10.1016\/j.mocell.2024.100140","article-title":"Recent Advances and Applications of Human Lung Alveolar Organoids","volume":"47","author":"Kim","year":"2024","journal-title":"Mol. Cells"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/s12016-013-8368-9","article-title":"Respiratory Syncytial Virus\u2014A Comprehensive Review","volume":"45","author":"Borchers","year":"2013","journal-title":"Clin. Rev. Allergy Immunol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1007\/s12098-023-04613-w","article-title":"Respiratory Syncytial Virus Infection: An Update","volume":"90","author":"Soni","year":"2023","journal-title":"Indian J. Pediatr."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"4897","DOI":"10.1038\/s41596-021-00603-4","article-title":"Multiplexed single-cell analysis of organoid signaling networks","volume":"16","author":"Sufi","year":"2021","journal-title":"Nat. Protoc."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"835","DOI":"10.15252\/msb.20156282","article-title":"Cytometry-Based Single-Cell Analysis of Intact Epithelial Signaling Reveals MAPK Activation Divergent from TNF-\u03b1-Induced Apoptosis In Vivo","volume":"11","author":"Simmons","year":"2015","journal-title":"Mol. Syst. Biol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"102488","DOI":"10.1016\/j.ceb.2025.102488","article-title":"High-Dimensional Signalling Analysis of Organoids","volume":"94","author":"Dobric","year":"2025","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/s41592-020-0737-8","article-title":"Cell-Type-Specific Signaling Networks in Heterocellular Organoids","volume":"17","author":"Qin","year":"2020","journal-title":"Nat. Methods"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/bs.mie.2023.07.006","article-title":"Mass Cytometry as a Tool in Target Validation and Drug Discovery","volume":"690","author":"Watson","year":"2023","journal-title":"Methods Enzymol."},{"key":"ref_117","first-page":"0078","article-title":"SARS-CoV-2 Spike Protein Post-Translational Modification Landscape and Its Impact on Protein Structure and Function via Computational Prediction","volume":"6","author":"Liang","year":"2023","journal-title":"Res. Wash. DC"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41580-020-0231-2","article-title":"Proteomic and Interactomic Insights into the Molecular Basis of Cell Functional Diversity","volume":"21","author":"Bludau","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Madahar, V., Dang, R., Zhang, Q., Liu, C., Rodgers, V.G.J., and Liao, J. (2023). Human Post-Translational SUMOylation Modification of SARS-CoV-2 Nucleocapsid Protein Enhances Its Interaction Affinity with Itself and Plays a Critical Role in Its Nuclear Translocation. Viruses, 15.","DOI":"10.3390\/v15071600"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"10053","DOI":"10.1038\/s41598-023-33088-0","article-title":"Site Specific N- and O-Glycosylation Mapping of the Spike Proteins of SARS-CoV-2 Variants of Concern","volume":"13","author":"Shajahan","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"100770","DOI":"10.1016\/j.mcpro.2024.100770","article-title":"Proteome, Lysine Acetylome, and Succinylome Identify Posttranslational Modification of STAT1 as a Novel Drug Target in Silicosis","volume":"23","author":"Zhang","year":"2024","journal-title":"Mol. Cell. Proteom."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"104518","DOI":"10.1016\/j.ebiom.2023.104518","article-title":"Proteomic and Phosphoproteomic Characteristics of the Cortex, Hippocampus, Thalamus, Lung, and Kidney in COVID-19-Infected Female K18-hACE2 Mice","volume":"90","author":"Liu","year":"2023","journal-title":"eBioMedicine"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"e2411720121","DOI":"10.1073\/pnas.2411720121","article-title":"Binding Mode-Guided Development of High-Performance Antibodies Targeting Site-Specific Posttranslational Modifications","volume":"122","author":"Riso","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Mann, G., Sulkshane, P., Sadhu, P., Ziv, T., Glickman, M.H., and Brik, A. (2022). Antibody for Serine 65 Phosphorylated Ubiquitin Identifies PLK1-Mediated Phosphorylation of Mitotic Proteins and APC1. Molecules, 27.","DOI":"10.3390\/molecules27154867"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1126\/science.abb9983","article-title":"Site-Specific Glycan Analysis of the SARS-CoV-2 Spike","volume":"369","author":"Watanabe","year":"2020","journal-title":"Science"},{"key":"ref_126","doi-asserted-by":"crossref","unstructured":"Merz, N., Schilling, K., Thomas, D., Hahnefeld, L., and Gr\u00f6sch, S. (2025). Cell Labeling with 15-YNE Is Useful for Tracking Protein Palmitoylation and Metabolic Lipid Flux in the Same Sample. Molecules, 30.","DOI":"10.3390\/molecules30020377"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"103068","DOI":"10.1016\/j.xpro.2024.103068","article-title":"Protocol to Identify S-Acylated Proteins in Hippocampal Neurons Using \u03c9-Alkynyl Fatty Acid Analogs and Click Chemistry","volume":"5","author":"Townsend","year":"2024","journal-title":"STAR Protoc."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"2766","DOI":"10.1093\/bioinformatics\/bty1051","article-title":"DeepPhos: Prediction of Protein Phosphorylation Sites with Deep Learning","volume":"35","author":"Luo","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"4668","DOI":"10.1093\/bioinformatics\/btab551","article-title":"PhosIDN: An Integrated Deep Neural Network for Improving Protein Phosphorylation Site Prediction by Combining Sequence and Protein\u2013Protein Interaction Information","volume":"37","author":"Yang","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Song, T., Yang, Q., Qu, P., Qiao, L., and Wang, X. (2024). Attenphos: General Phosphorylation Site Prediction Model Based on Attention Mechanism. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25031526"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"108079","DOI":"10.1016\/j.compbiomed.2024.108079","article-title":"DeepNphos: A Deep-Learning Architecture for Prediction of N-Phosphorylation Sites","volume":"170","author":"Chang","year":"2024","journal-title":"Comput. Biol. Med."},{"key":"ref_132","first-page":"73","article-title":"Prediction of Kinase-Substrate Associations Using the Functional Landscape of Kinases and Phosphorylation Sites","volume":"28","author":"Ayati","year":"2023","journal-title":"Pac. Symp. Biocomput. Pac. Symp. Biocomput."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"e16164","DOI":"10.7717\/peerj.16164","article-title":"KSFinder\u2014A Knowledge Graph Model for Link Prediction of Novel Phosphorylated Substrates of Kinases","volume":"11","author":"Anandakrishnan","year":"2023","journal-title":"PeerJ"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1021\/cb100218d","article-title":"SIRT3 Substrate Specificity Determined by Peptide Arrays and Machine Learning","volume":"6","author":"Smith","year":"2011","journal-title":"ACS Chem. Biol."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/s42004-025-01717-6","article-title":"Machine Learning-Driven Prediction of Substrates for Enzymes Introducing or Removing Protein Post-Translational Modifications","volume":"8","author":"Ridgeway","year":"2025","journal-title":"Commun. Chem."},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Bludau, I., Willems, S., Zeng, W.-F., Strauss, M.T., Hansen, F.M., Tanzer, M.C., Karayel, O., Schulman, B.A., and Mann, M. (2022). The Structural Context of Posttranslational Modifications at a Proteome-Wide Scale. PLoS Biol., 20.","DOI":"10.1371\/journal.pbio.3001636"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"100129","DOI":"10.1016\/j.mcpro.2021.100129","article-title":"Decoding Post-Translational Modification Crosstalk with Proteomics","volume":"20","author":"Leutert","year":"2021","journal-title":"Mol. Cell. Proteom."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.devcel.2021.11.007","article-title":"A Census of the Lung: CellCards from LungMAP","volume":"57","author":"Sun","year":"2022","journal-title":"Dev. Cell"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.trsl.2022.07.002","article-title":"Human Lung Organoids as a Model for Respiratory Virus Replication and Countermeasure Performance in Human Hosts","volume":"250","author":"Edwards","year":"2022","journal-title":"Transl. Res."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1002\/msb.201304521","article-title":"Evolution and Functional Cross-talk of Protein Post-translational Modifications","volume":"9","author":"Beltrao","year":"2013","journal-title":"Mol. Syst. Biol."},{"key":"ref_141","doi-asserted-by":"crossref","unstructured":"Boytz, R., and Laurent-Rolle, M. (2024). Balancing Acts: The Posttranslational Modification Tightrope of Flavivirus Replication. PLoS Pathog., 20.","DOI":"10.1371\/journal.ppat.1012626"},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Li, X., Kabza, A., Ives, A.N., Thiel, J., Waters, K.M., Qian, W.-J., Sims, A.C., and Zhang, T. (2025). Proteome-Wide Characterization of PTMs Reveals Host Cell Responses to Viral Infection and Identifies Putative Antiviral Drug Targets. Front. Immunol., 16, Correction in Front. Immunol. 2025, 16, 1672766. https:\/\/doi.org\/10.3389\/fimmu.2025.1672766.","DOI":"10.3389\/fimmu.2025.1672766"},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"Schmidt, H.M., and Horner, S.M. (2025). Towards a Universal Translator: Decoding the PTMs That Regulate Orthoflavivirus Infection. Viruses, 17.","DOI":"10.3390\/v17020287"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1590\/S0100-879X2012007500142","article-title":"Recombinant Vaccines and the Development of New Vaccine Strategies","volume":"45","author":"Nascimento","year":"2012","journal-title":"Braz. J. Med. Biol. Res."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1111\/j.1365-3024.2006.00902.x","article-title":"The Importance of Protein Glycosylation in Development of Novel Tick Vaccine Strategies","volume":"28","author":"Canales","year":"2006","journal-title":"Parasite Immunol."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1111\/j.1365-3024.2006.00806.x","article-title":"Exposed and Concealed Antigens as Vaccine Targets for Controlling Ticks and Tick-borne Diseases","volume":"28","author":"Nuttall","year":"2006","journal-title":"Parasite Immunol."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1002\/mas.21905","article-title":"Exploring the Dynamic Landscape of Immunopeptidomics: Unravelling Posttranslational Modifications and Navigating Bioinformatics Terrain","volume":"44","author":"Flender","year":"2025","journal-title":"Mass Spectrom. Rev."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"e41714","DOI":"10.1016\/j.heliyon.2025.e41714","article-title":"Computational Epitope-Based Vaccine Design with Bioinformatics Approach; a Review","volume":"11","author":"Basmenj","year":"2025","journal-title":"Heliyon"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/24\/12174\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T05:10:28Z","timestamp":1766380228000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/24\/12174"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,18]]},"references-count":148,"journal-issue":{"issue":"24","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["ijms262412174"],"URL":"https:\/\/doi.org\/10.3390\/ijms262412174","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,18]]}}}