{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T11:56:05Z","timestamp":1787313365812,"version":"build-2736575974"},"reference-count":163,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:00:00Z","timestamp":1748563200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011661","name":"Pacific Northwest National Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011661","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>Post-translational modifications (PTMs) are biochemical modifications that can significantly alter protein structure, function, stability, localization, and interactions with other molecules, thereby activating or inactivating intracellular processes. A growing body of research has begun to highlight the role of PTMs, including phosphorylation, ubiquitination, acetylation, and redox modifications, during virus-host interactions. Collectively, these PTMs regulate key steps in mounting the host immune response and control critical host pathways required for productive viral replication. This has led to the conception of antiviral therapeutics that focus on controlling host protein PTMs, potentially offering pathogen-agnostic treatment options and revolutionizing our capacity to prevent virus transmission. On the other hand, viruses can hijack the host cellular PTM machinery to modify viral proteins in promoting viral replication and evading immune surveillance. PTM regulation during virus-host interactions is complex and poorly mapped, and the development of effective PTM-targeted antiviral drugs will require a more comprehensive understanding of the cellular pathways essential for virus replication. In this review, we discuss the roles of PTMs in virus infection and how technological advances in mass spectrometry-based proteomics can capture systems-level PTM changes during viral infection. Additionally, we explore how such knowledge is leveraged to identify PTM-targeted candidates for developing antiviral drugs. Looking ahead, studies focusing on the discovery and functional elucidation of PTMs, either on the host or viral proteins, will not only deepen our understanding of molecular pathology but also pave the way for developing better drugs to fight emerging viruses.<\/jats:p>","DOI":"10.3389\/fimmu.2025.1587106","type":"journal-article","created":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T01:44:03Z","timestamp":1748569443000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets"],"prefix":"10.3389","volume":"16","author":[{"given":"Xiaolu","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Kabza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley N.","family":"Ives","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julianne","family":"Thiel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina M.","family":"Waters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei-Jun","family":"Qian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy C.","family":"Sims","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,5,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbagen.2019.05.012","article-title":"Exploitation of glycosylation in enveloped virus pathobiology","volume":"1863","author":"Watanabe","year":"2019","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01321-20","article-title":"Human cytomegalovirus induces the expression of the AMPKa2 subunit to drive glycolytic activation and support productive viral infection","volume":"95","author":"Dunn","year":"2021","journal-title":"J Virol"},{"key":"B3","doi-asserted-by":"publisher","first-page":"790","DOI":"10.3390\/pathogens11070790","article-title":"Antagonism of protein kinase R by large DNA viruses","volume":"11","author":"Olson","year":"2022","journal-title":"Pathogens"},{"key":"B4","doi-asserted-by":"publisher","first-page":"110690","DOI":"10.1016\/j.celrep.2022.110690","article-title":"Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling","volume":"39","author":"Johnson","year":"2022","journal-title":"Cell Rep"},{"key":"B5","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/s41580-021-00418-x","article-title":"Mechanisms of SARS-CoV-2 entry into cells","volume":"23","author":"Jackson","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"key":"B6","doi-asserted-by":"publisher","first-page":"113558","DOI":"10.1016\/j.celrep.2023.113558","article-title":"A quantitative model for virus uncoating predicts influenza A infectivity","volume":"42","author":"Artcibasova","year":"2023","journal-title":"Cell Rep"},{"key":"B7","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s41422-021-00581-y","article-title":"Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2","volume":"32","author":"Zhang","year":"2022","journal-title":"Cell Res"},{"key":"B8","doi-asserted-by":"publisher","first-page":"845","DOI":"10.3390\/v16060845","article-title":"Identifying protein interactions with viral DNA genomes during virus infection","volume":"16","author":"Packard","year":"2024","journal-title":"Viruses"},{"key":"B9","doi-asserted-by":"publisher","first-page":"e2206292119","DOI":"10.1073\/pnas.2206292119","article-title":"Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles","volume":"119","author":"Garmann","year":"2022","journal-title":"Proc Natl Acad Sci United States Am"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01474-0","article-title":"A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets","volume":"41","author":"Zhou","year":"2023","journal-title":"Nat Biotechnol"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.03.002","article-title":"Comprehensive characterization of human-virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs","volume":"20","author":"Li","year":"2022","journal-title":"Comput Struct Biotechnol J"},{"key":"B12","doi-asserted-by":"publisher","first-page":"11058","DOI":"10.3390\/ijms231911058","article-title":"Transcriptomics and RNA-based therapeutics as potential approaches to manage SARS-coV-2 infection","volume":"23","author":"Arriaga-Canon","year":"2022","journal-title":"Int J Mol Sci"},{"key":"B13","doi-asserted-by":"publisher","first-page":"6030","DOI":"10.1038\/s41467-023-41442-z","article-title":"Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets","volume":"14","author":"Haas","year":"2023","journal-title":"Nat Commun"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac820","article-title":"qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast","volume":"51","author":"Yu","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"B15","doi-asserted-by":"publisher","first-page":"11308","DOI":"10.3390\/ijms231911308","article-title":"Protein acetylation going viral: implications in antiviral immunity and viral infection","volume":"23","author":"Xue","year":"2022","journal-title":"Int J Mol Sci"},{"key":"B16","doi-asserted-by":"publisher","first-page":"4593","DOI":"10.3390\/ijms23094593","article-title":"The roles of ubiquitination in pathogenesis of influenza virus infection","volume":"23","author":"Park","year":"2022","journal-title":"Int J Mol Sci"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1101\/gad.11.20.2645","article-title":"The HIV transactivator TAT binds to the CDK-activating kinase and activates the phosphorylation of the carboxy-terminal domain of RNA polymerase II","volume":"11","author":"Cujec","year":"1997","journal-title":"Genes Dev"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00027-06","article-title":"Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action","volume":"70","author":"Garc\u00eda","year":"2006","journal-title":"Microbiol Mol Biol Rev"},{"key":"B19","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.cell.2020.06.034","article-title":"The global phosphorylation landscape of SARS-coV-2 infection","volume":"182","author":"Bouhaddou","year":"2020","journal-title":"Cell"},{"key":"B20","doi-asserted-by":"publisher","first-page":"e2300096","DOI":"10.1002\/pmic.202300096","article-title":"Global analysis of lysine acetylation in the brain cortex of K18-hACE2 mice infected with SARS-CoV-2","volume":"23","author":"Wang","year":"2023","journal-title":"Proteomics"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.76071","article-title":"Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target","volume":"11","author":"Neogi","year":"2022","journal-title":"Elife"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1021\/cr300163e","article-title":"Cysteine-mediated redox signaling: chemistry, biology, and tools for discovery","volume":"113","author":"Paulsen","year":"2013","journal-title":"Chem Rev"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202200194","article-title":"Thiol redox proteomics: Characterization of thiol-based post-translational modifications","volume":"23","author":"Li","year":"2023","journal-title":"Proteomics"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1016\/j.freeradbiomed.2022.10.300","article-title":"A deep redox proteome profiling workflow and its application to skeletal muscle of a duchene muscular dystrophy model","volume":"193","author":"Day","year":"2022","journal-title":"Free Radic Biol Med"},{"key":"B25","doi-asserted-by":"publisher","first-page":"e2201169119","DOI":"10.1073\/pnas.2201169119","article-title":"Viral evasion of PKR restriction by reprogramming cellular stress granules","volume":"119","author":"Gao","year":"2022","journal-title":"Proc Natl Acad Sci United States Am"},{"key":"B26","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1038\/s41467-023-36445-9","article-title":"APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection","volume":"14","author":"Manjunath","year":"2023","journal-title":"Nat Commun"},{"key":"B27","doi-asserted-by":"publisher","first-page":"e1009183","DOI":"10.1371\/journal.ppat.1009183","article-title":"Orthopoxvirus K3 orthologs show virus- and host-specific inhibition of the antiviral protein kinase PKR","volume":"17","author":"Park","year":"2021","journal-title":"PloS Pathog"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.232439","article-title":"ICP34.5 protein of herpes simplex virus facilitates the initiation of protein translation by bridging eukaryotic initiation factor 2alpha (eIF2alpha) and protein phosphatase 1","volume":"286","author":"Li","year":"2011","journal-title":"J Biol Chem"},{"key":"B29","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/s42003-023-04735-z","article-title":"WSSV exploits AMPK to activate mTORC2 signaling for proliferation by enhancing aerobic glycolysis","volume":"6","author":"Zhang","year":"2023","journal-title":"Commun Biol"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1007\/s11262-022-01888-7","article-title":"AMP-activated kinase regulates porcine reproductive and respiratory syndrome virus infection in vitro","volume":"58","author":"Fang","year":"2022","journal-title":"Virus Genes"},{"key":"B31","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1186\/s11658-022-00381-1","article-title":"5-Methoxyflavone-induced AMPK\u03b1 activation inhibits NF-\u03baB and P38 MAPK signaling to attenuate influenza A virus-mediated inflammation and lung injury in vitro and in vivo","volume":"27","author":"Yang","year":"2022","journal-title":"Cell Mol Biol Lett"},{"key":"B32","doi-asserted-by":"publisher","first-page":"e1002661","DOI":"10.1371\/journal.ppat.1002661","article-title":"AMP-activated kinase restricts Rift Valley fever virus infection by inhibiting fatty acid synthesis","volume":"8","author":"Moser","year":"2012","journal-title":"PloS Pathog"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00360-18","article-title":"Direct activation of adenosine monophosphate-activated protein kinase (AMPK) by PF-06409577 inhibits flavivirus infection through modification of host cell lipid metabolism","volume":"62","author":"Jim\u00e9nez de Oya","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"key":"B34","doi-asserted-by":"publisher","first-page":"e1450","DOI":"10.1002\/wrna.1450","article-title":"Regulation and function of CMTR1-dependent mRNA cap methylation","volume":"8","author":"Inesta-Vaquera","year":"2017","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"B35","doi-asserted-by":"publisher","first-page":"114405","DOI":"10.1016\/j.celrep.2024.114405","article-title":"CK2 phosphorylation of CMTR1 promotes RNA cap formation and influenza virus infection","volume":"43","author":"Lukoszek","year":"2024","journal-title":"Cell Rep"},{"key":"B36","doi-asserted-by":"publisher","first-page":"552","DOI":"10.3390\/v14030552","article-title":"Targeting of protein kinase CK2 elicits antiviral activity on bovine coronavirus infection","volume":"14","author":"Ram\u00f3n","year":"2022","journal-title":"Viruses"},{"key":"B37","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1111\/fim.2014.72.issue-1","article-title":"The role of the IKK complex in viral infections","volume":"72","author":"Amaya","year":"2014","journal-title":"Pathog Dis"},{"key":"B38","doi-asserted-by":"publisher","first-page":"164","DOI":"10.3390\/pathogens13020164","article-title":"The role of the nuclear factor-kappa B (NF-\u03baB) pathway in SARS-coV-2 infection","volume":"13","author":"Kesika","year":"2024","journal-title":"Pathogens"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.3390\/microorganisms8071067","article-title":"Regulation of host immune responses against influenza A virus infection by mitogen-activated protein kinases (MAPKs)","volume":"8","author":"Yu","year":"2020","journal-title":"Microorganisms"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1007\/s12026-023-09401-4","article-title":"Functions of MAP3Ks in antiviral immunity","volume":"71","author":"Guan","year":"2023","journal-title":"Immunol Res"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.80.7.3341-3348.2006","article-title":"Protein kinase B\/Akt is present in activated form throughout the entire replicative cycle of deltaU(S)3 mutant virus but only at early times after infection with wild-type herpes simplex virus 1","volume":"80","author":"Benetti","year":"2006","journal-title":"J Virol"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01671-10","article-title":"Dominant inhibition of Akt\/protein kinase B signaling by the matrix protein of a negative-strand RNA virus","volume":"85","author":"Dunn","year":"2011","journal-title":"J Virol"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1111\/cmi.12559","article-title":"Phosphorylation of influenza A virus NS1 protein at threonine 49 suppresses its interferon antagonistic activity","volume":"18","author":"Kathum","year":"2016","journal-title":"Cell Microbiol"},{"key":"B44","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1186\/s12985-019-1255-0","article-title":"The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon","volume":"16","author":"Cheng","year":"2019","journal-title":"Virol J"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1038\/nature05732","article-title":"TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity","volume":"446","author":"Gack","year":"2007","journal-title":"Nature"},{"key":"B46","doi-asserted-by":"publisher","first-page":"5536","DOI":"10.1038\/s41467-020-19318-3","article-title":"RNF115 plays dual roles in innate antiviral responses by catalyzing distinct ubiquitination of MAVS and MITA","volume":"11","author":"Zhang","year":"2020","journal-title":"Nat Commun"},{"key":"B47","doi-asserted-by":"publisher","first-page":"e1008702","DOI":"10.1371\/journal.ppat.1008702","article-title":"Dissecting distinct proteolytic activities of FMDV Lpro implicates cleavage and degradation of RLR signaling proteins, not its deISGylase\/DUB activity, in type I interferon suppression","volume":"16","author":"Visser","year":"2020","journal-title":"PloS Pathog"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.744348","article-title":"MAVS: A two-sided CARD mediating antiviral innate immune signaling and regulating immune homeostasis","volume":"12","author":"Chen","year":"2021","journal-title":"Front Microbiol"},{"key":"B49","doi-asserted-by":"publisher","first-page":"3410","DOI":"10.1016\/j.cell.2021.04.047","article-title":"TRIM7 inhibits enterovirus replication and promotes emergence of a viral variant with increased pathogenicity","volume":"184","author":"Fan","year":"2021","journal-title":"Cell"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.15252\/embj.201592586","article-title":"HDAC6 regulates cellular viral RNA sensing by deacetylation of RIG-I","volume":"35","author":"Choi","year":"2016","journal-title":"EMBO J"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3464","article-title":"Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity","volume":"17","author":"Li","year":"2016","journal-title":"Nat Immunol"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1922330117","article-title":"KAT5 acetylates cGAS to promote innate immune response to DNA virus","volume":"117","author":"Song","year":"2020","journal-title":"Proc Natl Acad Sci United States Am"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA117.001683","article-title":"Influenza A virus nucleoprotein is acetylated by histone acetyltransferases PCAF and GCN5","volume":"293","author":"Hatakeyama","year":"2018","journal-title":"J Biol Chem"},{"key":"B54","doi-asserted-by":"publisher","first-page":"392","DOI":"10.3390\/v10080392","article-title":"Redox biology of respiratory viral infections","volume":"10","author":"Khomich","year":"2018","journal-title":"Viruses"},{"key":"B55","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/s12866-020-01890-9","article-title":"Redox control in the pathophysiology of influenza virus infection","volume":"20","author":"Chen","year":"2020","journal-title":"BMC Microbiol"},{"key":"B56","doi-asserted-by":"publisher","first-page":"e1006778","DOI":"10.1371\/journal.ppat.1006778","article-title":"Prohibitin plays a critical role in Enterovirus 71 neuropathogenesis","volume":"14","author":"Too","year":"2018","journal-title":"PloS Pathog"},{"key":"B57","doi-asserted-by":"publisher","first-page":"e282","DOI":"10.1038\/cddis.2012.21","article-title":"HIV-1 Tat protein directly induces mitochondrial membrane permeabilization and inactivates cytochrome c oxidase","volume":"3","author":"Lecoeur","year":"2012","journal-title":"Cell Death Dis"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.6.2840-2846.2000","article-title":"Hepatitis B virus X protein colocalizes to mitochondria with a human voltage-dependent anion channel, HVDAC3, and alters its transmembrane potential","volume":"74","author":"Rahmani","year":"2000","journal-title":"J Virol"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.810376","article-title":"Infection of endothelial cells by dengue virus induces ROS production by different sources affecting virus replication, cellular activation, death and vascular permeability","volume":"13","author":"Meuren","year":"2022","journal-title":"Front Immunol"},{"key":"B60","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1038\/s41467-017-00057-x","article-title":"Endosomal NOX2 oxidase exacerbates virus pathogenicity and is a target for antiviral therapy","volume":"8","author":"To","year":"2017","journal-title":"Nat\u00a0Commun"},{"key":"B61","doi-asserted-by":"publisher","first-page":"102563","DOI":"10.1016\/j.redox.2022.102563","article-title":"New insights into extracellular and intracellular redox status in COVID-19 patients","volume":"59","author":"Tavassolifar","year":"2023","journal-title":"Redox Biol"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.13904","article-title":"Oxidative stress, a trigger of hepatitis C and B virus-induced liver carcinogenesis","volume":"8","author":"Ivanov","year":"2017","journal-title":"Oncotarget"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2014.03.034","article-title":"ROS function in redox signaling and oxidative stress","volume":"24","author":"Schieber","year":"2014","journal-title":"Curr Biol"},{"key":"B64","doi-asserted-by":"publisher","first-page":"8416763","DOI":"10.1155\/2017\/8416763","article-title":"Oxidative stress: harms and benefits for human health","volume":"2017","author":"Pizzino","year":"2017","journal-title":"Oxid Med Cell Longev"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2021.12.011","article-title":"Mitochondria-mediated oxidative stress\u00a0during viral infection","volume":"30","author":"Foo","year":"2022","journal-title":"Trends Microbiol"},{"key":"B66","doi-asserted-by":"publisher","first-page":"102296","DOI":"10.1016\/j.isci.2021.102296","article-title":"Distinct roles and actions of protein disulfide isomerase family enzymes in catalysis of nascent-chain disulfide bond formation","volume":"24","author":"Hirayama","year":"2021","journal-title":"iScience"},{"key":"B67","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/s12985-020-01325-x","article-title":"Disulfide isomerase ERp57 improves the stability and immunogenicity of H3N2 influenza virus hemagglutinin","volume":"17","author":"Wu","year":"2020","journal-title":"Virol J"},{"key":"B68","doi-asserted-by":"publisher","first-page":"101129","DOI":"10.1016\/j.redox.2019.101129","article-title":"Lung epithelial protein disulfide isomerase A3 (PDIA3) plays an important role in influenza infection, inflammation, and airway mechanics","volume":"22","author":"Chamberlain","year":"2019","journal-title":"Redox Biol"},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.8b02676","article-title":"Gene expression profiling of endoplasmic reticulum stress in hepatitis C virus-containing cells treated with an inhibitor of protein disulfide isomerases","volume":"3","author":"\u00d6zcelik","year":"2018","journal-title":"ACS Omega"},{"key":"B70","doi-asserted-by":"publisher","first-page":"155","DOI":"10.3390\/v11020155","article-title":"Protein disulfide isomerase inhibitor suppresses viral replication and production during antibody-dependent enhancement of dengue virus infection in human monocytic cells","volume":"11","author":"Rawarak","year":"2019","journal-title":"Viruses"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026406","article-title":"Relationship between the occurrence of cysteine in proteins and the complexity of organisms","volume":"17","author":"Miseta","year":"2000","journal-title":"Mol Biol Evol"},{"key":"B72","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb2762","article-title":"Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2","volume":"367","author":"Yan","year":"2020","journal-title":"Science"},{"key":"B73","doi-asserted-by":"publisher","first-page":"104614","DOI":"10.1016\/j.isci.2022.104614","article-title":"Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways","volume":"25","author":"Richard","year":"2022","journal-title":"iScience"},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb3405","article-title":"Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved \u03b1-ketoamide inhibitors","volume":"368","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"B75","doi-asserted-by":"publisher","first-page":"e0209421","DOI":"10.1128\/mBio.02094-21","article-title":"Regulation of the dimerization and activity of SARS-coV-2 main protease through reversible glutathionylation of cysteine 300","volume":"12","author":"Davis","year":"2021","journal-title":"mBio"},{"key":"B76","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/s41467-023-44621-0","article-title":"Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design","volume":"15","author":"Funk","year":"2024","journal-title":"Nat Commun"},{"key":"B77","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-021-00966-5","article-title":"Widespread occurrence of covalent lysine-cysteine redox switches in proteins","volume":"18","author":"Rabe von Pappenheim","year":"2022","journal-title":"Nat\u00a0Chem Biol"},{"key":"B78","doi-asserted-by":"publisher","first-page":"668","DOI":"10.3390\/v13040668","article-title":"Top-down and bottom-up proteomics methods to study RNA virus biology","volume":"13","author":"Simanjuntak","year":"2021","journal-title":"Viruses"},{"key":"B79","doi-asserted-by":"publisher","first-page":"100712","DOI":"10.1016\/j.mcpro.2024.100712","article-title":"Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023","volume":"23","author":"Lou","year":"2024","journal-title":"Mol Cell Proteomics"},{"key":"B80","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.201800650","article-title":"A review on quantitative multiplexed proteomics","volume":"20","author":"Pappireddi","year":"2019","journal-title":"Chembiochem"},{"key":"B81","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.aca.2017.01.059","article-title":"A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition","volume":"964","author":"Vidova","year":"2017","journal-title":"Anal Chim Acta"},{"key":"B82","doi-asserted-by":"publisher","first-page":"463352","DOI":"10.1016\/j.chroma.2022.463352","article-title":"Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications","volume":"1678","author":"Brandi","year":"2022","journal-title":"J\u00a0Chromatogr A"},{"key":"B83","doi-asserted-by":"publisher","DOI":"10.1152\/ajpcell.00040.2020","article-title":"Characterization of cellular oxidative stress response by stoichiometric redox proteomics","volume":"320","author":"Zhang","year":"2021","journal-title":"Am J Physiol Cell Physiol"},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-3922-1_12","article-title":"Automated immunoprecipitation workflow for comprehensive acetylome analysis","volume":"2823","author":"Gritsenko","year":"2024","journal-title":"Methods Mol Biol"},{"key":"B85","doi-asserted-by":"publisher","first-page":"100754","DOI":"10.1016\/j.mcpro.2024.100754","article-title":"Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics","volume":"23","author":"Bortel","year":"2024","journal-title":"Mol Cell Proteomics"},{"key":"B86","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-8706-1_23","article-title":"Ubiquitin diGLY proteomics as an approach to identify and quantify the ubiquitin-modified proteome","volume":"1844","author":"Fulzele","year":"2018","journal-title":"Methods Mol Biol"},{"key":"B87","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/s41467-019-14175-1","article-title":"Rapid and deep-scale ubiquitylation profiling for biology and translational research","volume":"11","author":"Udeshi","year":"2020","journal-title":"Nat Commun"},{"key":"B88","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.O114.047555","article-title":"Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow","volume":"14","author":"Svinkina","year":"2015","journal-title":"Mol Cell Proteomics"},{"key":"B89","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M114.041160","article-title":"Proteome-wide light\/dark modulation of thiol oxidation in cyanobacteria revealed by quantitative site-specific redox proteomics*","volume":"13","author":"Guo","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"B90","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.0c00473","article-title":"21-plex diLeu isobaric tags for high-throughput quantitative proteomics","volume":"92","author":"Frost","year":"2020","journal-title":"Anal Chem"},{"key":"B91","doi-asserted-by":"publisher","first-page":"rs2","DOI":"10.1126\/scisignal.2002548","article-title":"Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast","volume":"5","author":"Dephoure","year":"2012","journal-title":"Sci Signal"},{"key":"B92","doi-asserted-by":"publisher","DOI":"10.1021\/ac502040v","article-title":"MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes","volume":"86","author":"McAlister","year":"2014","journal-title":"Anal Chem"},{"key":"B93","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1038\/s41467-020-20509-1","article-title":"Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology","volume":"12","author":"Hansen","year":"2021","journal-title":"Nat Commun"},{"key":"B94","doi-asserted-by":"publisher","first-page":"2539","DOI":"10.1038\/s41467-021-22759-z","article-title":"A data-independent acquisition-based global phosphoproteomics system enables deep profiling","volume":"12","author":"Kitata","year":"2021","journal-title":"Nat Commun"},{"key":"B95","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/s41467-020-14609-1","article-title":"Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries","volume":"11","author":"Bekker-Jensen","year":"2020","journal-title":"Nat Commun"},{"key":"B96","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.3c00416","article-title":"Top-down proteomics and the challenges of true proteoform characterization","volume":"22","author":"Po","year":"2023","journal-title":"J Proteome Res"},{"key":"B97","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M115.054460","article-title":"Systems level analysis of histone H3 post-translational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation","volume":"15","author":"Schw\u00e4mmle","year":"2016","journal-title":"Mol Cell Proteomics"},{"key":"B98","doi-asserted-by":"publisher","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 Proteomics"},{"key":"B99","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.3390\/v12121409","article-title":"Mapping influenza-induced posttranslational modifications on histones from CD8+ T cells","volume":"12","author":"Rezinciuc","year":"2020","journal-title":"Viruses"},{"key":"B100","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb9983","article-title":"Site-specific glycan\u00a0analysis of the SARS-CoV-2 spike","volume":"369","author":"Watanabe","year":"2020","journal-title":"Science"},{"key":"B101","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.1c02713","article-title":"Structural O-glycoform heterogeneity of the SARS-coV-2 spike protein receptor-binding domain revealed by top-down mass spectrometry","volume":"143","author":"Roberts","year":"2021","journal-title":"J Am Chem Soc"},{"key":"B102","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.9b00797","article-title":"Individual ion mass spectrometry enhances the sensitivity and sequence coverage of top-down mass spectrometry","volume":"19","author":"Kafader","year":"2020","journal-title":"J Proteome Res"},{"key":"B103","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0764-5","article-title":"Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes","volume":"17","author":"Kafader","year":"2020","journal-title":"Nat Methods"},{"key":"B104","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.1c00353","article-title":"Heterogeneity of glycan processing on trimeric SARS-coV-2 spike protein revealed by charge detection mass spectrometry","volume":"143","author":"Miller","year":"2021","journal-title":"J Am Chem Soc"},{"key":"B105","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.coviro.2019.02.006","article-title":"Mass spectrometry-based studies of virus assembly","volume":"36","author":"Ashcroft","year":"2019","journal-title":"Curr Opin Virol"},{"key":"B106","doi-asserted-by":"publisher","first-page":"2079449","DOI":"10.1080\/19420862.2022.2079449","article-title":"A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies","volume":"14","author":"de Graaf","year":"2022","journal-title":"MAbs"},{"key":"B107","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cwaa018","article-title":"Understanding the role of antibody glycosylation through the lens of severe viral and bacterial diseases","volume":"30","author":"Irvine","year":"2020","journal-title":"Glycobiology"},{"key":"B108","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.3c01426","article-title":"Added value of internal fragments for top-down mass spectrometry of intact\u00a0monoclonal antibodies and antibody-drug conjugates","volume":"95","author":"Wei","year":"2023","journal-title":"Anal Chem"},{"key":"B109","doi-asserted-by":"publisher","first-page":"3114","DOI":"10.1038\/s41467-024-47337-x","article-title":"Antigen-specific Fab profiling achieves molecular-resolution analysis of human autoantibody repertoires in rheumatoid arthritis","volume":"15","author":"Stork","year":"2024","journal-title":"Nat Commun"},{"key":"B110","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1021\/acs.analchem.1c03656","article-title":"Comparative analysis of antibodies and heavily glycosylated macromolecular immune complexes by size-exclusion chromatography multi-angle light scattering, native charge detection mass spectrometry, and mass photometry","volume":"94","author":"den Boer","year":"2022","journal-title":"Anal Chem"},{"key":"B111","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.1c00882","article-title":"Next-generation serology by mass spectrometry: readout of the SARS-coV-2 antibody repertoire","volume":"21","author":"Melani","year":"2022","journal-title":"J Proteome Res"},{"key":"B112","doi-asserted-by":"publisher","first-page":"3679","DOI":"10.1038\/s41467-018-06119-y","article-title":"Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target","volume":"9","author":"Y\u00e1ng\u00fcez","year":"2018","journal-title":"Nat Commun"},{"key":"B113","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.3c00182","article-title":"Investigation of the host kinome response to coronavirus infection reveals PI3K\/mTOR inhibitors as betacoronavirus antivirals","volume":"22","author":"Fritch","year":"2023","journal-title":"J Proteome Res"},{"key":"B114","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s12014-024-09457-w","article-title":"Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients","volume":"21","author":"Kaneko","year":"2024","journal-title":"Clin Proteomics"},{"key":"B115","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.0c00758","article-title":"Ubiquitin-modified proteome of SARS-coV-2-infected host cells reveals insights into virus-host interaction and pathogenesis","volume":"20","author":"Zhang","year":"2021","journal-title":"J Proteome Res"},{"key":"B116","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/s41392-022-01156-y","article-title":"Multiomics approach reveals the ubiquitination-specific processes hijacked by SARS-CoV-2","volume":"7","author":"Xu","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"B117","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1603435113","article-title":"p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1","volume":"113","author":"Ma-Lauer","year":"2016","journal-title":"Proc Natl Acad Sci United States Am"},{"key":"B118","doi-asserted-by":"publisher","first-page":"4967","DOI":"10.1038\/s41467-018-07179-w","article-title":"Orchestration of protein acetylation as a toggle for cellular defense and virus replication","volume":"9","author":"Murray","year":"2018","journal-title":"Nat Commun"},{"key":"B119","doi-asserted-by":"publisher","first-page":"e0051023","DOI":"10.1128\/msystems.00510-23","article-title":"Sirtuin 2 promotes human cytomegalovirus replication by regulating cell cycle progression","volume":"8","author":"Betsinger","year":"2023","journal-title":"mSystems"},{"key":"B120","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.C113.511261","article-title":"Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins","volume":"288","author":"Feldman","year":"2013","journal-title":"J Biol Chem"},{"key":"B121","doi-asserted-by":"publisher","DOI":"10.1007\/s11262-024-02104-4","article-title":"Effect of HDAC9-induced deacetylation of glycolysis-related GAPDH lysine 219 on rotavirus replication in rotavirus-infected Caco-2 cells","volume":"60","author":"Song","year":"2024","journal-title":"Virus Genes"},{"key":"B122","doi-asserted-by":"publisher","first-page":"e313","DOI":"10.1002\/ctm2.v11.3","article-title":"Quantitative acetylome analysis reveals histone modifications that may predict prognosis in hepatitis B-related hepatocellular carcinoma","volume":"11","author":"Chai","year":"2021","journal-title":"Clin Transl Med"},{"key":"B123","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03493-4","article-title":"Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV","volume":"594","author":"Stukalov","year":"2021","journal-title":"Nature"},{"key":"B124","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.3390\/v13071415","article-title":"Acetylation, methylation and allysine modification profile of viral and host proteins during influenza A virus infection","volume":"13","author":"Ahmed","year":"2021","journal-title":"Viruses"},{"key":"B125","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1341599","article-title":"Role of protein Post-translational modifications in enterovirus infection","volume":"15","author":"Zhao","year":"2024","journal-title":"Front Microbiol"},{"key":"B126","doi-asserted-by":"publisher","first-page":"323","DOI":"10.3390\/ijms22010323","article-title":"Role of host-mediated post-translational modifications (PTMs) in RNA virus pathogenesis","volume":"22","author":"Kumar","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"B127","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00305-20","article-title":"Nonproteolytic K29-linked ubiquitination of the PB2 replication protein of influenza A viruses by proviral cullin 4-based E3 ligases","volume":"11","author":"Karim","year":"2020","journal-title":"mBio"},{"key":"B128","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01473-06","article-title":"Kaposi\u2019s sarcoma-associated herpesvirus-encoded protein kinase and its interaction with K-bZIP","volume":"81","author":"Izumiya","year":"2007","journal-title":"J Virol"},{"key":"B129","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(19)88697-0","article-title":"MAK3 encodes an N-acetyltransferase whose modification of the L-A gag NH2 terminus is necessary for virus particle assembly","volume":"267","author":"Tercero","year":"1992","journal-title":"J\u00a0Biol Chem"},{"key":"B130","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01369-10","article-title":"Viral serine\/threonine protein kinases","volume":"85","author":"Jacob","year":"","journal-title":"J Virol"},{"key":"B131","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M805747200","article-title":"Glycogen synthase kinase-3 regulates the phosphorylation of severe acute respiratory syndrome coronavirus nucleocapsid protein and viral replication","volume":"284","author":"Wu","year":"2009","journal-title":"J. Biol. Chem."},{"key":"B132","doi-asserted-by":"publisher","first-page":"e2113401118","DOI":"10.1073\/pnas.2113401118","article-title":"Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition","volume":"118","author":"Liu","year":"2021","journal-title":"Proc Natl Acad Sci USA."},{"key":"B133","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.09.009","article-title":"Nucleocapsid phosphorylation and RNA helicase DDX1 recruitment enables coronavirus transition from discontinuous to continuous transcription","volume":"16","author":"Wu","year":"2014","journal-title":"Cell Host Microbe"},{"key":"B134","doi-asserted-by":"publisher","first-page":"e0000222","DOI":"10.1128\/jvi.00002-22","article-title":"Host cellular RNA helicases regulate SARS-coV-2 infection","volume":"96","author":"Ariumi","year":"2022","journal-title":"J Virol"},{"key":"B135","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02369-20","article-title":"Phosphorylation of influenza A virus NS1 at serine 205 mediates its viral polymerase-enhancing function","volume":"95","author":"Patil","year":"2021","journal-title":"J Virol"},{"key":"B136","doi-asserted-by":"publisher","first-page":"2275606","DOI":"10.1080\/22221751.2023.2275606","article-title":"PLK3 facilitates replication of swine influenza virus by phosphorylating viral NP protein","volume":"12","author":"Ren","year":"2023","journal-title":"Emerg Microbes Infect"},{"key":"B137","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.1065211","article-title":"Viruses utilize ubiquitination systems to escape TLR\/RLR-mediated innate immunity","volume":"13","author":"Huang","year":"2022","journal-title":"Front Immunol"},{"key":"B138","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/s41467-023-36389-0","article-title":"The ubiquitination landscape of the influenza A virus polymerase","volume":"14","author":"G\u00fcnl","year":"2023","journal-title":"Nat Commun"},{"key":"B139","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/s41392-021-00509-3","article-title":"SARS-CoV-2 non-structural protein 13 (nsp13) hijacks host deubiquitinase USP13 and counteracts host antiviral immune response","volume":"6","author":"Guo","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"B140","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.02194-20","article-title":"The FAT10 post-translational modification is involved in the lytic replication of Kaposi\u2019s sarcoma-associated herpesvirus","volume":"95","author":"Sugimoto","year":"2021","journal-title":"J Virol"},{"key":"B141","doi-asserted-by":"publisher","first-page":"100881","DOI":"10.1016\/j.mcpro.2024.100881","article-title":"Integrative multi-PTM proteomics reveals dynamic global, redox, phosphorylation, and acetylation regulation in cytokine-treated pancreatic beta cells","volume":"23","author":"Gluth","year":"2024","journal-title":"Mol Cell Proteomics"},{"key":"B142","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1038\/s41467-023-37547-0","article-title":"Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues","volume":"14","author":"Abelin","year":"2023","journal-title":"Nat Commun"},{"key":"B143","doi-asserted-by":"publisher","first-page":"7246","DOI":"10.1038\/s41467-022-34919-w","article-title":"Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry","volume":"13","author":"Orsburn","year":"2022","journal-title":"Nat Commun"},{"key":"B144","doi-asserted-by":"publisher","DOI":"10.1038\/s41423-021-00754-0","article-title":"Multiomics: unraveling the\u00a0panoramic landscapes of SARS-CoV-2 infection","volume":"18","author":"Wang","year":"2021","journal-title":"Cell Mol Immunol"},{"key":"B145","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1038\/s41597-024-03124-3","article-title":"A compendium of multi-omics data illuminating host responses to lethal human virus infections","volume":"11","author":"Eisfeld","year":"2024","journal-title":"Sci Data"},{"key":"B146","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1186\/s13059-017-1215-1","article-title":"Multi-omics approaches to disease","volume":"18","author":"Hasin","year":"2017","journal-title":"Genome Biol"},{"key":"B147","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac376","article-title":"OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics","volume":"50","author":"Zhou","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"B148","doi-asserted-by":"publisher","DOI":"10.1038\/s41416-024-02706-7","article-title":"Graph machine learning for integrated multi-omics analysis","volume":"131","author":"Valous","year":"2024","journal-title":"Br J Cancer"},{"key":"B149","doi-asserted-by":"publisher","first-page":"vbae151","DOI":"10.1093\/bioadv\/vbae151","article-title":"mosGraphGen: a novel tool to generate multi-omics signaling graphs to facilitate integrative and interpretable graph AI model development","volume":"4","author":"Zhang","year":"2024","journal-title":"Bioinform Adv"},{"key":"B150","doi-asserted-by":"publisher","first-page":"e202300712","DOI":"10.1002\/cbic.202300712","article-title":"TAC-tics for leveraging proximity biology in drug discovery","volume":"25","author":"Nalawansha","year":"2024","journal-title":"Chembiochem"},{"key":"B151","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-022-01149-6","article-title":"Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection","volume":"19","author":"Oh","year":"2023","journal-title":"Nat Chem Biol"},{"key":"B152","doi-asserted-by":"publisher","first-page":"e2120419119","DOI":"10.1073\/pnas.2120419119","article-title":"Thiol-based chemical probes exhibit antiviral activity against SARS-CoV-2 via allosteric disulfide disruption in the spike glycoprotein","volume":"119","author":"Shi","year":"2022","journal-title":"Proc Natl Acad Sci United States America"},{"key":"B153","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a033910","article-title":"Redox-mediated regulatory mechanisms of endoplasmic reticulum homeostasis","volume":"11","author":"Ushioda","year":"2019","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"B154","doi-asserted-by":"publisher","first-page":"e158978","DOI":"10.1172\/JCI158978","article-title":"An allosteric inhibitor of sirtuin 2 deacetylase activity exhibits broad-spectrum antiviral activity","volume":"133","author":"Roche","year":"2023","journal-title":"J Clin Invest"},{"key":"B155","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1038\/s43856-025-00863-1","article-title":"Targeted protein degraders of SARS-CoV-2 Mpro are more active than enzymatic inhibition alone with activity against nirmatrelvir resistant virus","volume":"5","author":"Pan","year":"2025","journal-title":"Commun Med (Lond)"},{"key":"B156","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1415449","article-title":"Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes","volume":"15","author":"Pastor","year":"2024","journal-title":"Front Microbiol"},{"key":"B157","doi-asserted-by":"publisher","DOI":"10.1007\/s12250-019-00131-2","article-title":"Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection","volume":"34","author":"Miao","year":"2019","journal-title":"Virol Sin"},{"key":"B158","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1717944115","article-title":"Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories","volume":"115","author":"Criglar","year":"2018","journal-title":"Proc Natl Acad Sci United States Am"},{"key":"B159","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00972-20","article-title":"A genetically engineered rotavirus NSP2 phosphorylation mutant impaired in viroplasm formation and replication shows an early interaction between vNSP2 and cellular lipid droplets","volume":"94","author":"Criglar","year":"2020","journal-title":"J\u00a0Virol"},{"key":"B160","doi-asserted-by":"publisher","DOI":"10.7150\/thno.50992","article-title":"Virus-induced p38 MAPK activation facilitates viral infection","volume":"10","author":"Cheng","year":"2020","journal-title":"Theranostics"},{"key":"B161","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/s41467-023-35874-w","article-title":"Master mitotic kinases regulate viral genome delivery during papillomavirus cell entry","volume":"14","author":"Rizzato","year":"2023","journal-title":"Nat Commun"},{"key":"B162","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02565-19","article-title":"Serine-arginine protein kinase 1 regulates ebola virus transcription","volume":"11","author":"Takamatsu","year":"2020","journal-title":"mBio"},{"key":"B163","doi-asserted-by":"publisher","first-page":"e0112523","DOI":"10.1128\/jvi.01125-23","article-title":"Protein kinase Cdc7 supports viral replication by phosphorylating Avibirnavirus VP3 protein","volume":"97","author":"Deng","year":"2023","journal-title":"J Virol"}],"updated-by":[{"DOI":"10.3389\/fimmu.2025.1672766","type":"corrigendum","label":"Corrigendum","source":"publisher","updated":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T00:00:00Z","timestamp":1754956800000}}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1587106\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T13:16:44Z","timestamp":1755004604000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1587106\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,30]]},"references-count":163,"alternative-id":["10.3389\/fimmu.2025.1587106"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2025.1587106","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,30]]},"article-number":"1587106"}}