{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T23:11:29Z","timestamp":1788390689244,"version":"build-2803163510"},"reference-count":217,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T00:00:00Z","timestamp":1747785600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Positive sense single strand RNA (+ssRNA) viruses are one of the evolutionary successful organisms and many of them pose a significant threat to human health. Diseases caused by +ssRNA viruses such as COVID-19, Flu and acute viral hepatitis are major public health concern worldwide. Therefore, a lot of research is focused at decoding the life cycle of +ssRNA viruses and develop specific antiviral therapeutics against them. Interaction of the viral RNA with virus-encoded proteins and host proteins drives the lifecycle and pathogenesis of +ssRNA viruses. Recent developments in computational and high-throughput omics-based experimental technologies offer the sensitivity and specificity for molecular characterization of these RNA-protein complexes. These are promising tools to revolutionize the field of +ssRNA virus research and pave the way for antiviral discovery. This review summarizes the current scientific resources available to characterize the RNA-protein interactome of +ssRNA viruses and provides an overview of the drug discovery pipeline for developing antivirals against pathogenic +ssRNA viruses.<\/jats:p>","DOI":"10.3389\/fcimb.2025.1580337","type":"journal-article","created":{"date-parts":[[2025,6,13]],"date-time":"2025-06-13T16:57:44Z","timestamp":1749833864000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Emerging RNA-centric technologies to probe RNA-protein interactions: importance in decoding the life cycle of positive sense single strand RNA viruses and antiviral discovery"],"prefix":"10.3389","volume":"15","author":[{"given":"Sreemoyee","family":"Ghosh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shivam","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohit","family":"Verma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shabnam","family":"Ansari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samrat","family":"Chatterjee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milan","family":"Surjit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,5,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1006\/viro.2000.0819","article-title":"The 3\u2032 end of hepatitis E virus (HEV) genome binds specifically to the viral RNA-dependent RNA polymerase (RdRp)","volume":"282","author":"Agrawal","year":"2001","journal-title":"Virology"},{"key":"B2","doi-asserted-by":"publisher","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"Aleksander","year":"2023","journal-title":"Genetics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"7854","DOI":"10.1128\/JVI.75.17.7854-7863.2001","article-title":"Activity of the hepatitis A virus IRES requires association between the cap-binding translation initiation factor (eIF4E) and eIF4G","volume":"75","author":"Ali","year":"2001","journal-title":"J. Virol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1128\/JVI.00584-06","article-title":"Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains","volume":"81","author":"Al-Sunaidi","year":"2007","journal-title":"J. Virol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"17021","DOI":"10.1074\/jbc.M109.006239","article-title":"The polypyrimidine tract-binding protein is required for efficient dengue virus propagation and associates with the viral replication machinery","volume":"284","author":"Anwar","year":"2009","journal-title":"J. Biol. Chem."},{"key":"B6","doi-asserted-by":"publisher","first-page":"3104","DOI":"10.1093\/bioinformatics\/btx361","article-title":"omiXcore: a web server for prediction of protein interactions with large RNA","volume":"33","author":"Armaos","year":"2017","journal-title":"Bioinformatics"},{"key":"B7","article-title":"RxList - The Internet Drug Index for prescription drug information, interactions, and side effects","volume-title":"RxList","year":""},{"key":"B8","doi-asserted-by":"publisher","first-page":"D1276","DOI":"10.1093\/nar\/gkac1085","article-title":"DrugCentral 2023 extends human clinical data and integrates veterinary drugs","volume":"51","author":"Avram","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1093\/emboj\/20.6.1439","article-title":"5\u2032 cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis","volume":"20","author":"Barton","year":"2001","journal-title":"EMBO J"},{"key":"B10","doi-asserted-by":"publisher","first-page":"D1549","DOI":"10.1093\/nar\/gkac971","article-title":"RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins","volume":"51","author":"Benoit Bouvrette","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B11","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1007\/s00018-022-04646-y","article-title":"The endocytic recycling compartment serves as a viral factory for hepatitis E virus","volume":"79","author":"Bentaleb","year":"2022","journal-title":"Cell. Mol. Life Sci."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006295","article-title":"Correction: G3BP1, G3BP2 and CAPRIN1 are required for translation of interferon stimulated mRNAs and are targeted by a dengue virus non-coding RNA","volume":"13","author":"Bidet","year":"2017","journal-title":"PloS Pathog."},{"key":"B13","doi-asserted-by":"publisher","first-page":"11115","DOI":"10.1073\/pnas.93.20.11115","article-title":"Poly (rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5'noncoding region: identification by automated liquid chromatography-tandem mass spectrometry","volume":"93","author":"Blyn","year":"1996","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B14","doi-asserted-by":"publisher","first-page":"7952","DOI":"10.1021\/acs.chemrev.1c00356","article-title":"Integration of mass spectrometry data for structural biology","volume":"122","author":"Britt","year":"2021","journal-title":"Chem. Rev."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1128\/jvi.68.2.1066-1074.1994","article-title":"In vitro characterization of an internal ribosomal entry site (IRES) present within the 5'nontranslated region of hepatitis A virus RNA: comparison with the IRES of encephalomyocarditis virus","volume":"68","author":"Brown","year":"1994","journal-title":"J. Virol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"3254","DOI":"10.1128\/JVI.79.6.3254-3266.2005","article-title":"Functional interaction of heterogeneous nuclear ribonucleoprotein C with poliovirus RNA synthesis initiation complexes","volume":"79","author":"Brunner","year":"2005","journal-title":"J. Virol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"D425","DOI":"10.1093\/nar\/gkaa1040","article-title":"RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions","volume":"49","author":"Caudron-Herger","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.virol.2012.09.041","article-title":"P-body components LSM1, GW182, DDX3, DDX6 and XRN1 are recruited to WNV replication sites and positively regulate viral replication","volume":"436","author":"Chahar","year":"2013","journal-title":"Virology"},{"key":"B19","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/nrmicro.2016.45","article-title":"Viral evasion of intracellular DNA and RNA sensing","volume":"14","author":"Chan","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"5907","DOI":"10.1128\/JVI.03404-13","article-title":"Dengue virus-and hepatitis C virus-induced replication and assembly compartments: the enemy inside\u2014caught in the web","volume":"88","author":"Chatel-Chaix","year":"2014","journal-title":"J. Virol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1007\/s13238-014-0026-3","article-title":"SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3-TBK1 complex","volume":"5","author":"Chen","year":"2014","journal-title":"Protein Cell"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1705","DOI":"10.1111\/j.1462-5822.2007.00904.x","article-title":"Specific interaction of HeLa cell proteins with coxsackievirus B3 3\u2032 UTR: La autoantigen binds the 3\u2032 and 5\u2032 UTR independently of the poly (A) tail","volume":"9","author":"Cheung","year":"2007","journal-title":"Cell. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1752-0509-8-S4-S11","article-title":"cytoHubba: identifying hub objects and sub-networks from complex interactome","volume":"8","author":"Chin","year":"2014","journal-title":"BMC Syst. Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"12143","DOI":"10.1073\/pnas.1919528117","article-title":"Split-TurboID enables contact-dependent proximity labeling in cells","volume":"117","author":"Cho","year":"2020","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.2147\/JIR.S295706","article-title":"Activation and inhibition of the NLRP3 inflammasome by RNA viruses","volume":"14","author":"Choudhury","year":"2021","journal-title":"J. Inflammation Res."},{"key":"B26","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.cell.2015.03.025","article-title":"Systematic discovery of Xist RNA binding proteins","volume":"161","author":"Chu","year":"2015","journal-title":"Cell"},{"key":"B27","doi-asserted-by":"publisher","first-page":"D301","DOI":"10.1093\/nar\/gkq1069","article-title":"RBPDB: a database of RNA-binding specificities","volume":"39","author":"Cook","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1568","DOI":"10.1261\/rna.1031408","article-title":"The cis-acting replication elements define human enterovirus and rhinovirus species","volume":"14","author":"Cordey","year":"2008","journal-title":"Rna"},{"key":"B29","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.molcel.2020.03.011","article-title":"How RNA-binding proteins interact with RNA: molecules and mechanisms","volume":"78","author":"Corley","year":"2020","journal-title":"Mol. Cell"},{"key":"B30","doi-asserted-by":"publisher","first-page":"9068","DOI":"10.1093\/nar\/gkx519","article-title":"Polypyrimidine tract-binding protein (PTB) and PTB-associated splicing factor in CVB3 infection: an ITAF for an ITAF","volume":"45","author":"Dave","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B31","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkm791","article-title":"ChEBI: a database and ontology for chemical entities of biological interest","volume":"36","author":"Degtyarenko","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"12803","DOI":"10.1128\/JVI.01467-07","article-title":"Degradation of nuclear factor kappa B during foot-and-mouth disease virus infection","volume":"81","author":"de Los Santos","year":"2007","journal-title":"J. Virol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1002\/feb2.2017.591.issue-2","article-title":"Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions","volume":"591","author":"De Munter","year":"2017","journal-title":"FEBS Lett."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-020-07239-w","article-title":"Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure","volume":"21","author":"Deng","year":"2020","journal-title":"BMC Genomics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12985-020-01329-7","article-title":"Role of RNA-binding proteins during the late stages of Flavivirus replication cycle","volume":"17","author":"Diosa-Toro","year":"2020","journal-title":"Virol. J."},{"key":"B36","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/nrm760","article-title":"Messenger-RNA-binding proteins and the messages they carry","volume":"3","author":"Dreyfuss","year":"2002","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"4908","DOI":"10.1128\/JVI.03668-13","article-title":"3Cpro of foot-and-mouth disease virus antagonizes the interferon signaling pathway by blocking STAT1\/STAT2 nuclear translocation","volume":"88","author":"Du","year":"2014","journal-title":"J. Virol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"4250","DOI":"10.1080\/07391102.2020.1854861","article-title":"DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site","volume":"40","author":"Du","year":"2022","journal-title":"J. Biomolecular Structure Dynamics"},{"key":"B39","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1038\/346818a0","article-title":"In vitro selection of RNA molecules that bind specific ligands","volume":"346","author":"Ellington","year":"1990","journal-title":"nature"},{"key":"B40","doi-asserted-by":"publisher","first-page":"4229","DOI":"10.1128\/JVI.02198-09","article-title":"Mechanistic consequences of hnRNP C binding to both RNA termini of poliovirus negative-strand RNA intermediates","volume":"84","author":"Ertel","year":"2010","journal-title":"J. Virol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"2394","DOI":"10.1016\/j.cell.2021.03.012","article-title":"Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions","volume":"184","author":"Flynn","year":"2021","journal-title":"Cell"},{"key":"B42","doi-asserted-by":"publisher","first-page":"6689","DOI":"10.1128\/JVI.02220-08","article-title":"Severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of IRF3 and NF-\u03baB signaling","volume":"83","author":"Frieman","year":"2009","journal-title":"J. Virol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"167515","DOI":"10.1016\/j.jmb.2022.167515","article-title":"RBPBind: quantitative prediction of protein-RNA interactions","volume":"434","author":"Gaither","year":"2022","journal-title":"J. Mol. Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"2219","DOI":"10.1128\/JVI.74.5.2219-2226.2000","article-title":"Interactions of viral protein 3CD and poly (rC) binding protein with the 5\u2032 untranslated region of the poliovirus genome","volume":"74","author":"Gamarnik","year":"2000","journal-title":"J. Virol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"10979","DOI":"10.1128\/JVI.75.22.10979-10990.2001","article-title":"Biochemical and genetic studies of the initiation of human rhinovirus 2 RNA replication: identification of a cis-replicating element in the coding sequence of 2Apro","volume":"75","author":"Gerber","year":"2001","journal-title":"J. Virol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1038\/nrg3813","article-title":"A census of human RNA-binding proteins","volume":"15","author":"Gerstberger","year":"2014","journal-title":"Nat. Rev. Genet."},{"key":"B47","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1101\/gr.247494.118","article-title":"Deep neural networks for interpreting RNA-binding protein target preferences","volume":"30","author":"Ghanbari","year":"2020","journal-title":"Genome Res."},{"key":"B48","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1080\/1062936X.2019.1650827","article-title":"Could deep learning in neural networks improve the QSAR models","volume":"30","author":"Gini","year":"2019","journal-title":"SAR QSAR Environ. Res."},{"key":"B49","doi-asserted-by":"publisher","first-page":"4590","DOI":"10.1128\/JVI.74.10.4590-4600.2000","article-title":"Identification of a cis-acting replication element within the poliovirus coding region","volume":"74","author":"Goodfellow","year":"2000","journal-title":"J. Virol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"5317","DOI":"10.1038\/s41467-019-13235-w","article-title":"In-cell identification and measurement of RNA-protein interactions","volume":"10","author":"Graindorge","year":"2019","journal-title":"Nat. Commun."},{"key":"B51","doi-asserted-by":"publisher","first-page":"7099","DOI":"10.1093\/nar\/gkaa530","article-title":"DeepCLIP: predicting the effect of mutations on protein\u2013RNA binding with deep learning","volume":"48","author":"Gr\u00f8nning","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B52","doi-asserted-by":"publisher","first-page":"8094","DOI":"10.1073\/pnas.1921485117","article-title":"Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors","volume":"117","author":"Hackbart","year":"2020","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B53","doi-asserted-by":"publisher","first-page":"5561","DOI":"10.1128\/JVI.01857-06","article-title":"A phylogenetically conserved RNA structure in the poliovirus open reading frame inhibits the antiviral endoribonuclease RNase L","volume":"81","author":"Han","year":"2007","journal-title":"J. Virol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"22068","DOI":"10.1073\/pnas.2006617117","article-title":"RNA\u2013protein interaction mapping via MS2-or Cas13-based APEX targeting","volume":"117","author":"Han","year":"2020","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B55","doi-asserted-by":"publisher","first-page":"2921","DOI":"10.1111\/j.1462-5822.2007.01006.x","article-title":"The mengovirus leader protein blocks interferon-\u03b1\/\u03b2 gene transcription and inhibits activation of interferon regulatory factor 3","volume":"9","author":"Hato","year":"2007","journal-title":"Cell. Microbiol."},{"key":"B56","doi-asserted-by":"publisher","first-page":"lqad010","DOI":"10.1093\/nargab\/lqad010","article-title":"A computational map of the human-SARS-CoV-2 protein\u2013RNA interactome predicted at single-nucleotide resolution","volume":"5","author":"Horlacher","year":"2023","journal-title":"NAR Genomics Bioinf."},{"key":"B57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-017-2338-4","article-title":"Determination of the cell permissiveness spectrum, mode of RNA replication, and RNA-protein interaction of Zika virus","volume":"17","author":"Hou","year":"2017","journal-title":"BMC Infect. Dis."},{"key":"B58","doi-asserted-by":"publisher","first-page":"5009","DOI":"10.1128\/JVI.75.11.5009-5017.2001","article-title":"Heterogeneous nuclear ribonucleoprotein a1 binds to the 3\u2032-untranslated region and mediates potential 5\u2032-3\u2032-end cross talks of mouse hepatitis virus RNA","volume":"75","author":"Huang","year":"2001","journal-title":"J. Virol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"2051","DOI":"10.1042\/BCJ20161037","article-title":"Encephalomyocarditis virus 3C protease attenuates type I interferon production through disrupting the TANK\u2013TBK1\u2013IKK\u03f5\u2013IRF3 complex","volume":"474","author":"Huang","year":"2017","journal-title":"Biochem. J."},{"key":"B60","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.1016\/j.molcel.2023.06.019","article-title":"HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence","volume":"83","author":"Jin","year":"2023","journal-title":"Mol. Cell"},{"key":"B61","doi-asserted-by":"publisher","first-page":"2851","DOI":"10.1016\/j.molcel.2021.05.023","article-title":"Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection","volume":"81","author":"Kamel","year":"2021","journal-title":"Mol. Cell"},{"key":"B62","doi-asserted-by":"publisher","first-page":"2021","DOI":"10.1101\/2021.10.06.463336","article-title":"Compositional analysis of Sindbis virus ribonucleoproteins reveals an extensive co-opting of key nuclear RNA-binding proteins","author":"Kamel","year":"2021","journal-title":"BioRxiv"},{"key":"B63","doi-asserted-by":"publisher","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B64","first-page":"1","article-title":"BCB: Bioinformatics, Computational Biology and Biomedicine","author":"Karin","year":"2021"},{"key":"B65","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1016\/j.cell.2018.09.043","article-title":"Identification, characterization, and heritability of murine metastable epialleles: implications for non-genetic inheritance","volume":"175","author":"Kazachenka","year":"2018","journal-title":"Cell"},{"key":"B66","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.virol.2020.12.010","article-title":"Programmed\u2013 1 ribosomal frameshifting in coronaviruses: a therapeutic target","volume":"554","author":"Kelly","year":"2021","journal-title":"Virology"},{"key":"B67","doi-asserted-by":"publisher","first-page":"5538","DOI":"10.1128\/JVI.00737-15","article-title":"Commandeering the ribosome: Lessons learned from dicistroviruses about translation","volume":"90","author":"Kerr","year":"2016","journal-title":"J. Virol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1002\/wrna.2015.6.issue-2","article-title":"Understanding the potential of hepatitis C virus internal ribosome entry site domains to modulate translation initiation via their structure and function","volume":"6","author":"Khawaja","year":"2015","journal-title":"Wiley Interdiscip. Reviews: RNA"},{"key":"B69","doi-asserted-by":"publisher","first-page":"6719","DOI":"10.1128\/JVI.75.14.6719-6728.2001","article-title":"Essential role of cyclization sequences in flavivirus RNA replication","volume":"75","author":"Khromykh","year":"2001","journal-title":"J. Virol."},{"key":"B70","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1016\/j.molcel.2020.04.013","article-title":"Discovery of widespread host protein interactions with the pre-replicated genome of CHIKV using VIR-CLASP","volume":"78","author":"Kim","year":"2020","journal-title":"Mol. Cell"},{"key":"B71","doi-asserted-by":"publisher","first-page":"D1373","DOI":"10.1093\/nar\/gkac956","article-title":"PubChem 2023 update","volume":"51","author":"Kim","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B72","doi-asserted-by":"publisher","first-page":"13123","DOI":"10.1074\/jbc.RA120.014260","article-title":"N6-Methyladenosine modification of hepatitis B and C viral RNAs attenuates host innate immunity via RIG-I signaling","volume":"295","author":"Kim","year":"2020","journal-title":"J. Biol. Chem."},{"key":"B73","doi-asserted-by":"publisher","first-page":"D1265","DOI":"10.1093\/nar\/gkad976","article-title":"DrugBank 6.0: the drugBank knowledgebase for 2024","volume":"52","author":"Knox","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B74","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1007\/978-1-0716-2768-6_12","article-title":"ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks","volume-title":"RNA Structure Prediction","author":"Koo","year":"2023"},{"key":"B75","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/nature11661","article-title":"Control of somatic tissue differentiation by the long non-coding RNA TINCR","volume":"493","author":"Kretz","year":"2013","journal-title":"Nature"},{"key":"B76","doi-asserted-by":"publisher","first-page":"btac815","DOI":"10.1093\/bioinformatics\/btac815","article-title":"konnect2prot: a web application to explore the protein properties in a functional protein\u2013protein interaction network","volume":"39","author":"Kumar","year":"2023","journal-title":"Bioinformatics"},{"key":"B77","doi-asserted-by":"publisher","first-page":"e02827","DOI":"10.1128\/spectrum.02827-22","article-title":"RNA-protein interactome at the Hepatitis E virus internal ribosome entry site","volume":"11","author":"Kumar","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"B78","doi-asserted-by":"publisher","first-page":"W171","DOI":"10.1093\/nar\/gkz365","article-title":"CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing","volume":"47","author":"Labun","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B79","doi-asserted-by":"publisher","first-page":"D601","DOI":"10.1093\/nar\/gky967","article-title":"RNAct: Protein\u2013RNA interaction predictions for model organisms with supporting experimental data","volume":"47","author":"Lang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B80","doi-asserted-by":"publisher","first-page":"11356","DOI":"10.1128\/JVI.02677-08","article-title":"Identification of RNA helicase A as a new host factor in the replication cycle of foot-and-mouth disease virus","volume":"83","author":"Lawrence","year":"2009","journal-title":"J. Virol."},{"key":"B81","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1016\/j.tim.2017.01.010","article-title":"Regulation mechanisms of viral IRES-driven translation","volume":"25","author":"Lee","year":"2017","journal-title":"Trends Microbiol."},{"key":"B82","doi-asserted-by":"publisher","first-page":"e48","DOI":"10.1093\/nar\/gkae334","article-title":"Massively parallel dissection of RNA in RNA\u2013protein interactions in vivo","volume":"52","author":"Lee","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B83","doi-asserted-by":"publisher","first-page":"5416","DOI":"10.1073\/pnas.1302807110","article-title":"RNA\u2013protein analysis using a conditional CRISPR nuclease","volume":"110","author":"Lee","year":"2013","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B84","doi-asserted-by":"publisher","first-page":"3190","DOI":"10.1002\/feb2.2017.591.issue-20","article-title":"RNA-virus proteases counteracting host innate immunity","volume":"591","author":"Lei","year":"2017","journal-title":"FEBS Lett."},{"key":"B85","doi-asserted-by":"publisher","first-page":"8051","DOI":"10.1128\/JVI.02491-09","article-title":"The 3C protein of enterovirus 71 inhibits retinoid acid-inducible gene I-mediated interferon regulatory factor 3 activation and type I interferon responses","volume":"84","author":"Lei","year":"2010","journal-title":"J. Virol."},{"key":"B86","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.4161\/rna.25107","article-title":"High-affinity interaction of hnRNP A1 with conserved RNA structural elements is required for translation and replication of enterovirus 71","volume":"10","author":"Levengood","year":"2013","journal-title":"RNA Biol."},{"key":"B87","doi-asserted-by":"publisher","first-page":"D277","DOI":"10.1093\/nar\/gkq1108","article-title":"PRIDB: a protein\u2013RNA interface database","volume":"39","author":"Lewis","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B88","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1128\/JVI.73.1.772-777.1999","article-title":"Polypyrimidine tract-binding protein binds to the leader RNA of mouse hepatitis virus and serves as a regulator of viral transcription","volume":"73","author":"Li","year":"1999","journal-title":"J. Virol."},{"key":"B89","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.celrep.2021.109091","article-title":"METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection","volume":"35","author":"Li","year":"2021","journal-title":"Cell Rep."},{"key":"B90","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.1080\/15476286.2021.1873620","article-title":"CBRPP: a new RNA-centric method to study RNA\u2013protein interactions","volume":"18","author":"Li","year":"2021","journal-title":"RNA Biol."},{"key":"B91","doi-asserted-by":"publisher","first-page":"2020","DOI":"10.1101\/2020.02.28.970442","article-title":"In vivo discovery of RNA proximal proteins in human cells via proximity-dependent biotinylation","author":"Lin","year":"2020","journal-title":"BioRxiv"},{"key":"B92","doi-asserted-by":"publisher","first-page":"2540","DOI":"10.1099\/vir.0.2008\/003673-0","article-title":"Heterogeneous nuclear ribonuclear protein K interacts with the enterovirus 71 5\u2032 untranslated region and participates in virus replication","volume":"89","author":"Lin","year":"2008","journal-title":"J. Gen. Virol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.1099\/jgv.0.000443","article-title":"Coxsackievirus counters the host innate immune response by blocking type III interferon expression","volume":"97","author":"Lind","year":"2016","journal-title":"J. Gen. Virol."},{"key":"B94","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009863","article-title":"Inferring RNA-binding protein target preferences using adversarial domain adaptation","volume":"18","author":"Liu","year":"2022","journal-title":"PloS Comput. Biol."},{"key":"B95","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1261\/rna.261807","article-title":"A U-turn motif-containing stem\u2013loop in the coronavirus 5\u2032 untranslated region plays a functional role in replication","volume":"13","author":"Liu","year":"2007","journal-title":"Rna"},{"key":"B96","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00453","article-title":"Structures and functions of the 3\u2032 untranslated regions of positive-sense single-stranded RNA viruses infecting humans and animals","volume":"10","author":"Liu","year":"2020","journal-title":"Front. Cell. infection Microbiol."},{"key":"B97","doi-asserted-by":"publisher","first-page":"1834","DOI":"10.1007\/s12010-015-1680-5","article-title":"Identification of lncRNA MEG3 binding protein using MS2-tagged RNA affinity purification and mass spectrometry","volume":"176","author":"Liu","year":"2015","journal-title":"Appl. Biochem. Biotechnol."},{"key":"B98","doi-asserted-by":"publisher","first-page":"3222","DOI":"10.1111\/febs.v286.16","article-title":"Interaction of coronavirus nucleocapsid protein with the 5\u2032-and 3\u2032-ends of the coronavirus genome is involved in genome circularization and negative-strand RNA synthesis","volume":"286","author":"Lo","year":"2019","journal-title":"FEBS J."},{"key":"B99","doi-asserted-by":"publisher","first-page":"11560","DOI":"10.1073\/pnas.96.20.11560","article-title":"A coding RNA sequence acts as a replication signal in cardioviruses","volume":"96","author":"Lobert","year":"1999","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B100","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1038\/nrm2178","article-title":"RNA-binding proteins: modular design for efficient function","volume":"8","author":"Lunde","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"B101","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003721","article-title":"DDX24 negatively regulates cytosolic RNA-mediated innate immune signaling","volume":"9","author":"Ma","year":"2013","journal-title":"PloS Pathog."},{"key":"B102","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.coviro.2015.02.005","article-title":"Mechanisms of innate immune evasion in re-emerging RNA viruses","volume":"12","author":"Ma","year":"2015","journal-title":"Curr. Opin. Virol."},{"key":"B103","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/bs.aivir.2016.08.007","article-title":"Coronavirus cis-acting RNA elements","volume":"96","author":"Madhugiri","year":"2016","journal-title":"Adv. Virus Res."},{"key":"B104","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2022.970494","article-title":"Optimal COVID-19 therapeutic candidate discovery using the CANDO platform","volume":"13","author":"Mangione","year":"2022","journal-title":"Front. Pharmacol."},{"key":"B105","doi-asserted-by":"publisher","first-page":"pdb","DOI":"10.1101\/pdb.prot072934","article-title":"SELEX to identify protein-binding sites on RNA","volume":"2013","author":"Manley","year":"2013","journal-title":"Cold Spring Harbor Protoc."},{"key":"B106","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1126\/science.aab3369","article-title":"Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness","volume":"350","author":"Manokaran","year":"2015","journal-title":"Science"},{"key":"B107","doi-asserted-by":"publisher","first-page":"9686","DOI":"10.1128\/JVI.76.19.9686-9694.2002","article-title":"Identification and characterization of a cis-acting replication element (cre) adjacent to the internal ribosome entry site of foot-and-mouth disease virus","volume":"76","author":"Mason","year":"2002","journal-title":"J. Virol."},{"key":"B108","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.ymeth.2016.10.005","article-title":"A versatile tandem RNA isolation procedure to capture in vivo formed mRNA-protein complexes","volume":"118","author":"Matia-Gonz\u00e1lez","year":"2017","journal-title":"Methods"},{"key":"B109","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2014-15-1-r17","article-title":"GraphProt: modeling binding preferences of RNA-binding proteins","volume":"15","author":"Maticzka","year":"2014","journal-title":"Genome Biol."},{"key":"B110","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1038\/nature14443","article-title":"The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3","volume":"521","author":"McHugh","year":"2015","journal-title":"Nature"},{"key":"B111","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1017\/S1355838298981006","article-title":"The rhinovirus type 14 genome contains an internally located RNA structure that is required for viral replication","volume":"4","author":"Mcknight","year":"1998","journal-title":"Rna"},{"key":"B112","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1080\/15476286.2020.1814556","article-title":"Secondary structure of the SARS-coV-2 5\u2019-UTR","volume":"18","author":"Miao","year":"2021","journal-title":"RNA Biol."},{"key":"B113","doi-asserted-by":"publisher","first-page":"D672","DOI":"10.1093\/nar\/gkad1025","article-title":"The reactome pathway knowledgebase 2024","volume":"52","author":"Milacic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B114","doi-asserted-by":"publisher","first-page":"aab2276","DOI":"10.1126\/science.aab2276","article-title":"A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation","volume":"349","author":"Minajigi","year":"2015","journal-title":"Science"},{"key":"B115","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1016\/j.drudis.2014.06.018","article-title":"CANDO and the infinite drug discovery frontier","volume":"19","author":"Minie","year":"2014","journal-title":"Drug Discov. Today"},{"key":"B116","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1038\/s41592-024-02372-w","article-title":"Geometric deep learning of protein\u2013DNA binding specificity","volume":"21","author":"Mitra","year":"2024","journal-title":"Nat. Methods"},{"key":"B117","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1021\/ct700324x","article-title":"The MARTINI coarse-grained force field: extension to proteins","volume":"4","author":"Monticelli","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"B118","doi-asserted-by":"publisher","first-page":"12863","DOI":"10.1073\/pnas.1820737116","article-title":"\u03b2-Actin mRNA interactome mapping by proximity biotinylation","volume":"116","author":"Mukherjee","year":"2019","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B119","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nrmicro2692","article-title":"The dependence of viral RNA replication on co-opted host factors","volume":"10","author":"Nagy","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"B120","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nrmicro3288","article-title":"Functional long-range RNA\u2013RNA interactions in positive-strand RNA viruses","volume":"12","author":"Nicholson","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"B121","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.cell.2017.03.028","article-title":"Multidimensional tracking of GPCR signaling via peroxidase-catalyzed proximity labeling","volume":"169","author":"Paek","year":"2017","journal-title":"Cell"},{"key":"B122","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-020-07291-6","article-title":"RBPsuite: RNA-protein binding sites prediction suite based on deep learning","volume":"21","author":"Pan","year":"2020","journal-title":"BMC Genomics"},{"key":"B123","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.virol.2009.08.009","article-title":"The viral RNA recognition sensor RIG-I is degraded during encephalomyocarditis virus (EMCV) infection","volume":"393","author":"Papon","year":"2009","journal-title":"Virology"},{"key":"B124","doi-asserted-by":"publisher","first-page":"bbac538","DOI":"10.1093\/bib\/bbac538","article-title":"Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile","volume":"24","author":"Patiyal","year":"2023","journal-title":"Briefings Bioinf."},{"key":"B125","doi-asserted-by":"publisher","first-page":"10359","DOI":"10.1128\/JVI.74.22.10359-10370.2000","article-title":"Identification of an RNA hairpin in poliovirus RNA that serves as the primary template in the in vitro uridylylation of VPg","volume":"74","author":"Paul","year":"2000","journal-title":"J. Virol."},{"key":"B126","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1007\/978-1-0716-1851-6_3","article-title":"RBPmap: a tool for mapping and predicting the binding sites of RNA-binding proteins considering the motif environment","volume":"2404","author":"Paz","year":"2022","journal-title":"Post-Transcriptional Gene Regul."},{"key":"B127","doi-asserted-by":"publisher","first-page":"W568","DOI":"10.1093\/nar\/gkw454","article-title":"BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins","volume":"44","author":"Paz","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B128","doi-asserted-by":"publisher","DOI":"10.1021\/ed100697w","article-title":"ChemSpider: an online chemical information resource","volume":"87","author":"Pence","year":"2010","journal-title":"J. Chemical Education"},{"key":"B129","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1101\/gad.1040803","article-title":"Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA","volume":"17","author":"Pestova","year":"2003","journal-title":"Genes Dev."},{"key":"B130","doi-asserted-by":"publisher","first-page":"5419","DOI":"10.1021\/acs.jctc.8b00670","article-title":"QM\/MM calculations on protein\u2013RNA complexes: Understanding limitations of classical MD simulations and search for reliable cost-effective QM methods","volume":"14","author":"Pokorna","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"B131","doi-asserted-by":"publisher","first-page":"W221","DOI":"10.1093\/nar\/gky453","article-title":"SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data","volume":"46","author":"Polishchuk","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B132","doi-asserted-by":"publisher","first-page":"3976","DOI":"10.1093\/bioinformatics\/btab570","article-title":"NetControl4BioMed: a web-based platform for controllability analysis of protein\u2013protein interaction networks","volume":"37","author":"Popescu","year":"2021","journal-title":"Bioinformatics"},{"key":"B133","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/s41587-018-0001-2","article-title":"Comprehensive identification of RNA\u2013protein interactions in any organism using orthogonal organic phase separation (OOPS)","volume":"37","author":"Queiroz","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B134","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nmeth.4601","article-title":"RNA\u2013protein interaction detection in living cells","volume":"15","author":"Ramanathan","year":"2018","journal-title":"Nat. Methods"},{"key":"B135","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1261\/rna.076141.120","article-title":"RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look","volume":"26","author":"Rangan","year":"2020","journal-title":"Rna"},{"key":"B136","doi-asserted-by":"publisher","first-page":"1328","DOI":"10.1126\/science.1230593","article-title":"Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging","volume":"339","author":"Rhee","year":"2013","journal-title":"Science"},{"key":"B137","doi-asserted-by":"publisher","first-page":"3693","DOI":"10.1007\/s00018-018-2882-0","article-title":"Viral journeys on the intracellular highways","volume":"75","author":"Robinson","year":"2018","journal-title":"Cell. Mol. Life Sci."},{"key":"B138","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007135","article-title":"Innate immune sensor LGP2 is cleaved by the Leader protease of foot-and-mouth disease virus","volume":"14","author":"Rodr\u00edguez Pulido","year":"2018","journal-title":"PloS Pathog."},{"key":"B139","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1074\/mcp.R120.001941","article-title":"Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches","volume":"19","author":"Samavarchi-Tehrani","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"B140","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/s41564-020-00846-z","article-title":"The SARS-CoV-2 RNA\u2013protein interactome in infected human cells","volume":"6","author":"Schmidt","year":"2021","journal-title":"Nat. Microbiol."},{"key":"B141","doi-asserted-by":"publisher","first-page":"15690","DOI":"10.1038\/ncomms15690","article-title":"Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes","volume":"8","author":"Schopp","year":"2017","journal-title":"Nat. Commun."},{"key":"B142","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-018-2254-7","article-title":"Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links","volume":"19","author":"Seal","year":"2018","journal-title":"BMC Bioinf."},{"key":"B143","first-page":"101","article-title":"Advances in QSAR through artificial intelligence and machine learning methods","volume-title":"QSAR in Safety Evaluation and Risk Assessment","author":"Selvaraj","year":"2023"},{"key":"B144","doi-asserted-by":"publisher","first-page":"8496","DOI":"10.1073\/pnas.93.16.8496","article-title":"A three-hybrid system to detect RNA-protein interactions in vivo","volume":"93","author":"SenGupta","year":"1996","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B145","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.isci.2021.103381","article-title":"RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery","volume":"24","author":"Sharma","year":"2021","journal-title":"Iscience"},{"key":"B146","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cbpa.2011.10.014","article-title":"Split-protein systems: beyond binary protein\u2013protein interactions","volume":"15","author":"Shekhawat","year":"2011","journal-title":"Curr. Opin. Chem. Biol."},{"key":"B147","doi-asserted-by":"publisher","first-page":"1741","DOI":"10.1109\/TCBB.2019.2910513","article-title":"RNA-protein binding sites prediction via multi scale convolutional gated recurrent unit networks","volume":"17","author":"Shen","year":"2019","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"key":"B148","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1093\/bioinformatics\/btaa762","article-title":"CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets","volume":"37","author":"\u0160krlj","year":"2021","journal-title":"Bioinformatics"},{"key":"B149","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1146\/annurev-virology-100114-055218","article-title":"Continuous and discontinuous RNA synthesis in coronaviruses","volume":"2","author":"Sola","year":"2015","journal-title":"Annu. Rev. Virol."},{"key":"B150","doi-asserted-by":"publisher","first-page":"237","DOI":"10.4161\/rna.8.2.14991","article-title":"RNA-RNA and RNA-protein interactions in coronavirus replication and transcription","volume":"8","author":"Sola","year":"2011","journal-title":"RNA Biol."},{"key":"B151","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/mBio.03103-19","article-title":"The U-rich untranslated region of the hepatitis E virus induces differential type I and type III interferon responses in a host cell-dependent manner","volume":"11","author":"Sooryanarain","year":"2020","journal-title":"MBio"},{"key":"B152","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1134\/S0006297921090042","article-title":"Non-canonical translation initiation mechanisms employed by eukaryotic viral mRNAs","volume":"86","author":"Sorokin","year":"2021","journal-title":"Biochem. (Moscow)"},{"key":"B153","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1017\/S135583820100245X","article-title":"Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins","volume":"7","author":"Srisawat","year":"2001","journal-title":"Rna"},{"key":"B154","doi-asserted-by":"publisher","first-page":"9181","DOI":"10.1128\/JVI.00603-10","article-title":"Different strains of Theiler's murine encephalomyelitis virus antagonize different sites in the type I interferon pathway","volume":"84","author":"Stavrou","year":"2010","journal-title":"J. Virol."},{"key":"B155","doi-asserted-by":"publisher","first-page":"2324","DOI":"10.1021\/acs.jcim.5b00559","article-title":"ZINC 15\u2013ligand discovery for everyone","volume":"55","author":"Sterling","year":"2015","journal-title":"J. Chem. Inf. modeling"},{"key":"B156","doi-asserted-by":"publisher","first-page":"a033001","DOI":"10.1101\/cshperspect.a033001","article-title":"Translational control in virus-infected cells","volume":"11","author":"Stern-Ginossar","year":"2019","journal-title":"Cold Spring Harbor Perspect. Biol."},{"key":"B157","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B158","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1128\/JVI.78.1.320-328.2004","article-title":"The ORF2 protein of hepatitis E virus binds the 5\u2032 region of viral RNA","volume":"78","author":"Surjit","year":"2004","journal-title":"J. Virol."},{"key":"B159","doi-asserted-by":"publisher","first-page":"D380","DOI":"10.1093\/nar\/gkv1277","article-title":"STITCH 5: augmenting protein\u2013chemical interaction networks with tissue and affinity data","volume":"44","author":"Szklarczyk","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B160","doi-asserted-by":"publisher","first-page":"104217","DOI":"10.1016\/j.chemolab.2020.104217","article-title":"kDeepBind: prediction of RNA-Proteins binding sites using convolution neural network and k-gram features","volume":"208","author":"Tahir","year":"2021","journal-title":"Chemometrics Intelligent Lab. Syst."},{"key":"B161","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JVI.02190-20","article-title":"The global and local distribution of RNA structure throughout the SARS-CoV-2 genome","volume":"95","author":"Tavares","year":"2021","journal-title":"J. Virol."},{"key":"B162","doi-asserted-by":"publisher","first-page":"D160","DOI":"10.1093\/nar\/gkz969","article-title":"NPInter v4. 0: an integrated database of ncRNA interactions","volume":"48","author":"Teng","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B163","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1002\/pro.v31.1","article-title":"PANTHER: Making genome-scale phylogenetics accessible to all","volume":"31","author":"Thomas","year":"2022","journal-title":"Protein Sci."},{"key":"B164","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1002\/iub.v64.10","article-title":"The biological regulation of ABCE1","volume":"64","author":"Tian","year":"2012","journal-title":"IUBMB Life"},{"key":"B165","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1016\/j.cell.2018.11.004","article-title":"The human RNA-binding proteome and its dynamics during translational arrest","volume":"176","author":"Trendel","year":"2019","journal-title":"Cell"},{"key":"B166","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1146\/annurev-virology-031413-085505","article-title":"Cytoplasmic RNA granules and viral infection","volume":"1","author":"Tsai","year":"2014","journal-title":"Annu. Rev. Virol."},{"key":"B167","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1074\/mcp.M110.007385","article-title":"Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach","volume":"10","author":"Tsai","year":"2011","journal-title":"Mol. Cell. Proteomics"},{"key":"B168","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1126\/science.2200121","article-title":"Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase","volume":"249","author":"Tuerk","year":"1990","journal-title":"science"},{"key":"B169","doi-asserted-by":"publisher","first-page":"giab054","DOI":"10.1093\/gigascience\/giab054","article-title":"RNAProt: an efficient and feature-rich RNA binding protein binding site predictor","volume":"10","author":"Uhl","year":"2021","journal-title":"GigaScience"},{"key":"B170","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.ymeth.2019.09.013","article-title":"Fast and unbiased purification of RNA-protein complexes after UV cross-linking","volume":"178","author":"Urdaneta","year":"2020","journal-title":"Methods"},{"key":"B171","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/s41586-020-2077-3","article-title":"A large-scale binding and functional map of human RNA-binding proteins","volume":"583","author":"Van Nostrand","year":"2020","journal-title":"Nature"},{"key":"B172","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/msystems.00643-21","article-title":"RNA-protein interaction analysis of SARS-CoV-2 5\u2032 and 3\u2032 untranslated regions reveals a role of lysosome-associated membrane protein-2a during viral infection","volume":"6","author":"Verma","year":"2021","journal-title":"Msystems"},{"key":"B173","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1002\/0471250953.2015.49.issue-1","article-title":"Scoring large-scale affinity purification mass spectrometry datasets with MiST","volume":"49","author":"Verschueren","year":"2015","journal-title":"Curr. Protoc. Bioinf."},{"key":"B174","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004921","article-title":"Identification of RNA binding proteins associated with dengue virus RNA in infected cells reveals temporally distinct host factor requirements","volume":"10","author":"Viktorovskaya","year":"2016","journal-title":"PloS neglected Trop. Dis."},{"key":"B175","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.virusres.2008.07.016","article-title":"Genome cyclization as strategy for flavivirus RNA replication","volume":"139","author":"Villordo","year":"2009","journal-title":"Virus Res."},{"key":"B176","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/nrmicro2655","article-title":"Viral subversion of the host protein synthesis machinery","volume":"9","author":"Walsh","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"B177","doi-asserted-by":"publisher","first-page":"7028","DOI":"10.1128\/JVI.00205-15","article-title":"Enterovirus 71 proteins 2A and 3D antagonize the antiviral activity of gamma interferon via signaling attenuation","volume":"89","author":"Wang","year":"2015","journal-title":"J. Virol."},{"key":"B178","doi-asserted-by":"publisher","first-page":"3758","DOI":"10.1128\/JVI.02589-10","article-title":"The leader proteinase of foot-and-mouth disease virus negatively regulates the type I interferon pathway by acting as a viral deubiquitinase","volume":"85","author":"Wang","year":"2011","journal-title":"J. Virol."},{"key":"B179","doi-asserted-by":"publisher","first-page":"9311","DOI":"10.1128\/JVI.00722-12","article-title":"Foot-and-mouth disease virus 3C protease cleaves NEMO to impair innate immune signaling","volume":"86","author":"Wang","year":"2012","journal-title":"J. Virol."},{"key":"B180","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.bbrc.2010.07.044","article-title":"Foot-and-mouth disease virus leader proteinase inhibits dsRNA-induced type I interferon transcription by decreasing interferon regulatory factor 3\/7 in protein levels","volume":"399","author":"Wang","year":"2010","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B181","doi-asserted-by":"publisher","first-page":"2090","DOI":"10.1128\/JVI.02514-15","article-title":"Porcine epidemic diarrhea virus 3C-like protease regulates its interferon antagonism by cleaving NEMO","volume":"90","author":"Wang","year":"2016","journal-title":"J. Virol."},{"key":"B182","doi-asserted-by":"publisher","first-page":"3762","DOI":"10.1016\/j.csbj.2020.10.043","article-title":"RBinds: a user-friendly server for RNA binding site prediction","volume":"18","author":"Wang","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"B183","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.4161\/rna.8.6.17836","article-title":"Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3\u2019UTR structures","volume":"8","author":"Ward","year":"2011","journal-title":"RNA Biol."},{"key":"B184","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1038\/s41587-020-0456-9","article-title":"Massively parallel Cas13 screens reveal principles for guide RNA design","volume":"38","author":"Wessels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"B185","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1016\/j.molcel.2014.07.012","article-title":"The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites","volume":"55","author":"West","year":"2014","journal-title":"Mol. Cell"},{"key":"B186","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1002\/cpt.2350","article-title":"An evidence-based framework for evaluating pharmacogenomics knowledge for personalized medicine","volume":"110","author":"Whirl-Carrillo","year":"2021","journal-title":"Clin. Pharmacol. Ther."},{"key":"B187","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.tim.2012.02.001","article-title":"Regulation of stress granules in virus systems","volume":"20","author":"White","year":"2012","journal-title":"Trends Microbiol."},{"key":"B188","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1016\/S0092-8674(00)00055-6","article-title":"Initiation of protein synthesis from the A site of the ribosome","volume":"102","author":"Wilson","year":"2000","journal-title":"Cell"},{"key":"B189","doi-asserted-by":"publisher","first-page":"D901","DOI":"10.1093\/nar\/gkm958","article-title":"DrugBank: a knowledgebase for drugs, drug actions and drug targets","volume":"36","author":"Wishart","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"B190","doi-asserted-by":"publisher","first-page":"2034","DOI":"10.3390\/v13102034","article-title":"The autophagosomes containing dengue virus proteins and full-length genomic RNA are infectious","volume":"13","author":"Wu","year":"2021","journal-title":"Viruses"},{"key":"B191","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000323","article-title":"A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA\u2013based regulation of viral processes","volume":"5","author":"Wu","year":"2009","journal-title":"PloS Pathog."},{"key":"B192","doi-asserted-by":"publisher","first-page":"W468","DOI":"10.1093\/nar\/gkad353","article-title":"PrismNet: predicting protein\u2013RNA interaction using in vivo RNA structural information","volume":"51","author":"Xu","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B193","doi-asserted-by":"publisher","first-page":"vbac023","DOI":"10.1093\/bioadv\/vbac023","article-title":"Prediction of RNA\u2013protein interactions using a nucleotide language model","volume":"2","author":"Yamada","year":"2022","journal-title":"Bioinf. Adv."},{"key":"B194","doi-asserted-by":"publisher","first-page":"i276","DOI":"10.1093\/bioinformatics\/btaa456","article-title":"Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions","volume":"36","author":"Yan","year":"2020","journal-title":"Bioinformatics"},{"key":"B195","doi-asserted-by":"publisher","first-page":"bbaa174","DOI":"10.1093\/bib\/bbaa174","article-title":"RNA-binding protein recognition based on multi-view deep feature and multi-label learning","volume":"22","author":"Yang","year":"2021","journal-title":"Briefings Bioinf."},{"key":"B196","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-015-1273-2","article-title":"CLIPdb: a CLIP-seq database for protein-RNA interactions","volume":"16","author":"Yang","year":"2015","journal-title":"BMC Genomics"},{"key":"B197","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.virusres.2015.02.025","article-title":"The structure and functions of coronavirus genomic 3\u2032 and 5\u2032 ends","volume":"206","author":"Yang","year":"2015","journal-title":"Virus Res."},{"key":"B198","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ymeth.2019.09.006","article-title":"High throughput approaches to study RNA-protein interactions in vitro","volume":"178","author":"Ye","year":"2020","journal-title":"Methods"},{"key":"B199","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41592-020-0866-0","article-title":"CRISPR-assisted detection of RNA\u2013protein interactions in living cells","volume":"17","author":"Yi","year":"2020","journal-title":"Nat. Methods"},{"key":"B200","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.ymeth.2012.07.004","article-title":"MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs","volume":"58","author":"Yoon","year":"2012","journal-title":"Methods"},{"key":"B201","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1038\/s41592-019-0511-y","article-title":"BindSpace decodes transcription factor binding signals by large-scale sequence embedding","volume":"16","author":"Yuan","year":"2019","journal-title":"Nat. Methods"},{"key":"B202","doi-asserted-by":"publisher","first-page":"D1180","DOI":"10.1093\/nar\/gkad1004","article-title":"The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods","volume":"52","author":"Zdrazil","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B203","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1038\/nprot.2006.81","article-title":"A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells","volume":"1","author":"Zeng","year":"2006","journal-title":"Nat. Protoc."},{"key":"B204","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s41422-021-00581-y","article-title":"Comparison of viral RNA\u2013host 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":"B205","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1109\/TST.5971803","article-title":"NetEPD: a network-based essential protein discovery platform","volume":"25","author":"Zhang","year":"2020","journal-title":"Tsinghua Sci. Technol."},{"key":"B206","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s12859-022-04798-5","article-title":"DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites","volume":"23","author":"Zhang","year":"2022","journal-title":"BMC Bioinf."},{"key":"B207","doi-asserted-by":"publisher","first-page":"e52","DOI":"10.1093\/nar\/gkaa143","article-title":"Capturing RNA\u2013protein interaction via CRUIS","volume":"48","author":"Zhang","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B208","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1261\/rna.044776.114","article-title":"RAID: a comprehensive resource for human RNA-associated (RNA\u2013RNA\/RNA\u2013protein) interaction","volume":"20","author":"Zhang","year":"2014","journal-title":"Rna"},{"key":"B209","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1038\/s41594-021-00653-y","article-title":"Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome","volume":"28","author":"Zhang","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"B210","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-021-04430-y","article-title":"Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization","volume":"22","author":"Zhao","year":"2021","journal-title":"BMC Bioinf."},{"key":"B211","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1007\/978-1-4939-3591-8_4","article-title":"Detecting RNA\u2013protein interaction using end-labeled biotinylated RNA oligonucleotides and immunoblotting","volume":"1421","author":"Zheng","year":"2016","journal-title":"RNA-Protein Complexes Interactions: Methods Protoc."},{"key":"B212","doi-asserted-by":"publisher","first-page":"D1465","DOI":"10.1093\/nar\/gkad751","article-title":"TTD: Therapeutic Target Database describing target druggability information","volume":"52","author":"Zhou","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B213","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.virol.2016.12.005","article-title":"Porcine deltacoronavirus nsp5 inhibits interferon-\u03b2 production through the cleavage of NEMO","volume":"502","author":"Zhu","year":"2017","journal-title":"Virology"},{"key":"B214","doi-asserted-by":"publisher","first-page":"e2747","DOI":"10.1038\/cddis.2017.170","article-title":"Foot-and-mouth disease virus infection inhibits LGP2 protein expression to exaggerate inflammatory response and promote viral replication","volume":"8","author":"Zhu","year":"2017","journal-title":"Cell Death Dis."},{"key":"B215","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JVI.00003-17","article-title":"Porcine deltacoronavirus nsp5 antagonizes type I interferon signaling by cleaving STAT2","volume":"91","author":"Zhu","year":"2017","journal-title":"J. Virol."},{"key":"B216","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1016\/j.molcel.2020.11.004","article-title":"The short-and long-range RNA-RNA interactome of SARS-CoV-2","volume":"80","author":"Ziv","year":"2020","journal-title":"Mol. Cell"},{"key":"B217","doi-asserted-by":"publisher","first-page":"9664","DOI":"10.1128\/JVI.76.19.9664-9672.2002","article-title":"The mengovirus leader protein suppresses alpha\/beta interferon production by inhibition of the iron\/ferritin-mediated activation of NF-\u03baB","volume":"76","author":"Zoll","year":"2002","journal-title":"J. Virol."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1580337\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,13]],"date-time":"2025-06-13T16:57:46Z","timestamp":1749833866000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1580337\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,21]]},"references-count":217,"alternative-id":["10.3389\/fcimb.2025.1580337"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1580337","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,21]]},"article-number":"1580337"}}