{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T19:22:29Z","timestamp":1790796149966,"version":"4.1.0"},"reference-count":94,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,6,4]],"date-time":"2021-06-04T00:00:00Z","timestamp":1622764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Messenger RNA (mRNA) vaccines have recently emerged as a new type of vaccine technology, showing strong potential to combat the COVID-19 pandemic. In addition to SARS-CoV-2 which caused the pandemic, mRNA vaccines have been developed and tested to prevent infectious diseases caused by other viruses such as Zika virus, the dengue virus, the respiratory syncytial virus, influenza H7N9 and Flavivirus. Interestingly, mRNA vaccines may also be useful for preventing non-infectious diseases such as diabetes and cancer. This review summarises the current progresses of mRNA vaccines designed for a range of diseases including COVID-19. As epitope study is a primary component in the in silico design of mRNA vaccines, we also survey on advanced bioinformatics and machine learning algorithms which have been used for epitope prediction, and review on user-friendly software tools available for this purpose. Finally, we discuss some of the unanswered concerns about mRNA vaccines, such as unknown long-term side effects, and present with our perspectives on future developments in this exciting area.<\/jats:p>","DOI":"10.1093\/bfgp\/elab027","type":"journal-article","created":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T11:21:16Z","timestamp":1621336876000},"page":"289-303","source":"Crossref","is-referenced-by-count":38,"title":["Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design"],"prefix":"10.1093","volume":"20","author":[{"given":"Xinhui","family":"Cai","sequence":"first","affiliation":[{"name":"Data Science Institute, Faculty of Engineering & IT, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiao Jiao","family":"Li","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Brian","sequence":"additional","affiliation":[{"name":"Children\u2019s Cancer Institute Australia, University of New South Wales Sydney, Children\u2019s Cancer Institute Australia, Randwick, Sydney, 2031, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyan","family":"Li","sequence":"additional","affiliation":[{"name":"Data Science Institute, Faculty of Engineering & IT, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,6,4]]},"reference":[{"key":"2021091309112897700_ref1","author":"Iedb.org: Free epitope database and prediction resource"},{"key":"2021091309112897700_ref2","author":"How does testing in the u.s. compare to other countries"},{"key":"2021091309112897700_ref3","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1016\/j.ijbiomac.2020.06.213","article-title":"Designing a novel mrna vaccine against sars-cov-2: An immunoinformatics approach","volume":"162","author":"Ahammad","year":"2020","journal-title":"International Journal of Biological Macromolecules"},{"issue":"2","key":"2021091309112897700_ref4","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1006\/jmbi.1995.0293","article-title":"Ranking potential binding peptides to mhc molecules by a computational threading approach","volume":"249","author":"Altuvia","year":"1995","journal-title":"Journal of Molecular Biology"},{"key":"2021091309112897700_ref5","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gki587","article-title":"Pcleavage: an svm based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences","volume":"33","author":"Bhasin","year":"2005","journal-title":"Nucleic Acids Research"},{"issue":"7","key":"2021091309112897700_ref6","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1093\/cid\/ciy323","article-title":"Predicting Influenza H3N2 Vaccine Efficacy From Evolution of the Dominant Epitope","volume":"67","author":"Bonomo","year":"2018","journal-title":"Clinical Infectious Diseases"},{"key":"2021091309112897700_ref7","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/B978-012310920-0\/50012-7","article-title":"11 - epitope mapping with peptides","volume-title":"Peptides","author":"Bosshard","year":"1995"},{"key":"2021091309112897700_ref8","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1007\/s00251-005-0798-y","article-title":"Automated generation and evaluation of specific mhc binding predictive tools: Arb matrix applications","volume":"57","author":"Bui","year":"2005","journal-title":"Immunogenetics"},{"issue":"5","key":"2021091309112897700_ref9","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2020.04.022","article-title":"Laura M. Walker. Rational vaccine design in the time of covid-19","volume":"27","author":"Burton","year":"2020","journal-title":"Cell Host and Microbe"},{"key":"2021091309112897700_ref10","doi-asserted-by":"crossref","DOI":"10.1172\/JCI134915","article-title":"mrna vaccine-induced neoantigen-specific t cell immunity in patients with gastrointestinal cancer","volume":"130","author":"Cafri","year":"2020","journal-title":"The Journal of Clinical Investigation"},{"key":"2021091309112897700_ref11","first-page":"602","article-title":"B-cell epitope prediction for peptide-based vaccine design: Towards a paradigm of biological outcomes","author":"Caoili","year":"2010","journal-title":"Association for Computing Machinery, page"},{"issue":"03","key":"2021091309112897700_ref12","article-title":"An rna nanoparticle vaccine against zika virus elicits antibody and cd8+ t cell responses in a mouse model","volume":"7","author":"Chahal","year":"2017","journal-title":"Scientific Reports"},{"key":"2021091309112897700_ref13","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1080\/21645515.2019.1654807","article-title":"Combining immunoprofiling with machine learning to assess the effects of adjuvant formulation on human vaccine-induced immunity","volume":"16","author":"Chaudhury","year":"2019","journal-title":"Human Vaccines and Immunotherapeutics"},{"key":"2021091309112897700_ref14","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-020-2622-0","article-title":"Sars-cov-2 mrna vaccine design enabled by prototype pathogen preparedness","author":"Corbett","year":"2020","journal-title":"Nature"},{"key":"2021091309112897700_ref15","doi-asserted-by":"crossref","DOI":"10.1056\/NEJMoa2024671","article-title":"Evaluation of the mrna-1273 vaccine against sars-cov-2 in nonhuman primates","author":"Corbett","year":"2020","journal-title":"New England Journal of Medicine"},{"key":"2021091309112897700_ref16","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature12966","article-title":"Proof of principle for epitope-focused vaccine design","volume":"507","author":"Correia","year":"2014","journal-title":"Nature"},{"key":"2021091309112897700_ref17","doi-asserted-by":"crossref","DOI":"10.1056\/NEJMoa2101765","article-title":"Bnt162b2 mrna covid-19 vaccine in a nationwide mass vaccination setting","author":"Dagan","year":"2021","journal-title":"The New England Journal of Medicine"},{"issue":"02","key":"2021091309112897700_ref18","article-title":"Sepia, a knowledge-driven algorithm for predicting conformational b-cell epitopes from the amino acid sequence","volume":"18","author":"Dalkas","year":"2017","journal-title":"BMC Bioinformatics"},{"issue":"02","key":"2021091309112897700_ref19","article-title":"Modified mrna\/lipid nanoparticle-based vaccines expressing respiratory syncytial virus f protein variants are immunogenic and protective in rodent models of rsv infection","volume":"5","author":"Espeseth","year":"2020","journal-title":"npj Vaccines"},{"issue":"25","key":"2021091309112897700_ref20","doi-asserted-by":"crossref","first-page":"3326","DOI":"10.1016\/j.vaccine.2019.04.074","article-title":"mrna vaccines against h10n8 and h7n9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials","volume":"37","author":"Feldman","year":"2019","journal-title":"Vaccine"},{"key":"2021091309112897700_ref21","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.omtm.2019.10.015","article-title":"Nanoparticles versus dendritic cells as vehicles to deliver mrna encoding multiple epitopes for immunotherapy","volume":"16","author":"Firdessa-Fite","year":"2020","journal-title":"Molecular Therapy - Methods & Clinical Development"},{"key":"2021091309112897700_ref22","doi-asserted-by":"crossref","DOI":"10.1126\/science.abc1932","article-title":"Development of an inactivated vaccine candidate for sars-cov-2","author":"Gao","year":"2020","journal-title":"Science"},{"issue":"39","key":"2021091309112897700_ref23","doi-asserted-by":"crossref","first-page":"5299","DOI":"10.1016\/j.vaccine.2009.06.101","article-title":"Epitope-based vaccination against pneumonic tularemia","volume":"27","author":"Gregory","year":"2009","journal-title":"Vaccine"},{"key":"2021091309112897700_ref24","article-title":"A novel sars-cov-2 multitope protein\/peptide vaccine candidate is highly immunogenic and prevents lung infection in an adeno associated virus human angiotensin-converting enzyme 2 (aav hace2) mouse model","author":"Guirakhoo","year":"2020","journal-title":"bioRxiv"},{"issue":"39","key":"2021091309112897700_ref25","doi-asserted-by":"crossref","first-page":"E9153","DOI":"10.1073\/pnas.1810002115","article-title":"mrna vaccination with charge-altering releasable transporters elicits human t cell responses and cures established tumors in mice","volume":"115","author":"Haabeth","year":"2018","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2021091309112897700_ref26","doi-asserted-by":"crossref","first-page":"2558","DOI":"10.1110\/ps.062405906","article-title":"Prediction of residues in discontinuous b-cell epitopes using protein 3d structures","volume":"15","author":"Andersen","year":"2006","journal-title":"Protein Science: A Publication of the Protein Society"},{"key":"2021091309112897700_ref27","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1007\/s00262-005-0064-z","article-title":"Vaccination with mrnas encoding tumor-associated antigens and granulocyte-macrophage colony-stimulating factor efficiently primes ctl responses, but is insufficient to overcome tolerance to a model tumor\/self antigen","volume":"55","author":"Hess","year":"2005","journal-title":"Cancer Immunology, Immunotherapy"},{"key":"2021091309112897700_ref28","doi-asserted-by":"crossref","first-page":"e0229327","DOI":"10.1371\/journal.pone.0229327","article-title":"Hla class i restricted epitopes prediction of common tumor antigens in white and east asian populations: Implication on antigen selection for cancer vaccine design","volume":"15","author":"Hu","year":"2020","journal-title":"PLOS ONE"},{"issue":"1898","key":"2021091309112897700_ref29","article-title":"Antibody immunity induced by h7n9 avian influenza vaccines: Evaluation criteria, affecting factors, and implications for rational vaccine design","volume":"8","author":"Hu","year":"2017","journal-title":"Frontiers in Microbiology"},{"key":"2021091309112897700_ref30","doi-asserted-by":"crossref","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"Bepipred-2.0: improving sequence-based b-cell epitope prediction using conformational epitopes","volume":"45","author":"Jespersen","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"2021091309112897700_ref31","doi-asserted-by":"crossref","first-page":"S88","DOI":"10.1093\/infdis\/jiy745","article-title":"New vaccine design and delivery technologies","volume":"219","author":"Kanekiyo","year":"2019","journal-title":"The Journal of Infectious Diseases"},{"key":"2021091309112897700_ref32","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1186\/1471-2105-10-394","article-title":"Derivation of an amino acid similarity matrix for peptide:mhc binding and its application as a bayesian prior","volume":"10","author":"Kim","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"27","key":"2021091309112897700_ref33","doi-asserted-by":"crossref","first-page":"3516","DOI":"10.1016\/j.vaccine.2008.04.016","article-title":"Prediction of pertussis vaccine efficacy using a correlates of protection model","volume":"26","author":"Kohberger","year":"2008","journal-title":"Vaccine"},{"key":"2021091309112897700_ref34","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/nbt.1733","article-title":"Expression of therapeutic proteins after delivery of chemically modified mrna in mice","volume":"29","author":"Kormann","year":"2011","journal-title":"Nature Biotechnology"},{"key":"2021091309112897700_ref35","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/nbt.1733","article-title":"Expression of therapeutic proteins after delivery of chemically modified mrna in mice","volume":"29","author":"Kormann","year":"2011","journal-title":"Nature Biotechnology"},{"key":"2021091309112897700_ref36","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-020-2798-3","article-title":"Sars-cov-2 vaccines in development","author":"Krammer","year":"2020","journal-title":"Nature"},{"key":"2021091309112897700_ref37","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/S2055-6640(20)30330-7","article-title":"Current trends in zika vaccine development","volume":"3","author":"Lagunas-Rangel","year":"2017","journal-title":"Journal of Virus Eradication"},{"key":"2021091309112897700_ref38","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1287\/inte.2016.0862","article-title":"Machine learning for predicting vaccine immunogenicity","volume":"46","author":"Lee","year":"2016","journal-title":"Interfaces"},{"issue":"12","key":"2021091309112897700_ref39","doi-asserted-by":"crossref","first-page":"2635","DOI":"10.1016\/j.ymthe.2017.08.006","article-title":"Efficient targeting and activation of antigen-presenting cells in vivo after modified mrna vaccine administration in rhesus macaques","volume":"25","author":"Liang","year":"2017","journal-title":"Molecular Therapy"},{"key":"2021091309112897700_ref40","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1186\/1471-2105-10-302","article-title":"Prediction of antigenic epitopes on protein surfaces by consensus scoring","volume":"10","author":"Liang","year":"2009","journal-title":"BMC bioinformatics"},{"key":"2021091309112897700_ref41","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1186\/1471-2105-11-381","article-title":"Epsvr and epmeta: prediction of antigenic epitopes using support vector regression and multiple server results","volume":"11","author":"Liang","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2021091309112897700_ref42","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1186\/1471-2105-11-381","article-title":"Epsvr and epmeta: prediction of antigenic epitopes using support vector regression and multiple server results","volume":"11","author":"Liang","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2021091309112897700_ref43","doi-asserted-by":"crossref","first-page":"W254","DOI":"10.1093\/nar\/gkr434","article-title":"Pacomplex: a web server to infer peptide antigen families and binding models from tcr-pmhc complexes","volume":"39","author":"Liu","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"2021091309112897700_ref44","doi-asserted-by":"crossref","first-page":"37","DOI":"10.3390\/vaccines7020037","article-title":"A comparison of plasmid dna and mrna as vaccine technologies","volume":"7","author":"Liu","year":"2019","journal-title":"Vaccines"},{"key":"2021091309112897700_ref45","doi-asserted-by":"crossref","DOI":"10.1038\/s41422-020-00392-7","article-title":"A covid-19 mrna vaccine encoding sars-cov-2 virus-like particles induces a strong antiviral-like immune response in mice","author":"Lu","year":"2020","journal-title":"Cell Research"},{"key":"2021091309112897700_ref46","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1353\/bhm.0.0173","article-title":"The world\u2019s first immunization campaign: The spanish smallpox vaccine expedition, 1803\u20131813","volume":"83","author":"MARK","year":"2009","journal-title":"Bulletin of the History of Medicine"},{"issue":"4","key":"2021091309112897700_ref47","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1016\/j.ymthe.2019.01.020","article-title":"mrna as a transformative technology for vaccine development to control infectious diseases","volume":"27","author":"Maruggi","year":"2019","journal-title":"Molecular Therapy"},{"key":"2021091309112897700_ref48","doi-asserted-by":"crossref","first-page":"3179","DOI":"10.1016\/j.vaccine.2007.01.039","article-title":"Diversity of francisella tularensis schu4 antigens recognized by t lymphocytes after natural infections in humans: Identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine","volume":"25","author":"McMurry","year":"2007","journal-title":"Vaccine"},{"issue":"11","key":"2021091309112897700_ref49","article-title":"In silico design of an epitope-based vaccine ensemble for chagas disease","volume":"10","author":"Michel-Tod\u00f3","year":"2019","journal-title":"Frontiers in Immunology"},{"key":"2021091309112897700_ref50","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1038\/nbt1215","article-title":"A consensus epitope prediction approach identifies the breadth of murine t(cd8+)-cell responses to vaccinia virus","volume":"24","author":"Moutaftsi","year":"2006","journal-title":"Nature biotechnology"},{"key":"2021091309112897700_ref51","first-page":"1","article-title":"Phase 1\/2 study of covid-19 rna vaccine bnt162b1 in adults","author":"Mulligan","year":"2020","journal-title":"Nature"},{"issue":"1","key":"2021091309112897700_ref52","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.jim.2010.07.003","article-title":"An in vitro-transcribed-mrna polyepitope construct encoding 32 distinct hla class i-restricted epitopes from cmv, ebv, and influenza for use as a functional control in human immune monitoring studies","volume":"360","author":"Nielsen","year":"2010","journal-title":"Journal of Immunological Methods"},{"issue":"1","key":"2021091309112897700_ref53","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.cels.2020.06.010","article-title":"Mhcflurry 2.0: Improved pan-allele prediction of mhc class i-presented peptides by incorporating antigen processing","volume":"11","author":"O\u2019Donnell","year":"2020","journal-title":"Cell Systems"},{"issue":"07","key":"2021091309112897700_ref54","article-title":"Covid-19 coronavirus vaccine design using reverse vaccinology and machine learning","volume":"11","author":"Ong","year":"2020","journal-title":"Frontiers in Immunology"},{"key":"2021091309112897700_ref55","doi-asserted-by":"crossref","first-page":"117956","DOI":"10.1016\/j.lfs.2020.117956","article-title":"Vaccination strategies to combat novel corona virus sars-cov-2","volume":"256","author":"Pandey","year":"2020","journal-title":"Life Sciences"},{"key":"2021091309112897700_ref56","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nature21428","article-title":"Zika virus protection by a single low-dose nucleoside-modified mrna vaccination","volume":"543","author":"Pardi","year":"2017","journal-title":"Nature"},{"key":"2021091309112897700_ref57","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/nrd.2017.243","article-title":"mrna vaccines-a new era in vaccinology","volume":"17","author":"Pardi","year":"2018","journal-title":"Nature Reviews Drug Discovery"},{"issue":"1","key":"2021091309112897700_ref58","doi-asserted-by":"crossref","first-page":"163","DOI":"10.4049\/jimmunol.152.1.163","article-title":"Scheme for ranking potential hla-a2 binding peptides based on independent binding of individual peptide side-chains","volume":"152","author":"Parker","year":"1994","journal-title":"The Journal of Immunology"},{"key":"2021091309112897700_ref59","doi-asserted-by":"crossref","first-page":"120139","DOI":"10.1098\/rsob.120139","article-title":"T-cell epitope vaccine design by immunoinformatics","volume":"3","author":"Patronov","year":"2013","journal-title":"Open Biology"},{"key":"2021091309112897700_ref60","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1471-2105-6-132","article-title":"Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method","volume":"6","author":"Peters","year":"2005","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"2021091309112897700_ref61","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/j.molmed.2013.09.002","article-title":"Challenges and advances towards the rational design of mrna vaccines","volume":"19","author":"Pollard","year":"2013","journal-title":"Trends in Molecular Medicine"},{"key":"2021091309112897700_ref62","article-title":"Recognition of a highly conserved dsrcptq epitope in envelope protein of zika virus through in silico approaches","author":"Rahman","year":"2020","journal-title":"bioRxiv"},{"key":"2021091309112897700_ref63","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s002510050595","article-title":"Syfpeithi: database for mhc ligands and peptide motifs","volume":"50","author":"Rammensee","year":"1999","journal-title":"Immunogenetics"},{"issue":"9","key":"2021091309112897700_ref64","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/S0198-8859(02)00432-9","article-title":"Prediction of mhc class i binding peptides using profile motifs","volume":"63","author":"Reche","year":"2002","journal-title":"Human Immunology"},{"issue":"W1","key":"2021091309112897700_ref65","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Research"},{"key":"2021091309112897700_ref66","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1016\/j.cell.2017.02.017","article-title":"Modified mrna vaccines protect against zika virus infection","volume":"168","author":"Richner","year":"2017","journal-title":"Cell"},{"issue":"06","key":"2021091309112897700_ref67","article-title":"A modified mrna vaccine targeting immunodominant ns epitopes protects against dengue virus infection in hla class i transgenic mice","volume":"10","author":"Roth","year":"2019","journal-title":"Frontiers in Immunology"},{"key":"2021091309112897700_ref68","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1016\/j.molimm.2008.09.009","article-title":"A machine-learning approach for predicting b-cell epitopes","volume":"46","author":"Rubinstein","year":"2009","journal-title":"Molecular Immunology"},{"issue":"8","key":"2021091309112897700_ref69","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1093\/bioinformatics\/btu790","article-title":"PEASE: predicting B-cell epitopes utilizing antibody sequence","volume":"31","author":"Sela-Culang","year":"2014","journal-title":"Bioinformatics"},{"key":"2021091309112897700_ref70","doi-asserted-by":"crossref","DOI":"10.1126\/science.abd4250","article-title":"Viral epitope profiling of covid-19 patients reveals cross-reactivity and correlates of severity","author":"Shrock","year":"2020","journal-title":"Science"},{"issue":"8","key":"2021091309112897700_ref71","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btg108","article-title":"ProPred1: prediction of promiscuous MHC Class-I binding sites","volume":"19","author":"Singh","year":"2003","journal-title":"Bioinformatics"},{"key":"2021091309112897700_ref72","doi-asserted-by":"crossref","DOI":"10.7717\/peerj-cs.275","article-title":"Enhancement of conformational b-cell epitope prediction using clusmote","volume":"6","author":"Solihah","year":"2020","journal-title":"PeerJ Computer Science"},{"key":"2021091309112897700_ref73","volume-title":"stefs304\/mhclovac","author":"Stojanovic","year":"2021"},{"key":"2021091309112897700_ref74","doi-asserted-by":"crossref","first-page":"W612","DOI":"10.1093\/nar\/gkp417","article-title":"Seppa: a computational server for spatial epitope prediction of protein antigens","volume":"37","author":"Sun","year":"2009","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"2021091309112897700_ref75","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1080\/21645515.2019.1670035","article-title":"Computational tools for modern vaccine development","volume":"16","author":"Sunita","year":"2020","journal-title":"Human Vaccines & Immunotherapeutics"},{"key":"2021091309112897700_ref76","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1093\/bioinformatics\/btn199","article-title":"Pepito: improved discontinuous b-cell epitope prediction using multiple distance thresholds and half sphere exposure","volume":"24","author":"Sweredoski","year":"2008","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2021091309112897700_ref77","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1093\/protein\/gzn075","article-title":"Cobepro: a novel system for predicting continuous b-cell epitopes","volume":"22","author":"Sweredoski","year":"2009","journal-title":"Protein Engineering, Design and Selection"},{"key":"2021091309112897700_ref78","doi-asserted-by":"crossref","DOI":"10.1038\/s41422-020-0387-5","article-title":"A novel receptor-binding domain (rbd)-based mrna vaccine against sars-cov-2","author":"Tai","year":"2020","journal-title":"Cell Research"},{"key":"2021091309112897700_ref79","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1038\/mt.2015.103","article-title":"Sequence-engineered mrna without chemical nucleoside modifications enables an effective protein therapy in large animals","volume":"23","author":"Thess","year":"2015","journal-title":"Molecular Therapy"},{"key":"2021091309112897700_ref80","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/s41467-020-20653-8","article-title":"Sars-cov-2 spike glycoprotein vaccine candidate nvx-cov2373 immunogenicity in baboons and protection in mice","volume":"12","author":"Tian","year":"2021","journal-title":"Nature Communications"},{"key":"2021091309112897700_ref81","volume-title":"Mortality analyses","author":"John Hopkins University","year":"2020"},{"issue":"12","key":"2021091309112897700_ref82","doi-asserted-by":"crossref","first-page":"3382","DOI":"10.1016\/j.celrep.2018.11.082","article-title":"An mrna vaccine protects mice against multiple tick-transmitted flavivirus infections","volume":"25","author":"VanBlargan","year":"2018","journal-title":"Cell Reports"},{"key":"2021091309112897700_ref83","doi-asserted-by":"crossref","first-page":"100766","DOI":"10.1016\/j.nantod.2019.100766","article-title":"Three decades of messenger rna vaccine development","volume":"28","author":"Verbeke","year":"2019","journal-title":"Nano Today"},{"key":"2021091309112897700_ref84","doi-asserted-by":"crossref","DOI":"10.1056\/NEJMoa2027906","article-title":"Safety and immunogenicity of two rna-based covid-19 vaccine candidates","author":"Walsh","year":"2020","journal-title":"New England Journal of Medicine"},{"key":"2021091309112897700_ref85","doi-asserted-by":"publisher","journal-title":"medRxiv","DOI":"10.1101\/2020.11.04.20226282"},{"key":"2021091309112897700_ref86","volume-title":"Coronavirus toll update","author":"Worldometer","year":"2021"},{"issue":"6483","key":"2021091309112897700_ref87","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1126\/science.abb2507","article-title":"Cryo-em structure of the 2019-ncov spike in the prefusion conformation","volume":"367","author":"Wrapp","year":"2020","journal-title":"Science"},{"issue":"6239","key":"2021091309112897700_ref88","article-title":"Comprehensive serological profiling of human populations using a synthetic human virome","volume":"348","author":"George","year":"2015","journal-title":"Science"},{"issue":"04","key":"2021091309112897700_ref89","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0062249","article-title":"Conformational b-cell epitope prediction on antigen protein structures: A review of current algorithms and comparison with common binding site prediction methods","volume":"8","author":"Yao","year":"2013","journal-title":"PLoS ONE"},{"issue":"4","key":"2021091309112897700_ref90","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0062249","article-title":"Conformational b-cell epitope prediction on antigen protein structures: A review of current algorithms and comparison with common binding site prediction methods","volume":"8","author":"Yao","year":"2013","journal-title":"PLOS ONE"},{"issue":"3","key":"2021091309112897700_ref91","doi-asserted-by":"crossref","first-page":"100036","DOI":"10.1016\/j.xcrm.2020.100036","article-title":"Identification of sars-cov-2 vaccine epitopes predicted to induce long-term population-scale immunity","volume":"1","author":"Yarmarkovich","year":"2020","journal-title":"Cell Reports Medicine"},{"issue":"03","key":"2021091309112897700_ref92","article-title":"Advances in mrna vaccines for infectious diseases","volume":"10","author":"Zhang","year":"2019","journal-title":"Frontiers in Immunology"},{"key":"2021091309112897700_ref93","article-title":"Lineardesign: Efficient algorithms for optimized mrna sequence design","author":"He","year":"2020"},{"key":"2021091309112897700_ref94","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1016\/j.cell.2020.07.024","article-title":"A thermostable mrna vaccine against covid-19","volume":"182","author":"Zhang","year":"2020","journal-title":"Cell"}],"container-title":["Briefings in Functional Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bfg\/article-pdf\/20\/5\/289\/40349787\/elab027.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bfg\/article-pdf\/20\/5\/289\/40349787\/elab027.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,3]],"date-time":"2023-11-03T21:19:55Z","timestamp":1699046395000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bfg\/article\/20\/5\/289\/6292285"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,4]]},"references-count":94,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2021,6,4]]},"published-print":{"date-parts":[[2021,9,11]]}},"URL":"https:\/\/doi.org\/10.1093\/bfgp\/elab027","relation":{},"ISSN":["2041-2649","2041-2657"],"issn-type":[{"value":"2041-2649","type":"print"},{"value":"2041-2657","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,9]]},"published":{"date-parts":[[2021,6,4]]}}}