{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T19:04:46Z","timestamp":1793127886641,"version":"4.5.0"},"reference-count":59,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2020,8,1]],"date-time":"2020-08-01T00:00:00Z","timestamp":1596240000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,8,1]],"date-time":"2020-08-01T00:00:00Z","timestamp":1596240000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,8,26]],"date-time":"2021-08-26T00:00:00Z","timestamp":1629936000000},"content-version":"vor","delay-in-days":390,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100012728","name":"Frederick National Laboratory for Cancer Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012728","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Systems"],"published-print":{"date-parts":[[2020,8]]},"DOI":"10.1016\/j.cels.2020.06.009","type":"journal-article","created":{"date-parts":[[2020,7,27]],"date-time":"2020-07-27T11:08:43Z","timestamp":1595848123000},"page":"131-144.e6","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":72,"title":["Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions"],"prefix":"10.1016","volume":"11","author":[{"given":"Ge","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon","family":"Carter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trenton","family":"Bricken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddhartha","family":"Jain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathias","family":"Viard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Carrington","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David K.","family":"Gifford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cels.2020.06.009_bib1","article-title":"Design of multi epitope-based peptide vaccine against E protein of human 2019-nCoV: an immunoinformatics approach","author":"Abdelmageed","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib2","doi-asserted-by":"crossref","first-page":"254","DOI":"10.3390\/v12030254","article-title":"Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies","volume":"12","author":"Ahmed","year":"2020","journal-title":"Viruses"},{"key":"10.1016\/j.cels.2020.06.009_bib3","article-title":"Genome based evolutionary study of SARS-CoV-2 towards the prediction of epitope based chimeric vaccine","author":"Akhand","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib4","article-title":"Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by immuno-informatic analysis aiming to a suitable vaccine development","author":"Banerjee","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib5","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1002\/jmv.25698","article-title":"Immunoinformatics-aided identification of T\u00a0cell and B cell epitopes in the surface glycoprotein of 2019-nCoV","volume":"92","author":"Baruah","year":"2020","journal-title":"J.\u00a0Med. Virol."},{"key":"10.1016\/j.cels.2020.06.009_bib6","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1002\/jmv.25736","article-title":"Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): immunoinformatics approach","volume":"92","author":"Bhattacharya","year":"2020","journal-title":"J.\u00a0Med. Virol."},{"key":"10.1016\/j.cels.2020.06.009_bib7","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/1471-2105-7-153","article-title":"Predicting population coverage of T-cell epitope-based diagnostics and vaccines","volume":"7","author":"Bui","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.cels.2020.06.009_bib8","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1034\/j.1399-0039.2003.00112.x","article-title":"Sensitive quantitative predictions of peptide-MHC binding by a \u2018Query by Committee\u2019 artificial neural network approach","volume":"62","author":"Buus","year":"2003","journal-title":"Tissue Antigens"},{"key":"10.1016\/j.cels.2020.06.009_bib9","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1038\/358764a0","article-title":"Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size","volume":"358","author":"Chicz","year":"1992","journal-title":"Nature"},{"key":"10.1016\/j.cels.2020.06.009_bib10","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cels.2020.06.009_bib11","doi-asserted-by":"crossref","first-page":"104742","DOI":"10.1016\/j.antiviral.2020.104742","article-title":"The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade","volume":"176","author":"Coutard","year":"2020","journal-title":"Antiviral Res."},{"key":"10.1016\/j.cels.2020.06.009_bib12","doi-asserted-by":"crossref","first-page":"3112","DOI":"10.1073\/pnas.1815239116","article-title":"Most viral peptides displayed by class I MHC on infected cells are immunogenic","volume":"116","author":"Croft","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cels.2020.06.009_bib13","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1002\/gch2.1018","article-title":"Data, disease and diplomacy: GISAID\u2019s innovative contribution to global health","volume":"1","author":"Elbe","year":"2017","journal-title":"Global Chall."},{"key":"10.1016\/j.cels.2020.06.009_bib14","first-page":"921","article-title":"Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population","volume":"12","author":"Excoffier","year":"1995","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cels.2020.06.009_bib15","article-title":"Potential T-cell and B-cell epitopes of 2019-nCoV","author":"Fast","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib16","article-title":"The coding capacity of SARS-CoV-2","author":"Finkel","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib17","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.chom.2020.03.002","article-title":"A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2","volume":"27","author":"Grifoni","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cels.2020.06.009_bib18","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1016\/j.cell.2020.05.015","article-title":"Targets of T\u00a0cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals","volume":"181","author":"Grifoni","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.cels.2020.06.009_bib19","article-title":"Identification of potential vaccine candidates against SARS-CoV-2, a step forward to fight novel coronavirus 2019-nCoV: A reverse vaccinology approach","author":"Gupta","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib20","author":"Gupta"},{"key":"10.1016\/j.cels.2020.06.009_bib21","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cels.2020.06.009_bib23","doi-asserted-by":"crossref","first-page":"W173","DOI":"10.1093\/nar\/gkh424","article-title":"The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences","volume":"32","author":"Helmberg","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cels.2020.06.009_bib24","doi-asserted-by":"crossref","first-page":"4464","DOI":"10.1016\/j.vaccine.2020.04.034","article-title":"An effective CTL peptide vaccine for Ebola zaire based on survivors\u2019 CD8+ targeting of a particular nucleocapsid protein epitope with potential implications for COVID-19 vaccine design","volume":"38","author":"Herst","year":"2020","journal-title":"Vaccine"},{"key":"10.1016\/j.cels.2020.06.009_bib25","article-title":"Immuno-informatics characterization sars-cov-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine","author":"Ismail","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib26","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1111\/imm.12889","article-title":"Improved methods for predicting peptide binding affinity to MHC class II molecules","volume":"154","author":"Jensen","year":"2018","journal-title":"Immunology"},{"key":"10.1016\/j.cels.2020.06.009_bib27","doi-asserted-by":"crossref","first-page":"3360","DOI":"10.4049\/jimmunol.1700893","article-title":"NetMHCpan-4.0: improved peptide\u2013MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data","volume":"199","author":"Jurtz","year":"2017","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cels.2020.06.009_bib28","article-title":"Design of an epitope-based peptide vaccine against the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2): A vaccine informatics approach","author":"Khan","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib29","doi-asserted-by":"crossref","first-page":"145","DOI":"10.12688\/f1000research.22507.2","article-title":"In silico identification of vaccine targets for 2019-nCoV","volume":"9","author":"Lee","year":"2020","journal-title":"F1000Res."},{"key":"10.1016\/j.cels.2020.06.009_bib30","article-title":"Multi-epitope based peptide vaccine design against SARS-CoV-2 using its spike protein","author":"Mitra","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib31","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1080\/21645515.2015.1061159","article-title":"iVAX: an integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines","volume":"11","author":"Moise","year":"2015","journal-title":"Hum. Vaccin. Immunother."},{"key":"10.1016\/j.cels.2020.06.009_bib32","article-title":"Structure-based modeling of sars-cov-2 peptide\/hla-a02 antigens","author":"Nerli","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib33","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1110\/ps.0239403","article-title":"Reliable prediction of T-cell epitopes using neural networks with novel sequence representations","volume":"12","author":"Nielsen","year":"2003","journal-title":"Protein Sci."},{"key":"10.1016\/j.cels.2020.06.009_bib34","article-title":"A model of antigen processing improves prediction of MHC I-presented peptides","author":"O\u2019Donnell","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib35","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.cels.2018.05.014","article-title":"MHCflurry: open-source class I MHC binding affinity prediction","volume":"7","author":"O\u2019Donnell","year":"2018","journal-title":"Cell Syst."},{"key":"10.1016\/j.cels.2020.06.009_bib36","author":"World Health Organization"},{"key":"10.1016\/j.cels.2020.06.009_bib37","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J.\u00a0Mach. Learn. Res."},{"key":"10.1016\/j.cels.2020.06.009_bib38","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1146\/annurev-immunol-082119-124838","article-title":"T cell epitope predictions","volume":"38","author":"Peters","year":"2020","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.cels.2020.06.009_bib39","article-title":"Sequence-based prediction of vaccine targets for inducing T\u00a0cell responses to SARS-CoV-2 utilizing the bioinformatics predictor RECON","author":"Poran","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib40","article-title":"COVID-19 vaccine candidates: prediction and validation of 174 SARS-CoV-2 epitopes","author":"Prachar","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib41","article-title":"Insights into cross-species evolution of novel human coronavirus 2019-nCoV and defining immune determinants for vaccine development","author":"Ramaiah","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib42","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 Res."},{"key":"10.1016\/j.cels.2020.06.009_bib43","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1021\/acs.jproteome.9b00874","article-title":"Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data","volume":"19","author":"Reynisson","year":"2020","journal-title":"J.\u00a0Proteome Res."},{"key":"10.1016\/j.cels.2020.06.009_bib44","doi-asserted-by":"crossref","first-page":"561","DOI":"10.4049\/jimmunol.1300292","article-title":"HLA peptide length preferences control CD8+ T\u00a0cell responses","volume":"191","author":"Rist","year":"2013","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cels.2020.06.009_bib45","article-title":"In silico approach for designing of a multi-epitope based vaccine against novel coronavirus (SARS-COV-2)","author":"Saha","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib46","doi-asserted-by":"crossref","first-page":"5586","DOI":"10.4049\/jimmunol.153.12.5586","article-title":"The relationship between class I binding affinity and immunogenicity of potential cytotoxic T\u00a0cell epitopes","volume":"153","author":"Sette","year":"1994","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cels.2020.06.009_bib47","article-title":"Designing a multi-epitope peptide-based vaccine against SARS-CoV-2","author":"Singh","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib48","article-title":"Structural basis to design multi-epitope vaccines against Novel coronavirus 19 (COVID19) infection, the ongoing pandemic emergency: an in\u00a0silico approach","author":"Srivastava","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib50","article-title":"Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: immunoinformatics and in silico approaches","author":"Tahir ul Qamar","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib49","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.4049\/jimmunol.1501721","article-title":"The length distribution of class I\u2013restricted T\u00a0cell epitopes is determined by both peptide supply and MHC allele\u2013specific binding preference","volume":"196","author":"Trolle","year":"2016","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cels.2020.06.009_bib51","article-title":"Understanding the B and T\u00a0cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: a computational way to predict the immunogens","author":"Vashi","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib52","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cell.2020.02.058","article-title":"Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein","volume":"181","author":"Walls","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.cels.2020.06.009_bib53","first-page":"1","article-title":"A unique protease cleavage site predicted in the spike protein of the novel pneumonia coronavirus (2019-nCoV) potentially related to viral transmissibility","author":"Wang","year":"2020","journal-title":"Virol. Sin."},{"key":"10.1016\/j.cels.2020.06.009_bib54","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/nchembio.1403","article-title":"Adaptive immune activation: glycosylation does matter","volume":"9","author":"Wolfert","year":"2013","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/j.cels.2020.06.009_bib55","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"},{"key":"10.1016\/j.cels.2020.06.009_bib56","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. Rep. Med."},{"key":"10.1016\/j.cels.2020.06.009_bib57","article-title":"Design an efficient multi-epitope peptide vaccine candidate against sars-cov-2: an in\u00a0silico analysis","author":"Yazdani","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.cels.2020.06.009_bib58","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.cels.2019.05.004","article-title":"Quantification of uncertainty in peptide-MHC binding prediction improves high-affinity peptide selection for therapeutic design","volume":"9","author":"Zeng","year":"2019","journal-title":"Cell Syst"},{"key":"10.1016\/j.cels.2020.06.009_bib59","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.abb3405","article-title":"Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved \u03b1-ketoamide inhibitors","volume":"368","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.cels.2020.06.009_bib60","article-title":"Site-specific N-glycosylation characterization of recombinant SARS-CoV-2 spike proteins using high-resolution mass spectrometry","author":"Zhang","year":"2020","journal-title":"bioRxiv"}],"container-title":["Cell Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2405471220302386?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2405471220302386?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T07:17:36Z","timestamp":1762499856000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2405471220302386"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8]]},"references-count":59,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,8]]}},"alternative-id":["S2405471220302386"],"URL":"https:\/\/doi.org\/10.1016\/j.cels.2020.06.009","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.05.16.088989","asserted-by":"object"}]},"ISSN":["2405-4712"],"issn-type":[{"value":"2405-4712","type":"print"}],"subject":[],"published":{"date-parts":[[2020,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions","name":"articletitle","label":"Article Title"},{"value":"Cell Systems","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cels.2020.06.009","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}