{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T18:53:21Z","timestamp":1793300001882,"version":"4.5.0"},"reference-count":77,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2013,10,24]],"date-time":"2013-10-24T00:00:00Z","timestamp":1382572800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003266","type":"journal-article","created":{"date-parts":[[2013,10,24]],"date-time":"2013-10-24T22:11:09Z","timestamp":1382652669000},"page":"e1003266","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":862,"title":["Properties of MHC Class I Presented Peptides That Enhance Immunogenicity"],"prefix":"10.1371","volume":"9","author":[{"given":"Jorg J. A.","family":"Calis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matt","family":"Maybeno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason A.","family":"Greenbaum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Weiskopf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aruna D.","family":"De Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Sette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Can","family":"Ke\u015fmir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bjoern","family":"Peters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2013,10,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1084\/jem.20001021","article-title":"Estimating the precursor frequency of naive antigen-specific CD8 T cells","volume":"195","author":"JN Blattman","year":"2002","journal-title":"J Exp Med"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1126\/science.1124228","article-title":"Naive and memory CD4+ T cell survival controlled by clonal abundance","volume":"312","author":"J Hataye","year":"2006","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.4049\/jimmunol.181.3.2124","article-title":"Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance","volume":"181","author":"MF Kotturi","year":"2008","journal-title":"J Immunol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"4337","DOI":"10.4049\/jimmunol.0901607","article-title":"Quantitating T cell cross-reactivity for unrelated peptide antigens","volume":"183","author":"J Ishizuka","year":"2009","journal-title":"J Immunol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.immuni.2008.04.010","article-title":"Endogenous naive CD8+ T cell precursor frequency regulates primary and memory responses to infection","volume":"28","author":"JJ Obar","year":"2008","journal-title":"Immunity"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1182\/blood-2009-10-251124","article-title":"Enumeration of human antigen-specific naive CD8+ T cells reveals conserved precursor frequencies","volume":"115","author":"C Alanio","year":"2010","journal-title":"Blood"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s002510050595","article-title":"SYFPEITHI: database for MHC ligands and peptide motifs","volume":"50","author":"H Rammensee","year":"1999","journal-title":"Immunogenetics"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e65","DOI":"10.1371\/journal.pcbi.0020065","article-title":"A community resource benchmarking predictions of peptide binding to MHC-I molecules","volume":"2","author":"B Peters","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref9","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":"KC Parker","year":"1994","journal-title":"J Immunol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1186\/1471-2105-8-424","article-title":"Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction","volume":"8","author":"MV Larsen","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1093\/bioinformatics\/btg247","article-title":"Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules","volume":"19","author":"B Peters","year":"2003","journal-title":"Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1093\/bioinformatics\/bth100","article-title":"Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach","volume":"20","author":"M Nielsen","year":"2004","journal-title":"Bioinformatics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e796","DOI":"10.1371\/journal.pone.0000796","article-title":"NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence","volume":"2","author":"M Nielsen","year":"2007","journal-title":"PLoS ONE"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00251-008-0341-z","article-title":"NetMHCpan, a method for MHC class I binding prediction beyond humans","volume":"61","author":"I Hoof","year":"2009","journal-title":"Immunogenetics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/978-1-60327-118-9_5","article-title":"SYFPEITHI: database for searching and T-cell epitope prediction","volume":"409","author":"MM Schuler","year":"2007","journal-title":"Methods Mol Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"21140","DOI":"10.1074\/jbc.M000740200","article-title":"The human 26 S and 20 S proteasomes generate overlapping but different sets of peptide fragments from a model protein substrate","volume":"275","author":"NP Emmerich","year":"2000","journal-title":"J Biol Chem"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1084\/jem.194.1.1","article-title":"Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products","volume":"194","author":"RE Toes","year":"2001","journal-title":"J Exp Med"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.4049\/jimmunol.172.2.1083","article-title":"Quantitative analysis of prionprotein degradation by constitutive and immuno-20S proteasomes indicates differences correlated with disease susceptibility","volume":"172","author":"S Tenzer","year":"2004","journal-title":"J Immunol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"8976","DOI":"10.1073\/pnas.94.17.8976","article-title":"Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries","volume":"94","author":"S Uebel","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/S0161-5890(98)00059-5","article-title":"Substrate selection by transporters associated with antigen processing occurs during peptide binding to TAP","volume":"35","author":"B Gubler","year":"1998","journal-title":"Mol Immunol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1007\/s00018-011-0657-y","article-title":"The role of the proteasome in the generation of MHC class I ligands and immune responses","volume":"68","author":"EJAM Sijts","year":"2011","journal-title":"Cell Mol Life Sci"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S1074-7613(02)00511-3","article-title":"Peptide diffusion, protection, and degradation in nuclear and cytoplasmic compartments before antigen presentation by MHC class I","volume":"18","author":"E Reits","year":"2003","journal-title":"Immunity"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1093\/protein\/15.4.287","article-title":"Prediction of proteasome cleavage motifs by neural networks","volume":"15","author":"C Kesmir","year":"2002","journal-title":"Protein Engineering"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.4049\/jimmunol.171.4.1741","article-title":"Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors","volume":"171","author":"B Peters","year":"2003","journal-title":"J Immunol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1007\/s00018-005-4528-2","article-title":"Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding","volume":"62","author":"S Tenzer","year":"2005","journal-title":"Cell Mol Life Sci"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1097\/QAD.0b013e3282f15622","article-title":"An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs","volume":"22","author":"IM Schellens","year":"2008","journal-title":"AIDS"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1084\/jem.187.10.1647-b","article-title":"Protective immunity does not correlate with the hierarchy of virus-specific cytotoxic T cell responses to naturally processed peptides","volume":"187","author":"A Gallimore","year":"1998","journal-title":"J Exp Med"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"7680","DOI":"10.4049\/jimmunol.177.11.7680","article-title":"Immunoproteasome subunit deficiencies impact differentially on two immunodominant influenza virus-specific CD8+ T cell responses","volume":"177","author":"KC Pang","year":"2006","journal-title":"J Immunol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/ni.1728","article-title":"Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance","volume":"10","author":"S Tenzer","year":"2009","journal-title":"Nat Immunol"},{"key":"ref30","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 cell epitopes","volume":"153","author":"A Sette","year":"1994","journal-title":"J Immunol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.immuni.2005.05.009","article-title":"The kinetic stability of MHC class II:peptide complexes is a key parameter that dictates immunodominance","volume":"23","author":"CA Lazarski","year":"2005","journal-title":"Immunity"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1073\/pnas.0510429103","article-title":"A virus-specific CD8+ T cell immunodominance hierarchy determined by antigen dose and precursor frequencies","volume":"103","author":"NLL Gruta","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1084\/jem.193.11.1319","article-title":"Immunoproteasomes shape immunodominance hierarchies of antiviral CD8(+) T cells at the levels of T cell repertoire and presentation of viral antigens","volume":"193","author":"W Chen","year":"2001","journal-title":"J Exp Med"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1084\/jem.20022151","article-title":"Differential antigen presentation regulates the changing patterns of CD8+ T cell immunodominance in primary and secondary influenza virus infections","volume":"198","author":"SR Crowe","year":"2003","journal-title":"J Exp Med"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"13980","DOI":"10.1073\/pnas.0506768102","article-title":"HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation","volume":"102","author":"C Oseroff","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","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":"M Moutaftsi","year":"2006","journal-title":"Nat Biotechnol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e823","DOI":"10.1371\/journal.pone.0000823","article-title":"Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins","volume":"2","author":"M Rolland","year":"2007","journal-title":"PLoS One"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"e1831","DOI":"10.1371\/journal.pone.0001831","article-title":"Amino acid similarity accounts for T cell cross-reactivity and for \u201choles\u201d in the T cell repertoire","volume":"3","author":"S Frankild","year":"2008","journal-title":"PLoS ONE"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"59","DOI":"10.4049\/jimmunol.0804046","article-title":"Restricted autoantigen recognition associated with deletional and adaptive regulatory mechanisms","volume":"183","author":"JA Gebe","year":"2009","journal-title":"J Immunol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1002412","DOI":"10.1371\/journal.pcbi.1002412","article-title":"Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire","volume":"8","author":"JJA Calis","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1006\/jtbi.1994.1160","article-title":"T cell repertoires and competitive exclusion","volume":"169","author":"RJ de Boer","year":"1994","journal-title":"J Theor Biol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.immuni.2011.07.010","article-title":"CD8(+) T cells: foot soldiers of the immune system","volume":"35","author":"N Zhang","year":"2011","journal-title":"Immunity"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"7890","DOI":"10.4049\/jimmunol.178.12.7890","article-title":"A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection","volume":"178","author":"E Assarsson","year":"2007","journal-title":"J Immunol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e1000695","DOI":"10.1371\/journal.ppat.1000695","article-title":"A multivalent and cross-protective vaccine strategy against arenaviruses associated with human disease","volume":"5","author":"MF Kotturi","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"D854","DOI":"10.1093\/nar\/gkp1004","article-title":"The immune epitope database 2.0","volume":"38","author":"R Vita","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genomewide studies","volume":"100","author":"JD Storey","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"D202","DOI":"10.1093\/nar\/gkm998","article-title":"AAindex: amino acid index database, progress report 2008","volume":"36","author":"S Kawashima","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/j.coi.2009.07.008","article-title":"Structural alterations in peptide-MHC recognition by self-reactive T cell receptors","volume":"21","author":"KW Wucherpfennig","year":"2009","journal-title":"Curr Opin Immunol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1146\/annurev.immunol.23.021704.115658","article-title":"How TCRs bind MHCs, peptides, and coreceptors","volume":"24","author":"MG Rudolph","year":"2006","journal-title":"Annu Rev Immunol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"5389","DOI":"10.4049\/jimmunol.162.9.5389","article-title":"Peptide recognition by two HLA-A2\/Tax11-19-specific T cell clones in relationship to their MHC\/peptide\/TCR crystal structures","volume":"162","author":"S Hausmann","year":"1999","journal-title":"J Immunol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1084\/jem.20041251","article-title":"T cell cross-reactivity and conformational changes during TCR engagement","volume":"200","author":"JK Lee","year":"2004","journal-title":"J Exp Med"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1002\/eji.200425903","article-title":"Discovery and characterization of highly immunogenic and broadly recognized mimics of the HIV-1 CTL epitope Gag77-85","volume":"35","author":"C Boggiano","year":"2005","journal-title":"Eur J Immunol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1084\/jem.20050864","article-title":"The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation","volume":"202","author":"FE Tynan","year":"2005","journal-title":"J Exp Med"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"5383","DOI":"10.4049\/jimmunol.0903516","article-title":"Interdisciplinary analysis of HIV-specific CD8+ T cell responses against variant epitopes reveals restricted TCR promiscuity","volume":"184","author":"I Hoof","year":"2010","journal-title":"J Immunol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"4268","DOI":"10.4049\/jimmunol.1101970","article-title":"Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design","volume":"187","author":"D Weiskopf","year":"2011","journal-title":"J Immunol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"E2046","DOI":"10.1073\/pnas.1305227110","article-title":"Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells","volume":"110","author":"D Weiskopf","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1745-7580-5-3","article-title":"Of mice and humans: how good are HLA transgenic mice as a model of human immune responses?","volume":"5","author":"MF Kotturi","year":"2009","journal-title":"Immunome Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1002\/eji.201040339","article-title":"MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation","volume":"40","author":"JJA Calis","year":"2010","journal-title":"Eur J Immunol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.4049\/jimmunol.172.4.2324","article-title":"The impact of self-tolerance on the polyclonal CD8+ T cell repertoire","volume":"172","author":"HWHG Kessels","year":"2004","journal-title":"J Immunol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1016\/S1074-7613(94)80017-0","article-title":"Development of high potency universal DR-restricted helper epitopes by modification of high affinity DR-blocking peptides","volume":"1","author":"J Alexander","year":"1994","journal-title":"Immunity"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1007\/s00251-002-0530-0","article-title":"Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution","volume":"54","author":"A Sette","year":"2003","journal-title":"Immunogenetics"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1186\/1471-2105-12-446","article-title":"POPISK: T-cell reactivity prediction using support vector machines and string kernels","volume":"12","author":"CW Tung","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.cell.2005.05.013","article-title":"How the T cell repertoire becomes peptide and MHC specific","volume":"122","author":"ES Huseby","year":"2005","journal-title":"Cell"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"7244","DOI":"10.4049\/jimmunol.0902313","article-title":"MHC drives TCR repertoire shaping, but not maturation, in recent thymic emigrants","volume":"183","author":"EG Houston","year":"2009","journal-title":"J Immunol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"6731","DOI":"10.4049\/jimmunol.1000295","article-title":"Impact of TCR reactivity and HLA phenotype on naive CD8 T cell frequency in humans","volume":"184","author":"F Legoux","year":"2010","journal-title":"J Immunol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1016\/j.molimm.2007.02.017","article-title":"Analysis of the TCR alpha-chain rearrangement profile in human T lymphocytes","volume":"44","author":"P Fuschiotti","year":"2007","journal-title":"Mol Immunol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"19414","DOI":"10.1073\/pnas.1010586107","article-title":"Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire","volume":"107","author":"MF Quigley","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref68","article-title":"Half of the T-cell repertoire combinatorial diversity is genetically determined in humans and humanized mice","author":"HP Pham","year":"2011","journal-title":"Eur J Immunol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1038\/nature07812","article-title":"Germline-encoded amino acids in the alphabeta T-cell receptor control thymic selection","volume":"458","author":"JP Scott-Browne","year":"2009","journal-title":"Nature"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/ni.f.219","article-title":"The molecular basis of TCR germline bias for MHC is surprisingly simple","volume":"10","author":"KC Garcia","year":"2009","journal-title":"Nat Immunol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1038\/nm.2197","article-title":"Transgenic mice with a diverse human T cell antigen receptor repertoire","volume":"16","author":"LP Li","year":"2010","journal-title":"Nat Med"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1089\/088282403322396064","article-title":"A survival game of hide and seek: cytomegaloviruses and MHC class I antigen presentation pathways","volume":"16","author":"S Basta","year":"2003","journal-title":"Viral Immunol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"e12303","DOI":"10.1371\/journal.pone.0012303","article-title":"Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing","volume":"5","author":"W Fischer","year":"2010","journal-title":"PLoS One"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1002\/(SICI)1521-4141(199802)28:02<625::AID-IMMU625>3.0.CO;2-I","article-title":"Differential processing of influenza nucleoprotein in human and mouse cells","volume":"28","author":"VM Braud","year":"1998","journal-title":"Eur J Immunol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSIBLAST: a new generation of protein database search programs","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref76","unstructured":"R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.R-project.org\" xlink:type=\"simple\">http:\/\/www.R-project.org<\/ext-link>. ISBN 3-900051-07-0."},{"key":"ref77","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1145\/168173.168412","article-title":"A remark on algorithm 643: FEXACT: an algorithm for performing Fisher&apos;s exact test in r\u00d7c contingency tables","volume":"19","author":"DB Clarkson","year":"1993","journal-title":"ACM Trans Math Softw"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003266","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T11:53:03Z","timestamp":1688557983000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003266"}},"subtitle":[],"editor":[{"given":"Becca","family":"Asquith","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,10,24]]},"references-count":77,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2013,10,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003266","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10,24]]}}}