{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,7]],"date-time":"2026-11-07T07:49:51Z","timestamp":1794037791599,"version":"4.8.0"},"reference-count":54,"publisher":"Frontiers Media SA","funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007190","name":"Unilever","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007190","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000833","name":"Rosetrees Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000833","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"DOI":"10.3389\/fimmu.2017.01267","type":"journal-article","created":{"date-parts":[[2017,10,12]],"date-time":"2017-10-12T00:15:43Z","timestamp":1507767343000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":131,"title":["Quantitative Characterization of the T Cell Receptor Repertoire of Na\u00efve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile"],"prefix":"10.3389","volume":"8","author":[{"given":"Theres","family":"Oakes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Heather","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharine","family":"Best","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Byng-Maddick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Connor","family":"Husovsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mazlina","family":"Ismail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kroopa","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gavin","family":"Maxwell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahdad","family":"Noursadeghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Riddell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tabea","family":"Ruehl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolin T.","family":"Turner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Imran","family":"Uddin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benny","family":"Chain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2017,10,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ygeno.2015.11.003","article-title":"The sequence of sequencers: the history of sequencing DNA","volume":"107","author":"Heather","year":"2015","journal-title":"Genomics"},{"key":"B2","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1038\/cmi.2014.134","article-title":"\u03b1\u03b2 T cell receptors as predictors of health and disease","volume":"12","author":"Attaf","year":"2015","journal-title":"Cell Mol Immunol"},{"key":"B3","doi-asserted-by":"publisher","first-page":"15865","DOI":"10.1073\/pnas.1203916109","article-title":"Chromatin conformation governs T-cell receptor J\u03b2 gene segment usage","volume":"109","author":"Ndifon","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B4","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.coi.2013.09.017","article-title":"Immunosequencing: applications of immune repertoire deep sequencing","volume":"25","author":"Robins","year":"2013","journal-title":"Curr Opin Immunol"},{"key":"B5","doi-asserted-by":"publisher","first-page":"2733","DOI":"10.1016\/j.celrep.2016.02.056","article-title":"System-wide analysis of the T cell response","volume":"14","author":"Covacu","year":"2016","journal-title":"Cell Rep"},{"key":"B6","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/gene.2016.9","article-title":"Current status and recent advances of next generation sequencing techniques in immunological repertoire","volume":"17","author":"Hou","year":"2016","journal-title":"Genes Immun"},{"key":"B7","doi-asserted-by":"publisher","first-page":"413","DOI":"10.3389\/fimmu.2013.00413","article-title":"The past, present, and future of immune repertoire biology \u2013 the rise of next-generation repertoire analysis","volume":"4","author":"Six","year":"2013","journal-title":"Front Immunol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"bbw138","DOI":"10.1093\/bib\/bbw138","article-title":"High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities","author":"Heather","year":"2017","journal-title":"Brief Bioinform"},{"key":"B9","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/0003-2697(86)90606-8","article-title":"Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase","volume":"158","author":"Tessier","year":"1986","journal-title":"Anal Biochem"},{"key":"B10","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1126\/science.1170020","article-title":"High-throughput sequencing of the zebrafish antibody repertoire","volume":"324","author":"Weinstein","year":"2009","journal-title":"Science"},{"key":"B11","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/nmeth.2960","article-title":"Towards error-free profiling of immune repertoires","volume":"11","author":"Shugay","year":"2014","journal-title":"Nat Methods"},{"key":"B12","doi-asserted-by":"publisher","first-page":"456","DOI":"10.3389\/fimmu.2013.00456","article-title":"Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling","volume":"4","author":"Mamedov","year":"2013","journal-title":"Front Immunol"},{"key":"B13","doi-asserted-by":"publisher","first-page":"14629","DOI":"10.1038\/srep14629","article-title":"Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding","volume":"5","author":"Best","year":"2015","journal-title":"Sci Rep"},{"key":"B14","doi-asserted-by":"publisher","first-page":"8218","DOI":"10.4049\/jimmunol.175.12.8218","article-title":"Cytomegalovirus-specific CD4+ T cells in healthy carriers are continuously driven to replicative exhaustion","volume":"175","author":"Fletcher","year":"2005","journal-title":"J Immunol"},{"key":"B15","doi-asserted-by":"crossref","first-page":"394","DOI":"10.4049\/jimmunol.142.2.394","article-title":"Delineation of several DR-restricted tetanus toxin T cell epitopes","volume":"142","author":"Demotz","year":"1989","journal-title":"J Immunol"},{"key":"B16","doi-asserted-by":"publisher","first-page":"3253","DOI":"10.1002\/eji.201141841","article-title":"Transcriptional profiling of innate and adaptive human immune responses to mycobacteria in the tuberculin skin test","volume":"41","author":"Tomlinson","year":"2011","journal-title":"Eur J Immunol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"e1005469","DOI":"10.1371\/journal.ppat.1005469","article-title":"In vivo molecular dissection of the effects of HIV-1 in active tuberculosis","volume":"12","author":"Bell","year":"2016","journal-title":"PLoS Pathog"},{"key":"B18","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1182\/blood-2006-03-013318","article-title":"Efficiency of T-cell receptor expression in dual-specific T cells is controlled by the intrinsic qualities of the TCR chains within the TCR-CD3 complex","volume":"109","author":"Heemskerk","year":"2007","journal-title":"Blood"},{"key":"B19","doi-asserted-by":"publisher","first-page":"9823","DOI":"10.1073\/pnas.89.20.9823","article-title":"Ligation-anchored PCR: a simple amplification technique with single-sided specificity","volume":"89","author":"Troutt","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B20","doi-asserted-by":"publisher","first-page":"5227","DOI":"10.1093\/nar\/19.19.5227","article-title":"Oligodeoxyribonucleotide ligation to single-stranded cDNAs: a new tool for cloning 5' ends of mRNAs and for constructing cDNA libraries by in vitro amplification","volume":"19","author":"Edwards","year":"1991","journal-title":"Nucleic Acids Res"},{"key":"B21","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1146\/annurev.iy.05.040187.003101","article-title":"Genes of the T-cell antigen receptor in normal and malignant T cells","volume":"5","author":"Toyonaga","year":"1987","journal-title":"Annu Rev Immunol"},{"key":"B22","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1093\/bioinformatics\/btt004","article-title":"Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine","volume":"29","author":"Thomas","year":"2013","journal-title":"Bioinformatics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1145\/360825.360855","article-title":"Efficient string matching: an aid to bibliographic search","volume":"18","author":"Aho","year":"1975","journal-title":"Commun ACM"},{"key":"B24","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/S0022-1759(02)00336-8","article-title":"Tracking T cell clonotypes in complex T lymphocyte populations by real-time quantitative PCR using fluorogenic complementarity-determining region-3-specific probes","volume":"270","author":"Gallard","year":"2002","journal-title":"J Immunol Methods"},{"key":"B25","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.4049\/jimmunol.141.5.1769","article-title":"Transcription of T cell antigen receptor genes is induced by protein kinase C activation","volume":"141","author":"Lindsten","year":"1988","journal-title":"J Immunol"},{"key":"B26","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/0006-291X(92)90789-N","article-title":"Correlation between up-regulation of lymphokine mRNA and down-regulation of TcR, CD4, CD8 and lck mRNA as shown by the effect of CsA on activated T lymphocytes","volume":"186","author":"Paillard","year":"1992","journal-title":"Biochem Biophys Res Commun"},{"key":"B27","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1002\/j.1460-2075.1990.tb08312.x","article-title":"Transcriptional and post-transcriptional regulation of TcR, CD4 and CD8 gene expression during activation of normal human T lymphocytes","volume":"9","author":"Paillard","year":"1990","journal-title":"EMBO J"},{"key":"B28","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1002\/eji.1830260429","article-title":"The expansion and selection of T cell receptor \u03b1\u03b2 intestinal intraepithelial T cell clones","volume":"26","author":"Regnault","year":"1996","journal-title":"Eur J Immunol"},{"key":"B29","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/nmeth.3800","article-title":"T cell fate and clonality inference from single-cell transcriptomes","volume":"13","author":"Stubbington","year":"2016","journal-title":"Nat Methods"},{"key":"B30","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1186\/s13073-016-0335-7","article-title":"Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq","volume":"8","author":"Redmond","year":"2016","journal-title":"Genome Med"},{"key":"B31","doi-asserted-by":"publisher","first-page":"13139","DOI":"10.1073\/pnas.1409155111","article-title":"Diversity and clonal selection in the human T-cell repertoire","volume":"111","author":"Qi","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B32","doi-asserted-by":"publisher","first-page":"4099","DOI":"10.1182\/blood-2009-04-217604","article-title":"Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells","volume":"114","author":"Robins","year":"2009","journal-title":"Blood"},{"key":"B33","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.imlet.2010.06.011","article-title":"Human T-cell memory consists mainly of unexpanded clones","volume":"133","author":"Klarenbeek","year":"2010","journal-title":"Immunol Lett"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1073\/pnas.0913939107","article-title":"High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets","volume":"107","author":"Wang","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B35","doi-asserted-by":"publisher","first-page":"2093","DOI":"10.4049\/jimmunol.1100978","article-title":"Reversible senescence in human CD4+CD45RA+CD27-memory T cells","volume":"187","author":"Di Mitri","year":"2011","journal-title":"J Immunol"},{"key":"B36","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1073\/pnas.1512977112","article-title":"Fluctuating fitness shapes the clone-size distribution of immune repertoires","volume":"113","author":"Desponds","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B37","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1016\/j.bbmt.2012.12.004","article-title":"Fractal organization of the human T cell repertoire in health and after stem cell transplantation","volume":"19","author":"Meier","year":"2013","journal-title":"Biol Blood Marrow Transplant"},{"key":"B38","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/0303-2647(96)01618-8","article-title":"Zipf-scaling behavior in the immune system","volume":"39","author":"Burgos","year":"1996","journal-title":"Biosystems"},{"key":"B39","doi-asserted-by":"publisher","first-page":"e108658","DOI":"10.1371\/journal.pone.0108658","article-title":"Assessing T cell clonal size distribution: a non-parametric approach","volume":"9","author":"Bolkhovskaya","year":"2014","journal-title":"PLoS One"},{"key":"B40","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1140\/epjb\/e2007-00219-y","article-title":"Parameter estimation for power-law distributions by maximum likelihood methods","volume":"58","author":"Bauke","year":"2007","journal-title":"Eur Phys J B"},{"key":"B41","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1137\/070710111","article-title":"Power-law distributions in empirical data","volume":"51","author":"Clauset","year":"2009","journal-title":"SIAM Rev"},{"key":"B42","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1038\/ni.3483","article-title":"Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses","volume":"17","author":"Pulko","year":"2016","journal-title":"Nat Immunol"},{"key":"B43","doi-asserted-by":"publisher","first-page":"5363","DOI":"10.4049\/jimmunol.1203267","article-title":"Age-associated increase of low-avidity cytomegalovirus-specific CD8+ T cells that re-express CD45RA","volume":"190","author":"Griffiths","year":"2013","journal-title":"J Immunol"},{"key":"B44","doi-asserted-by":"publisher","first-page":"20140291","DOI":"10.1098\/rstb.2014.0291","article-title":"Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach","volume":"370","author":"Laydon","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"B45","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1016\/j.celrep.2017.03.072","article-title":"Sequence and structural analyses reveal distinct and highly diverse human CD8 + TCR repertoires to immunodominant viral antigens","volume":"19","author":"Chen","year":"2017","journal-title":"Cell Rep"},{"key":"B46","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat Methods"},{"key":"B47","doi-asserted-by":"publisher","first-page":"3098","DOI":"10.1093\/bioinformatics\/btw339","article-title":"RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data","volume":"32","author":"Gerritsen","year":"2016","journal-title":"Bioinformatics"},{"key":"B48","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1038\/nri2619","article-title":"The precursors of memory: models and controversies","volume":"9","author":"Ahmed","year":"2009","journal-title":"Nat Rev Immunol"},{"key":"B49","doi-asserted-by":"publisher","first-page":"5782","DOI":"10.4049\/jimmunol.164.11.5782","article-title":"Size estimate of the alpha beta TCR repertoire of naive mouse splenocytes","volume":"164","author":"Casrouge","year":"2000","journal-title":"J Immunol"},{"key":"B50","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.molimm.2017.01.026","article-title":"A new mechanism shapes the na\u00efve CD8 + T cell repertoire: the selection for full diversity","volume":"85","author":"Gon\u00e7alves","year":"2017","journal-title":"Mol Immunol"},{"key":"B51","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.jtbi.2015.10.016","article-title":"How many TCR clonotypes does a body maintain?","volume":"389","author":"Lythe","year":"2016","journal-title":"J Theor Biol"},{"key":"B52","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1126\/science.1124228","article-title":"Naive and memory CD4+ T cell survival controlled by clonal abundance","volume":"312","author":"Hataye","year":"2006","journal-title":"Science"},{"key":"B53","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1126\/science.1235454","article-title":"Disparate individual fates compose robust CD8+ T cell immunity","volume":"340","author":"Buchholz","year":"2013","journal-title":"Science"},{"key":"B54","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1016\/j.immuni.2007.10.012","article-title":"A single naive CD8+ T cell precursor can develop into diverse effector and memory subsets","volume":"27","author":"Stemberger","year":"2007","journal-title":"Immunity"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fimmu.2017.01267\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,26]],"date-time":"2023-08-26T20:49:52Z","timestamp":1693082992000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fimmu.2017.01267\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,12]]},"references-count":54,"alternative-id":["10.3389\/fimmu.2017.01267"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2017.01267","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,12]]},"article-number":"1267"}}