{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T09:04:20Z","timestamp":1783242260625,"version":"3.54.6"},"reference-count":106,"publisher":"Oxford University Press (OUP)","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Brief Bioinform"],"DOI":"10.1093\/bib\/bbw138","type":"journal-article","created":{"date-parts":[[2016,12,8]],"date-time":"2016-12-08T12:05:45Z","timestamp":1481198745000},"page":"bbw138","source":"Crossref","is-referenced-by-count":51,"title":["High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities"],"prefix":"10.1093","author":[{"given":"James M.","family":"Heather","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mazlina","family":"Ismail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theres","family":"Oakes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benny","family":"Chain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,1,10]]},"reference":[{"key":"2017011117202254000_bbw138v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/0167-5699(92)90043-7"},{"key":"2017011117202254000_bbw138v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.coi.2009.03.009"},{"key":"2017011117202254000_bbw138v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/S0968-0004(00)01606-6"},{"key":"2017011117202254000_bbw138v1.4","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.molimm.2016.07.002","article-title":"T cell receptor diversity in the human thymus","volume":"76","author":"Vanhanen","year":"2016","journal-title":"Mol Immunol"},{"key":"2017011117202254000_bbw138v1.5","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2009-04-217604"},{"key":"2017011117202254000_bbw138v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2015.11.003"},{"key":"2017011117202254000_bbw138v1.7","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2013.00185"},{"key":"2017011117202254000_bbw138v1.8","doi-asserted-by":"crossref","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":"2017011117202254000_bbw138v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.coi.2013.09.017"},{"key":"2017011117202254000_bbw138v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2014.09.004"},{"key":"2017011117202254000_bbw138v1.11","doi-asserted-by":"crossref","first-page":"242.","DOI":"10.5045\/br.2013.48.4.242","article-title":"Next generation sequencing: new tools in immunology and hematology","volume":"48","author":"Mori","year":"2013","journal-title":"Blood Res"},{"key":"2017011117202254000_bbw138v1.12","doi-asserted-by":"publisher","DOI":"10.1186\/gm502"},{"key":"2017011117202254000_bbw138v1.13","doi-asserted-by":"crossref","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":"2017011117202254000_bbw138v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/nature07517"},{"key":"2017011117202254000_bbw138v1.15","doi-asserted-by":"crossref","unstructured":"Heather JM Best K Oakes T , . Dynamic perturbations of the T-cell receptor repertoire in chronic hiv infection and following antiretroviral therapy. Front Immunol 2016; 6:","DOI":"10.3389\/fimmu.2015.00644"},{"key":"2017011117202254000_bbw138v1.16","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2013.00185"},{"key":"2017011117202254000_bbw138v1.17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh412"},{"key":"2017011117202254000_bbw138v1.18","first-page":"26","article-title":"IMGT\/HIGHV-QUEST: the IMGT web portal for immunoglobulin (Ig) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing","volume":"8","author":"Alamyar","year":"2012","journal-title":"Immunome Res"},{"key":"2017011117202254000_bbw138v1.19","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1093\/nar\/gkt382","article-title":"IgBLAST: an immunoglobulin variable domain sequence analysis tool","volume":"41","author":"Ye","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2017011117202254000_bbw138v1.20","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt004"},{"key":"2017011117202254000_bbw138v1.21","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-409"},{"key":"2017011117202254000_bbw138v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3364"},{"key":"2017011117202254000_bbw138v1.23","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.115.176735"},{"key":"2017011117202254000_bbw138v1.24","doi-asserted-by":"crossref","first-page":"btv309","DOI":"10.1093\/bioinformatics\/btv309","article-title":"IMSEQ\u2014a fast and error aware approach to immunogenetic sequence analysis","volume":"31","author":"Kuchenbecker","year":"2015","journal-title":"Bioinformatics"},{"key":"2017011117202254000_bbw138v1.25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1016"},{"key":"2017011117202254000_bbw138v1.26","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1400711"},{"key":"2017011117202254000_bbw138v1.27","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw339"},{"key":"2017011117202254000_bbw138v1.28","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1186\/s12859-016-1304-2","article-title":"TRIg: a robust alignment pipeline for non- regular T-cell receptor and immunoglobulin sequences","volume":"17","author":"Hung","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2017011117202254000_bbw138v1.29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/26.1.297"},{"key":"2017011117202254000_bbw138v1.30","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki010"},{"key":"2017011117202254000_bbw138v1.31","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn838"},{"key":"2017011117202254000_bbw138v1.32","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn316"},{"key":"2017011117202254000_bbw138v1.33","doi-asserted-by":"crossref","first-page":"2333.","DOI":"10.1038\/ncomms3333","article-title":"IMGT\/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling","volume":"4","author":"Li","year":"2013","journal-title":"Nat Commun"},{"key":"2017011117202254000_bbw138v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"2017011117202254000_bbw138v1.35","doi-asserted-by":"crossref","first-page":"3643","DOI":"10.3892\/ol.2016.4465","article-title":"Characterization of the T cell repertoire by deep T cell receptor sequencing in tissues and blood from patients with advanced colorectal cancer","volume":"11","author":"Tamura","year":"2016","journal-title":"Oncol Lett"},{"key":"2017011117202254000_bbw138v1.36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv309"},{"key":"2017011117202254000_bbw138v1.37","doi-asserted-by":"publisher","DOI":"10.1145\/360825.360855"},{"key":"2017011117202254000_bbw138v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2555"},{"key":"2017011117202254000_bbw138v1.39","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-13-3464"},{"key":"2017011117202254000_bbw138v1.40","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/ng.3581","article-title":"Landscape of tumor-infiltrating T cell repertoire of human cancers","volume":"48","author":"Li","year":"2016","journal-title":"Nat Genet"},{"key":"2017011117202254000_bbw138v1.41","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3800"},{"key":"2017011117202254000_bbw138v1.42","doi-asserted-by":"crossref","first-page":"125.","DOI":"10.1186\/s13073-015-0248-x","article-title":"Profiling tissue-resident T cell repertoires by RNA sequencing","volume":"7","author":"Brown","year":"2015","journal-title":"Genome Med"},{"key":"2017011117202254000_bbw138v1.43","doi-asserted-by":"crossref","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":"2017011117202254000_bbw138v1.44","doi-asserted-by":"publisher","DOI":"10.1038\/icb.2016.16"},{"key":"2017011117202254000_bbw138v1.45","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80195-6"},{"key":"2017011117202254000_bbw138v1.46","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp163"},{"key":"2017011117202254000_bbw138v1.47","unstructured":"Pag\u00e8s H Aboyoun P Gentleman R , . Biostrings: String Objects Representing Biological Sequences, and Matching Algorithms. R package version 2.42.1, 2016."},{"key":"2017011117202254000_bbw138v1.48","doi-asserted-by":"crossref","first-page":"22.","DOI":"10.3389\/fimmu.2014.00022","article-title":"Immunoglobulin and T Cell Receptor Genes: IMGT(\u00ae) and the Birth and Rise of Immunoinformatics","volume":"5","author":"Lefranc","year":"2014","journal-title":"Front Immunol"},{"key":"2017011117202254000_bbw138v1.49","doi-asserted-by":"publisher","DOI":"10.1016\/S0145-305X(02)00039-3"},{"key":"2017011117202254000_bbw138v1.50","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1105422108"},{"key":"2017011117202254000_bbw138v1.51","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/287430"},{"key":"2017011117202254000_bbw138v1.52","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":"2017011117202254000_bbw138v1.53","doi-asserted-by":"publisher","DOI":"10.1101\/gr.115428.110"},{"key":"2017011117202254000_bbw138v1.54","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-106"},{"key":"2017011117202254000_bbw138v1.55","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.3.186"},{"key":"2017011117202254000_bbw138v1.56","doi-asserted-by":"publisher","DOI":"10.1038\/ng.806"},{"key":"2017011117202254000_bbw138v1.57","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1303"},{"key":"2017011117202254000_bbw138v1.58","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.jim.2011.09.001","article-title":"Ultra-sensitive detection of rare T cell clones","volume":"375","author":"Robins","year":"2011","journal-title":"J Immunol Methods"},{"key":"2017011117202254000_bbw138v1.59","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201242517"},{"key":"2017011117202254000_bbw138v1.60","doi-asserted-by":"publisher","DOI":"10.1126\/science.1170020"},{"key":"2017011117202254000_bbw138v1.61","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1778"},{"key":"2017011117202254000_bbw138v1.62","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr217"},{"key":"2017011117202254000_bbw138v1.63","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1017621108"},{"key":"2017011117202254000_bbw138v1.64","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2960"},{"key":"2017011117202254000_bbw138v1.65","doi-asserted-by":"publisher","DOI":"10.1038\/srep14629"},{"key":"2017011117202254000_bbw138v1.66","first-page":"Unit 24.2","article-title":"Design, synthesis, and amplification of DNA pools for in vitro selection","volume":"Chapter 24","author":"Hall","year":"2009","journal-title":"Curr Protoc Mol Biol"},{"key":"2017011117202254000_bbw138v1.67","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1500215"},{"key":"2017011117202254000_bbw138v1.68","doi-asserted-by":"publisher","DOI":"10.1101\/gr.092924.109"},{"key":"2017011117202254000_bbw138v1.69","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr344"},{"key":"2017011117202254000_bbw138v1.70","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-S11-S1"},{"key":"2017011117202254000_bbw138v1.71","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-0976-y"},{"key":"2017011117202254000_bbw138v1.72","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1212755109"},{"key":"2017011117202254000_bbw138v1.73","doi-asserted-by":"publisher","DOI":"10.1002\/path.4284"},{"key":"2017011117202254000_bbw138v1.74","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2172-14-35"},{"key":"2017011117202254000_bbw138v1.75","doi-asserted-by":"publisher","DOI":"10.1089\/08892220050195838"},{"key":"2017011117202254000_bbw138v1.76","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2014.06.025"},{"key":"2017011117202254000_bbw138v1.77","doi-asserted-by":"publisher","DOI":"10.1128\/CDLI.7.6.953-959.2000"},{"key":"2017011117202254000_bbw138v1.78","doi-asserted-by":"publisher","DOI":"10.1309\/AJCPV2D1DDSGJDBW"},{"key":"2017011117202254000_bbw138v1.79","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1203916109"},{"key":"2017011117202254000_bbw138v1.80","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1304048110"},{"key":"2017011117202254000_bbw138v1.81","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004503"},{"key":"2017011117202254000_bbw138v1.82","doi-asserted-by":"crossref","first-page":"175.","DOI":"10.1186\/s12859-015-0613-1","article-title":"tcR: an R package for T cell receptor repertoire advanced data analysis","volume":"16","author":"Nazarov","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2017011117202254000_bbw138v1.83","doi-asserted-by":"crossref","unstructured":"Bystry V Reigl T Krejci A , . ARResT\/Interrogate: an interactive immunoprofiler for IG\/TR NGS data. Bioinformatics 2016; btw634.","DOI":"10.1093\/bioinformatics\/btw634"},{"key":"2017011117202254000_bbw138v1.84","doi-asserted-by":"crossref","first-page":"339","DOI":"10.3389\/fimmu.2016.00339","article-title":"IMGT\/StatClonotype for pairwise evaluation and visualization of NGS IG and TR IMGT clonotype (AA) diversity or expression from IMGT\/HighV-QUEST","volume":"7","author":"Aouinti","year":"2016","journal-title":"Front Immunol"},{"key":"2017011117202254000_bbw138v1.85","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3003656"},{"key":"2017011117202254000_bbw138v1.86","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-13-3231"},{"key":"2017011117202254000_bbw138v1.87","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1111\/bjh.13981","article-title":"Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis","volume":"173","author":"Ferret","year":"2016","journal-title":"Br J Haematol"},{"key":"2017011117202254000_bbw138v1.88","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1409572111"},{"key":"2017011117202254000_bbw138v1.89","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw112"},{"key":"2017011117202254000_bbw138v1.90","doi-asserted-by":"crossref","unstructured":"Mora T Walczak AM. Quantifying lymphocyte receptor diversity. bioRxiv 2016.","DOI":"10.1101\/046870"},{"key":"2017011117202254000_bbw138v1.91","doi-asserted-by":"crossref","unstructured":"Laydon DJ Bangham CRM Asquith B. Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach. Philos Trans R Soc Lond B Biol Sci 2015; 370.","DOI":"10.1098\/rstb.2014.0291"},{"key":"2017011117202254000_bbw138v1.92","doi-asserted-by":"publisher","DOI":"10.1111\/j.2006.0030-1299.14714.x"},{"key":"2017011117202254000_bbw138v1.93","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2013.11.018"},{"key":"2017011117202254000_bbw138v1.94","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-015-0169-8"},{"key":"2017011117202254000_bbw138v1.95","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1003898"},{"key":"2017011117202254000_bbw138v1.96","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2011-01-328781"},{"key":"2017011117202254000_bbw138v1.97","doi-asserted-by":"crossref","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":"2017011117202254000_bbw138v1.98","doi-asserted-by":"publisher","DOI":"10.1101\/gr.170753.113"},{"key":"2017011117202254000_bbw138v1.99","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1001198"},{"key":"2017011117202254000_bbw138v1.100","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1172\/JCI83792","article-title":"Public T cell receptors confer high-avidity CD4 responses to HIV controllers","volume":"126","author":"Benati","year":"2016","journal-title":"J Clin Invest"},{"key":"2017011117202254000_bbw138v1.101","doi-asserted-by":"crossref","first-page":"245","DOI":"10.3184\/003685011X13139280383942","article-title":"Specific T-cell activation in an unspecific T-cell repertoire","volume":"94","author":"Van Den Berg","year":"2011","journal-title":"Sci Prog"},{"key":"2017011117202254000_bbw138v1.102","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1074\/jbc.M111.289488","article-title":"A single autoimmune T cell receptor recognizes more than a million different peptides","volume":"287","author":"Wooldridge","year":"2011","journal-title":"J Biol Chem"},{"key":"2017011117202254000_bbw138v1.103","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.03.047"},{"key":"2017011117202254000_bbw138v1.104","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0808081105"},{"key":"2017011117202254000_bbw138v1.105","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt250"},{"key":"2017011117202254000_bbw138v1.106","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401279101"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","deposited":{"date-parts":[[2023,8,21]],"date-time":"2023-08-21T06:38:45Z","timestamp":1692599925000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article-lookup\/doi\/10.1093\/bib\/bbw138"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,10]]},"references-count":106,"alternative-id":["10.1093\/bib\/bbw138"],"URL":"https:\/\/doi.org\/10.1093\/bib\/bbw138","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,10]]}}}