{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T23:29:47Z","timestamp":1768001387152,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,1,10]],"date-time":"2017-01-10T00:00:00Z","timestamp":1484006400000},"content-version":"vor","delay-in-days":5,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006112","name":"Microsoft Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006112","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001658","name":"Minerva Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001658","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor \u03b2 chain complementarity determining region 3 (CDR3\u03b2) sequences following immunization with ovalbumin administered with complete Freund\u2019s adjuvant (CFA) or CFA alone.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The CDR3\u03b2 sequences were deconstructed into short stretches of overlapping contiguous amino acids. The motifs were ranked according to a one-dimensional Bayesian classifier score comparing their frequency in the repertoires of the two immunization classes. The top ranking motifs were selected and used to create feature vectors which were used to train a support vector machine. The support vector machine achieved high classification scores in a leave-one-out validation test reaching\u2009&amp;gt;90% in some cases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The study describes a novel two-stage classification strategy combining a one-dimensional Bayesian classifier with a support vector machine. Using this approach we demonstrate that the frequency of a small number of linear motifs three amino acids in length can accurately identify a CD4 T cell response to ovalbumin against a background response to the complex mixture of antigens which characterize Complete Freund\u2019s Adjuvant.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The sequence data is available at www.ncbi.nlm.nih.gov\/sra\/?term\u00bcSRP075893. The Decombinator package is available at github.com\/innate2adaptive\/Decombinator. The R package e1071 is available at the CRAN repository https:\/\/cran.r-project.org\/web\/packages\/e1071\/index.html.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw771","type":"journal-article","created":{"date-parts":[[2016,12,5]],"date-time":"2016-12-05T20:05:40Z","timestamp":1480968340000},"page":"951-955","source":"Crossref","is-referenced-by-count":78,"title":["Feature selection using a one dimensional na\u00efve Bayes\u2019 classifier increases the accuracy of support vector machine classification of CDR3 repertoires"],"prefix":"10.1093","volume":"33","author":[{"given":"Mattia","family":"Cinelli","sequence":"first","affiliation":[{"name":"Division of Infection and Immunity, UCL, London, UK"}]},{"given":", Yuxin","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Computer Science, UCL, London, UK"}]},{"given":"Katharine","family":"Best","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, UCL, London, UK"},{"name":"Complex, UCL, London, UK"}]},{"given":"James M","family":"Heather","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, UCL, London, UK"}]},{"given":"Shlomit","family":"Reich-Zeliger","sequence":"additional","affiliation":[{"name":"Department of Immunology, Weizmann Institute, Rehovot, Israel"}]},{"given":"Eric","family":"Shifrut","sequence":"additional","affiliation":[{"name":"Department of Immunology, Weizmann Institute, Rehovot, Israel"}]},{"given":"Nir","family":"Friedman","sequence":"additional","affiliation":[{"name":"Department of Immunology, Weizmann Institute, Rehovot, Israel"}]},{"given":"John","family":"Shawe-Taylor","sequence":"additional","affiliation":[{"name":"Department of Computer Science, UCL, London, UK"}]},{"given":"Benny","family":"Chain","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, UCL, London, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,1,5]]},"reference":[{"key":"2023020205010227200_btw771-B1","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/BF00994018","article-title":"Support-vector networks","volume":"20","author":"Cortes","year":"1995","journal-title":"Mach. Learn"},{"key":"2023020205010227200_btw771-B2","volume-title":"Support Vector Machines","author":"Cristianini","year":"2000"},{"key":"2023020205010227200_btw771-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1749-6632.1995.tb44477.x","article-title":"T-cell receptor V-region usage and antigen specificity. The cytochrome c model system","volume":"756","author":"Davis","year":"1995","journal-title":"Ann. N. Y. Acad. Sci"},{"key":"2023020205010227200_btw771-B4","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/0167-5699(95)80118-9","article-title":"The injured cell: the role of the dendritic cell system as a sentinel receptor pathway","volume":"16","author":"Ibrahim","year":"1995","journal-title":"Immunol. Today"},{"key":"2023020205010227200_btw771-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/SQB.1989.054.01.003","article-title":"Approaching the asymptote? Evolution and revolution in immunology","volume":"54","author":"Janeway","year":"1989","journal-title":"Cold Spring Harb. Symp. Quant. Biol"},{"key":"2023020205010227200_btw771-B6","doi-asserted-by":"crossref","first-page":"4942","DOI":"10.1073\/pnas.0401279101","article-title":"Conserved T cell receptor usage in primary and recall responses to an immunodominant influenza virus nucleoprotein epitope","volume":"101","author":"Kedzierska","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020205010227200_btw771-B7","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1101\/gr.170753.113","article-title":"T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity","volume":"24","author":"Madi","year":"2014","journal-title":"Genome Res"},{"key":"2023020205010227200_btw771-B8","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/icb.2010.139","article-title":"Bias in the \u03b1\u03b2 T-cell repertoire: implications for disease pathogenesis and vaccination","volume":"89","author":"Miles","year":"2011","journal-title":"Immunol. Cell Biol"},{"key":"2023020205010227200_btw771-B9","doi-asserted-by":"crossref","first-page":"16161","DOI":"10.1073\/pnas.1212755109","article-title":"Statistical inference of the generation probability of T-cell receptors from sequence repertoires","volume":"109","author":"Murugan","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020205010227200_btw771-B10","doi-asserted-by":"crossref","first-page":"15865","DOI":"10.1073\/pnas.1203916109","article-title":"Chromatin conformation governs T-cell receptor Jbeta gene segment usage","volume":"109","author":"Ndifon","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020205010227200_btw771-B11","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":"Quigley","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020205010227200_btw771-B12","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1084\/jem.158.2.303","article-title":"Antigen recognition by H-2-restricted T cells. I. Cell-free antigen processing","volume":"158","author":"Shimonkevitz","year":"1983","journal-title":"J. Exp. Med"},{"key":"2023020205010227200_btw771-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/btu523","article-title":"Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence","volume":"30","author":"Thomas","year":"2014","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/7\/951\/49038553\/bioinformatics_33_7_951.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/7\/951\/49038553\/bioinformatics_33_7_951.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:03:16Z","timestamp":1675314196000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/7\/951\/2883387"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,1,5]]},"references-count":13,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2017,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw771","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,4,1]]},"published":{"date-parts":[[2017,1,5]]}}}