{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T22:26:34Z","timestamp":1773699994098,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T00:00:00Z","timestamp":1589241600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["31771458"],"award-info":[{"award-number":["31771458"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["31822030"],"award-info":[{"award-number":["31822030"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["31801113"],"award-info":[{"award-number":["31801113"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFA0700403"],"award-info":[{"award-number":["2017YFA0700403"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2018M632830"],"award-info":[{"award-number":["2018M632830"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2019M652623"],"award-info":[{"award-number":["2019M652623"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>T-cell receptors (TCRs) function to recognize antigens and play vital roles in T-cell immunology. Surveying TCR repertoires by characterizing complementarity-determining region 3 (CDR3) is a key issue. Due to the high diversity of CDR3 and technological limitation, accurate characterization of CDR3 repertoires remains a great challenge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a computational method named CATT for ultra-sensitive and precise TCR CDR3 sequences detection. CATT can be applied on TCR sequencing, RNA-Seq and single-cell TCR(RNA)-Seq data to characterize CDR3 repertoires. CATT integrated de Bruijn graph-based micro-assembly algorithm, data-driven error correction model and Bayesian inference algorithm, to self-adaptively and ultra-sensitively characterize CDR3 repertoires with high performance. Benchmark results of datasets from in silico and experimental data demonstrated that CATT showed superior recall and precision compared with existing tools, especially for data with short read length and small size and single-cell sequencing data. Thus, CATT will be a useful tool for TCR analysis in researches of cancer and immunology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>http:\/\/bioinfo.life.hust.edu.cn\/CATT or https:\/\/github.com\/GuoBioinfoLab\/CATT.<\/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\/btaa432","type":"journal-article","created":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T15:18:10Z","timestamp":1588778290000},"page":"4255-4262","source":"Crossref","is-referenced-by-count":19,"title":["An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8076-0576","authenticated-orcid":false,"given":"Si-Yi","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chun-Jie","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, China"},{"name":"Department of Biotechnology, College of Life Sciences, Anhui Normal University , Wuhu, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5099-7465","authenticated-orcid":false,"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,12]]},"reference":[{"key":"2023062312040887800_btaa432-B1","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":"2023062312040887800_btaa432-B2","doi-asserted-by":"crossref","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":"2023062312040887800_btaa432-B3","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/nbt.3979","article-title":"Antigen receptor repertoire profiling from RNA-seq data","volume":"35","author":"Bolotin","year":"2017","journal-title":"Nat. Biotechnol"},{"key":"2023062312040887800_btaa432-B4","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":"2023062312040887800_btaa432-B5","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1007\/s00109-014-1145-2","article-title":"Molecules in medicine mini review: the \u03b1\u03b2 T cell receptor","volume":"92","author":"Clambey","year":"2014","journal-title":"J. Mol. Med"},{"key":"2023062312040887800_btaa432-B6","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023062312040887800_btaa432-B7","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s40169-017-0145-6","article-title":"Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis","volume":"6","author":"Ellsworth","year":"2017","journal-title":"Clin. Transl. Med"},{"key":"2023062312040887800_btaa432-B8","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1093\/bioinformatics\/btv272","article-title":"Polyester: simulating RNA-seq datasets with differential transcript expression","volume":"31","author":"Frazee","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062312040887800_btaa432-B9","doi-asserted-by":"crossref","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":"2023062312040887800_btaa432-B10","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/nature22976","article-title":"Identifying specificity groups in the T cell receptor repertoire","volume":"547","author":"Glanville","year":"2017","journal-title":"Nature"},{"key":"2023062312040887800_btaa432-B11","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/j.tips.2015.11.004","article-title":"Adoptive T cell therapies: a comparison of T cell receptors and chimeric antigen receptors","volume":"37","author":"Harris","year":"2016","journal-title":"Trends Pharmacol. Sci"},{"key":"2023062312040887800_btaa432-B12","doi-asserted-by":"crossref","first-page":"3009","DOI":"10.1200\/JCO.2017.35.15_suppl.3009","article-title":"A phase I\/II clinical trial of E6 T-cell receptor gene therapy for human papillomavirus (HPV)-associated epithelial cancers","volume":"35","author":"Hinrichs","year":"2017","journal-title":"J.\u00a0Clin. Oncol"},{"key":"2023062312040887800_btaa432-B13","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1038\/s41588-018-0339-x","article-title":"Landscape of B cell immunity and related immune evasion in human cancers","volume":"51","author":"Hu","year":"2019","journal-title":"Nat. Genet"},{"key":"2023062312040887800_btaa432-B14","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"28","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062312040887800_btaa432-B15","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/1471-2105-8-131","article-title":"Statistical significance of quantitative PCR","volume":"8","author":"Karlen","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023062312040887800_btaa432-B16","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1038\/ni1001-957","article-title":"Immunotherapy through TCR gene transfer","volume":"2","author":"Kessels","year":"2001","journal-title":"Nat. Immunol"},{"key":"2023062312040887800_btaa432-B17","doi-asserted-by":"crossref","first-page":"2963","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":"2023062312040887800_btaa432-B18","doi-asserted-by":"crossref","first-page":"D413","DOI":"10.1093\/nar\/gku1056","article-title":"IMGT\u00ae, the international ImMunoGeneTics information system\u00ae 25 years on","volume":"43","author":"Lefranc","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062312040887800_btaa432-B19","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1172\/JCI83465","article-title":"Targeting human melanoma neoantigens by T cell receptor gene therapy","volume":"126","author":"Leisegang","year":"2016","journal-title":"J. Clin. Invest"},{"key":"2023062312040887800_btaa432-B20","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows\u2013Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinform. Oxf. Engl"},{"key":"2023062312040887800_btaa432-B21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-02832-w","article-title":"High-throughput immune repertoire analysis with IGoR","volume":"9","author":"Marcou","year":"2018","journal-title":"Nat. Commun"},{"key":"2023062312040887800_btaa432-B22","doi-asserted-by":"crossref","first-page":"eaar5894","DOI":"10.1126\/scitranslmed.aar5894","article-title":"High-throughput sequencing of the T cell receptor \u03b2 gene identifies aggressive early-stage mycosis fungoides","volume":"10","author":"De Masson","year":"2018","journal-title":"Sci. Transl. Med"},{"key":"2023062312040887800_btaa432-B23","first-page":"1902880","article-title":"ImmuCellAI: a unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunothreapy","volume":"2020","author":"Mao","year":"2019","journal-title":"Adv. Sci"},{"key":"2023062312040887800_btaa432-B24","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/S0952-7915(97)80152-5","article-title":"Innate immunity: impact on the adaptive immune response","volume":"9","author":"Medzhitov","year":"1997","journal-title":"Curr. Opin. Immunol"},{"key":"2023062312040887800_btaa432-B25","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature22991","article-title":"An immunogenic personal neoantigen vaccine for patients with melanoma","volume":"547","author":"Ott","year":"2017","journal-title":"Nature"},{"key":"2023062312040887800_btaa432-B26","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1158\/2326-6066.CIR-16-0013","article-title":"Deep sequencing of T-cell receptor DNA as a biomarker of clonally expanded TILs in breast cancer after immunotherapy","volume":"4","author":"Page","year":"2016","journal-title":"Cancer Immunol. Res"},{"key":"2023062312040887800_btaa432-B27","doi-asserted-by":"crossref","first-page":"e3000314","DOI":"10.1371\/journal.pbio.3000314","article-title":"Detecting T cell receptors involved in immune responses from single repertoire snapshots","volume":"17","author":"Pogorelyy","year":"2019","journal-title":"PLoS Biol"},{"key":"2023062312040887800_btaa432-B28","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/s41586-018-0326-5","article-title":"Reprogramming human T cell function and specificity with non-viral genome targeting","volume":"559","author":"Roth","year":"2018","journal-title":"Nature"},{"key":"2023062312040887800_btaa432-B29","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1038\/bcj.2011.6","article-title":"Highly skewed T-cell receptor V-beta chain repertoire in the bone marrow is associated with response to immunosuppressive drug therapy in children with very severe aplastic anemia","volume":"1","author":"Schuster","year":"2011","journal-title":"Blood Cancer J"},{"key":"2023062312040887800_btaa432-B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-02727-8","article-title":"A high-throughput assay for quantitative measurement of PCR errors","volume":"7","author":"Shagin","year":"2017","journal-title":"Sci. Rep"},{"key":"2023062312040887800_btaa432-B31","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res"},{"key":"2023062312040887800_btaa432-B32","doi-asserted-by":"crossref","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":"2023062312040887800_btaa432-B33","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/s41591-018-0057-z","article-title":"A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade","volume":"24","author":"Thommen","year":"2018","journal-title":"Nat. Med"},{"key":"2023062312040887800_btaa432-B34","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1038\/nri1977","article-title":"Structural determinants of T-cell receptor bias in immunity","volume":"6","author":"Turner","year":"2006","journal-title":"Nat. Rev. Immunol"},{"key":"2023062312040887800_btaa432-B35","doi-asserted-by":"crossref","first-page":"119","DOI":"10.7150\/ijbs.7823","article-title":"\u03b3\u03b4 T cells and their potential for immunotherapy","volume":"10","author":"Wu","year":"2014","journal-title":"Int. J. Biol. Sci"},{"key":"2023062312040887800_btaa432-B36","doi-asserted-by":"crossref","first-page":"W34","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":"2023062312040887800_btaa432-B37","doi-asserted-by":"crossref","first-page":"1500","DOI":"10.3389\/fimmu.2017.01500","article-title":"Quantification of inter-sample differences in T-cell receptor repertoires using sequence-based information","volume":"8","author":"Yokota","year":"2017","journal-title":"Front. Immunol"},{"key":"2023062312040887800_btaa432-B38","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.1093\/nar\/gkv1016","article-title":"LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins","volume":"44","author":"Yu","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062312040887800_btaa432-B39","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1038\/s41591-018-0040-8","article-title":"Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer","volume":"24","author":"Zacharakis","year":"2018","journal-title":"Nat. Med"},{"key":"2023062312040887800_btaa432-B40","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","article-title":"PEAR: a fast and accurate Illumina Paired-End reAd mergeR","volume":"30","author":"Zhang","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062312040887800_btaa432-B41","article-title":"Tools for fundamental analysis functions of TCR repertoires: a systematic comparison","author":"Zhang","year":"2019","journal-title":"Brief. Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa432\/33515230\/btaa432.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/15\/4255\/50671674\/bioinformatics_36_15_4255.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/15\/4255\/50671674\/bioinformatics_36_15_4255.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T17:52:47Z","timestamp":1687629167000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/15\/4255\/5836504"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,5,12]]},"references-count":41,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2020,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa432","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/740340","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,8,1]]},"published":{"date-parts":[[2020,5,12]]}}}