{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T17:53:05Z","timestamp":1776707585782,"version":"3.51.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,4,5]],"date-time":"2018-04-05T00:00:00Z","timestamp":1522886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"National Health and Medical Research Council of Australia"},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1121643"],"award-info":[{"award-number":["1121643"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1113904"],"award-info":[{"award-number":["1113904"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Centre for HIV and HCV Research"},{"name":"UIPA"},{"DOI":"10.13039\/501100001773","name":"UNSW","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001773","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AGRTP"},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1130128"],"award-info":[{"award-number":["1130128"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1043067"],"award-info":[{"award-number":["1043067"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1128416"],"award-info":[{"award-number":["1128416"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NSW Health Early-Mid Career Fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region. VDJPuzzle successfully reconstructed BCRs from 100% (n=117) human and 96.5% (n=200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>VDJPuzzle is available at https:\/\/bitbucket.org\/kirbyvisp\/vdjpuzzle2.<\/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\/bty203","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T15:12:36Z","timestamp":1522854756000},"page":"2846-2847","source":"Crossref","is-referenced-by-count":96,"title":["B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3881-8759","authenticated-orcid":false,"given":"Simone","family":"Rizzetto","sequence":"first","affiliation":[{"name":"Kirby Institute for Infection and Immunity, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David N P","family":"Koppstein","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jerome","family":"Samir","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mandeep","family":"Singh","sequence":"additional","affiliation":[{"name":"Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanne H","family":"Reed","sequence":"additional","affiliation":[{"name":"Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Curtis H","family":"Cai","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew R","family":"Lloyd","sequence":"additional","affiliation":[{"name":"School of Medical Sciences, UNSW, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Auda A","family":"Eltahla","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher C","family":"Goodnow","sequence":"additional","affiliation":[{"name":"Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabio","family":"Luciani","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW, Sydney, Australia"},{"name":"Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,4,5]]},"reference":[{"key":"2023012712593457300_bty203-B1","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1093\/nar\/gkx615","article-title":"Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state","volume":"45","author":"Afik","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012712593457300_bty203-B2","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1093\/bioinformatics\/btw631","article-title":"BASIC: BCR assembly from single cells","volume":"33","author":"Canzar","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012712593457300_bty203-B3","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1038\/icb.2016.16","article-title":"Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells","volume":"94","author":"Eltahla","year":"2016","journal-title":"Immunol. Cell Biol"},{"key":"2023012712593457300_bty203-B4","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1084\/jem.181.3.1245","article-title":"kappa+lambda+ dual receptor B cells are present in the human peripheral repertoire","volume":"181","author":"Giachino","year":"1995","journal-title":"J. Exp. Med"},{"key":"2023012712593457300_bty203-B5","doi-asserted-by":"crossref","first-page":"D413","DOI":"10.1093\/nar\/gku1056","article-title":"IMGT(R), the international ImMunoGeneTics information system(R) 25 years on","volume":"43","author":"Lefranc","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012712593457300_bty203-B6","author":"Lindeman","year":"2017"},{"key":"2023012712593457300_bty203-B7","first-page":"A132","article-title":"Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes","volume":"4","author":"Lizotte","year":"2016","journal-title":"JCI Insight"},{"key":"2023012712593457300_bty203-B8","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":"2023012712593457300_bty203-B9","first-page":"12781","author":"Rizzetto","year":"2017"},{"key":"2023012712593457300_bty203-B10","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":"2023012712593457300_bty203-B11","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/302575a0","article-title":"Somatic generation of antibody diversity","volume":"302","author":"Tonegawa","year":"1983","journal-title":"Nature"},{"key":"2023012712593457300_bty203-B12","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1084\/jem.20161056","article-title":"Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE","volume":"214","author":"Wu","year":"2017","journal-title":"J. Exp. Med"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/16\/2846\/48917938\/bioinformatics_34_16_2846.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/16\/2846\/48917938\/bioinformatics_34_16_2846.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T08:43:55Z","timestamp":1751532235000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/16\/2846\/4961426"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,4,5]]},"references-count":12,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2018,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty203","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/181156","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":[[2018,8,15]]},"published":{"date-parts":[[2018,4,5]]}}}