{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T10:46:35Z","timestamp":1767869195098,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":84,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Cancer Genome Atlas","award":["U24-CA143848-06"],"award-info":[{"award-number":["U24-CA143848-06"]}]},{"name":"National Cancer Institute Breast SPORE","award":["P50-CA58223-09A1"],"award-info":[{"award-number":["P50-CA58223-09A1"]}]},{"name":"National Cancer Institute Breast SPORE","award":["RO1-CA195740-01"],"award-info":[{"award-number":["RO1-CA195740-01"]}]},{"DOI":"10.13039\/100001006","name":"Breast Cancer Research Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100001006","id-type":"DOI","asserted-by":"crossref"}]},{"name":"University of North Carolina University Cancer Research Fund"},{"name":"UNC Oncology Clinical Translational Research Training Program","award":["5K12CA120780"],"award-info":[{"award-number":["5K12CA120780"]}]},{"name":"William Guy Forbeck Research Foundation Collaborative Research Grant"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Motivation: B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions. While this approach has proven to be effective, it is frequently not feasible due to cost or limited sample material. Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not.<\/jats:p>\n               <jats:p>Results: We present here V\u2019DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V\u2019DJer\u2019s ability to accurately reconstruct BCR repertoires from short read mRNA-seq data.<\/jats:p>\n               <jats:p>Availability and Implementation: V\u2019DJer is implemented in C\/C\u2009++, freely available for academic use and can be downloaded from Github: https:\/\/github.com\/mozack\/vdjer<\/jats:p>\n               <jats:p>Contact: \u00a0benjamin_vincent@med.unc.edu or parkerjs@email.unc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw526","type":"journal-article","created":{"date-parts":[[2016,8,25]],"date-time":"2016-08-25T02:49:07Z","timestamp":1472093347000},"page":"3729-3734","source":"Crossref","is-referenced-by-count":70,"title":["Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V\u2019DJer"],"prefix":"10.1093","volume":"32","author":[{"given":"Lisle E.","family":"Mose","sequence":"first","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara R.","family":"Selitsky","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa M.","family":"Bixby","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"},{"name":"2Division of Hematology\/Oncology, Department of Internal Medicine,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David L.","family":"Marron","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael D.","family":"Iglesia","sequence":"additional","affiliation":[{"name":"3Curriculum in Genetics and Molecular Biology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan S.","family":"Serody","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"},{"name":"2Division of Hematology\/Oncology, Department of Internal Medicine,"},{"name":"4Department of Microbiology\/Immunology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles M.","family":"Perou","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"},{"name":"5Departments of Genetics and Pathology and Laboratory Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin G.","family":"Vincent","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"},{"name":"2Division of Hematology\/Oncology, Department of Internal Medicine,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joel S.","family":"Parker","sequence":"additional","affiliation":[{"name":"1Lineberger Comprehensive Cancer Center"},{"name":"6Departments of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,8,24]]},"reference":[{"key":"2023020114085453300_btw526-B1","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1126\/science.286.5441.958","article-title":"A direct estimate of the human alphabeta T cell receptor diversity","volume":"286","author":"Arstila","year":"1999","journal-title":"Science"},{"key":"2023020114085453300_btw526-B2","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1089\/cmb.2015.0226","article-title":"CRISPR detection from short reads using partial overlap graphs","volume":"23","author":"Ben-Bassat","year":"2016","journal-title":"J. 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