{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:14:08Z","timestamp":1783689248604,"version":"3.55.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"St John\u2019s College"},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006662","name":"NIHR","doi-asserted-by":"publisher","award":["CL-2021-13-002"],"award-info":[{"award-number":["CL-2021-13-002"]}],"id":[{"id":"10.13039\/100006662","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Brain Tumour Charity Future Leaders Fellowship","award":["FL_2023_\/1_10774"],"award-info":[{"award-number":["FL_2023_\/1_10774"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/V002503\/1"],"award-info":[{"award-number":["MR\/V002503\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["204969\/Z\/16\/Z"],"award-info":[{"award-number":["204969\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005150","name":"Chinese Academy of Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005150","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Innovation Fund for Medical Science","award":["2024-I2M-2-001-1"],"award-info":[{"award-number":["2024-I2M-2-001-1"]}]},{"DOI":"10.13039\/100006662","name":"NIHR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006662","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Oxford Biomedical Research Centre"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>High-throughput sequencing of B and T cell repertoires provides unprecedented insights into adaptive immunity but generates high-dimensional feature sets that are challenging to interpret. Standard dimensionality reduction techniques are often suboptimal for adaptive immune receptor repertoire (AIRR) data, which exhibits multi-collinearity, heterogeneous data types, and missingness.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present VDJ-REMIX, an R package implementing a robust, network-based framework to deconstruct complex repertoire feature matrices into biologically interpretable modules. By refactoring weighted correlation network analysis (WGCNA), VDJ-REMIX provides a tailored workflow for preprocessing, imputation, and modularization of immune repertoire data. We demonstrate its utility across diverse contexts, including autoimmunity, inflammation, and acute infection. In autoimmune patients, VDJ-REMIX identified distinct B cell signatures that stratified diseases and revealed opposing dynamic responses to B cell-depleting versus anti-proliferative therapies. In COVID-19 and non-COVID-19 sepsis patients, it distinguished disease-specific signatures from shared severe infection responses and identified modules correlated with severity. Analysis of flow-sorted B cell populations stratified by FCGR2B genotype recapitulated known tolerance defects and uncovered population-specific repertoire signatures linked to inhibitory receptor dysfunction, providing orthogonal validation of module biological coherence. Finally, applied to a single-cell multi-omics dataset of immune cells in pancreatic ductal adenocarcinoma (PDAC) combining gene expression with AIRR-seq, VDJ-REMIX recovered modules linking BCR isotype usage and clonality to cytotoxic, interferon-responsive, and regulatory immune programmes. VDJ-REMIX is a versatile tool enabling systematic exploration of immunological variation and biomarker discovery from complex immune repertoire data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>VDJ-REMIX is freely available at https:\/\/github.com\/Bashford-Rogers-lab\/vdjremix.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag326","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T16:33:43Z","timestamp":1783442023000},"source":"Crossref","is-referenced-by-count":0,"title":["VDJ-REMIX: REpertoire Module Identification and eXploration"],"prefix":"10.1093","volume":"42","author":[{"given":"Sakina","family":"Amin","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Oxford , Oxford OX1 3QU,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Overend","sequence":"additional","affiliation":[{"name":"Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford , Oxford OX3 7BN,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felicia","family":"Tucci","sequence":"additional","affiliation":[{"name":"Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford , Oxford OX3 7BN,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5507-6657","authenticated-orcid":false,"given":"Bo","family":"Sun","sequence":"additional","affiliation":[{"name":"Nuffield Department of Clinical Neuroscience, University of Oxford , Oxford OX3 9DU,","place":["United 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