{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T09:34:36Z","timestamp":1774517676353,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:00:00Z","timestamp":1773100800000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Fundation of China","doi-asserted-by":"crossref","award":["32270687"],"award-info":[{"award-number":["32270687"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Key R&D\u00b7Program of China","award":["2023YFC3403200"],"award-info":[{"award-number":["2023YFC3403200"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>B-cell receptors (BCRs) and gene expression profiles are two distinct yet complementary modalities of B cells. However, most analyses treat them independently. Here, we present CoMBCR, a B-cell embedding tool that co-learns BCRs and gene expressions, representing data within a unified latent space for downstream analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We applied CoMBCR to 126,791 B cells from diverse datasets with matched BCRs and gene expressions. First, CoMBCR outperforms the methods solely encoding BCRs in capturing B-cell biological features, achieving at least 0.1 improvement in Matthews Correlation Coefficient on a SARS-CoV-2 binding prediction task. Second, CoMBCR reveals active immune responses and CDR3 motif preferences through modality gap analysis in SARS-CoV-2-specific memory B cells. Moreover, when supported by spatial transcriptomics data, CoMBCR accurately traces the developmental trajectories of malignant B cells and uncovers transcriptional patterns associated with their survival within lymphoma patients.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The CoMBCR software is publicly available under the MIT License at https:\/\/github.com\/deepomicslab\/CoMBCR.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>shuaicli@cityu.edu.hk<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag115","type":"journal-article","created":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T12:47:01Z","timestamp":1772714821000},"source":"Crossref","is-referenced-by-count":0,"title":["CoMBCR: Co-Learning Multi-Modalities of BCRs and gene expressions"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7522-6088","authenticated-orcid":false,"given":"Yiping","family":"Zou","sequence":"first","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Kowloon Tong , Hong Kong,","place":["China"]},{"name":"City University of Hong Kong Shenzhen Research Institute , Nanshan District , Shenzhen, 518057,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5453-6431","authenticated-orcid":false,"given":"Jiaqi","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Kowloon Tong , Hong Kong,","place":["China"]},{"name":"City University of Hong Kong Shenzhen Research Institute , Nanshan District , Shenzhen, 518057,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6246-6349","authenticated-orcid":false,"given":"Shuaicheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Kowloon Tong , Hong Kong,","place":["China"]},{"name":"City University of Hong Kong Shenzhen Research Institute , Nanshan District , Shenzhen, 518057,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,9]]},"reference":[{"key":"2026032604202177600_btag115-B1","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1007\/s00428-019-02695-6","article-title":"Characterisation of tumour microenvironment and immune checkpoints in primary central nervous system diffuse large B cell lymphomas","volume":"476","author":"Alame","year":"2020","journal-title":"Virchows 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