{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T16:47:23Z","timestamp":1754153243672,"version":"3.41.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,7,17]],"date-time":"2025-07-17T00:00:00Z","timestamp":1752710400000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Shenzhen Science and Technology Program","award":["JCYJ20200109143216036"],"award-info":[{"award-number":["JCYJ20200109143216036"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>B-cell lineage trees describe the evolutionary process of immunoglobulin genes during affinity maturation. Existing methods for building B-cell lineage trees generally do not guarantee the parent-to-child inheritance and accumulation of advantageous mutations under successive rounds of somatic hypermutation (SHM) and selection, and are often incompatible with repertoire input.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address previous limitations, we developed AffMB (Affinity Maturation of B-cell receptor), a comprehensive toolkit for tracking affinity maturation through the generation and visualization of SHM-ordered, inheritance-based B-cell lineage trees from single-cell or bulk B-cell receptor sequencing data. The SHM-ordered inheritance tree algorithm outperformed state-of-the-art benchmarks in simulations. When applied to single-cell data from BNT162b2 vaccination (n\u2009=\u200942), AffMB demonstrated the ability to infer immunization responses and showed the feasibility of identifying potential high-affinity antibody sequences.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>AffMB is an open-source Python package that supports contig FASTA or AIRR rearrangement TSV inputs. The source code for AffMB is freely available at https:\/\/github.com\/deepomicslab\/AffMB.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf346","type":"journal-article","created":{"date-parts":[[2025,7,17]],"date-time":"2025-07-17T18:49:53Z","timestamp":1752778193000},"source":"Crossref","is-referenced-by-count":0,"title":["AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5453-6431","authenticated-orcid":false,"given":"Jiaqi","family":"Luo","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, 518000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7522-6088","authenticated-orcid":false,"given":"Yiping","family":"Zou","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, 518000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6246-6349","authenticated-orcid":false,"given":"Shuai Cheng","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, 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