{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T13:19:42Z","timestamp":1761225582664,"version":"build-2065373602"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:00:00Z","timestamp":1759968000000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"SNSF Ambizione","award":["PZ00P3_208734"],"award-info":[{"award-number":["PZ00P3_208734"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The rapid advancements in immune repertoire sequencing, powered by single-cell technologies and artificial intelligence, have created unprecedented opportunities to study B cell evolution at a novel scale and resolution. However, fully leveraging these data requires specialized software capable of performing inter- and intra-repertoire analyses to unravel the complex dynamics of B cell repertoire evolution during immune responses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present AntibodyForests, software to infer B cell lineages, quantify inter- and intra-antibody repertoire evolution, and analyze somatic hypermutation using protein language models and protein structure.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>This R package is available on CRAN and Github at https:\/\/github.com\/alexyermanos\/AntibodyForests, a vignette is available at https:\/\/cran.case.edu\/web\/packages\/AntibodyForests\/vignettes\/AntibodyForests_vignette.html.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf560","type":"journal-article","created":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T11:49:19Z","timestamp":1759837759000},"source":"Crossref","is-referenced-by-count":0,"title":["Delineating inter- and intra-antibody repertoire evolution with AntibodyForests"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5893-7096","authenticated-orcid":false,"given":"Daphne","family":"van Ginneken","sequence":"first","affiliation":[{"name":"University Medical Center Utrecht Center for Translational Immunology, , Lundlaan 6 , 3584 EA Utrecht,","place":["The Netherlands"]}]},{"given":"Valentijn","family":"Tromp","sequence":"additional","affiliation":[{"name":"University Medical Center Utrecht Center for Translational Immunology, , Lundlaan 6 , 3584 EA Utrecht,","place":["The 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and Engineering, , Klingelbergstrasse 48 , 4056 Basel,","place":["Switzerland"]},{"name":"Botnar Institute of Immune Engineering , Klingelbergstrasse 48 , 4056 Basel,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6238-0588","authenticated-orcid":false,"given":"Alexander","family":"Yermanos","sequence":"additional","affiliation":[{"name":"University Medical Center Utrecht Center for Translational Immunology, , Lundlaan 6 , 3584 EA Utrecht,","place":["The Netherlands"]},{"name":"ETH Zurich Department of Biosystems Science and Engineering, , Klingelbergstrasse 48 , 4056 Basel,","place":["Switzerland"]},{"name":"Botnar Institute of Immune Engineering , Klingelbergstrasse 48 , 4056 Basel,","place":["Switzerland"]}]}],"member":"286","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"2025102308572321300_btaf560-B1","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.1093\/bioinformatics\/btac016","article-title":"ABlooper: fast accurate 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