ArticleBioinformatics (Oxford, England)2025
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- Protein language model pseudolikelihoods capture features of in vivo B cell selection and evolution.Briefings in bioinformatics · 2025Article
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8 authors.
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Abstract
motivationThe 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.
resultsHere, 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. AVAILABILITY AND IMPLEMENTATION: 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.
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