Delineating inter- and intra-antibody repertoire evolution with AntibodyForests
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Publication date
2025-10-01
Authors
van Ginneken, Daphne
Tromp, Valentijn
Stalder, Lucas
Cotet, Tudor Stefan
Bakker, Sophie
Samant, Anamay
Reddy, Sai T.
Yermanos, Alexander
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Document Type
Article
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cc_by
Abstract
Motivation: 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. Results: 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.
Keywords
Statistics and Probability, Biochemistry, Molecular Biology, Computer Science Applications, Computational Theory and Mathematics, Computational Mathematics
Citation
van Ginneken, D, Tromp, V, Stalder, L, Cotet, T S, Bakker, S, Samant, A, Reddy, S T & Yermanos, A 2025, 'Delineating inter- and intra-antibody repertoire evolution with AntibodyForests', Bioinformatics, vol. 41, no. 10, btaf560. https://doi.org/10.1093/bioinformatics/btaf560