ArticlePLoS computational biology2020
Using B cell receptor lineage structures to predict affinity.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Dynamics of memory B cells and plasmablasts in healthy individuals.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Increased immunogen valency improves the maturation of vaccine-elicited HIV-1 VRC01-like antibodies.PLoS pathogens · 2025Article
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
- Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses.PLoS pathogens · 2023Article
- Inference of B cell clonal families using heavy/light chain pairing information.PLoS computational biology · 2022Article
- Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning.Bioinformatics (Oxford, England) · 2022Article
- AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses.PLoS computational biology · 2022Article
- Protective Human Anti-Poxvirus Monoclonal Antibodies Are Generated from Rare Memory B Cells Isolated by Multicolor Antigen Tetramers.Vaccines · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis. Comments Please post comments or questions on this paper as new issues at https://git.io/Jvxkn.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.