ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2015
Quantifying evolutionary constraints on B-cell affinity maturation.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 60 citations in OpenAlex.
- Dynamics of memory B cells and plasmablasts in healthy individuals.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.bioRxiv : the preprint server for biology · 2025Article
- Article
- A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer-Encoder.Molecular biology and evolution · 2025Article
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
- Inference of B cell clonal families using heavy/light chain pairing information.PLoS computational biology · 2022Article
- Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies.PLoS computational biology · 2022Article
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.Frontiers in immunology · 2022Article
- Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data.Nucleic acids research · 2020Article
- Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.PLoS computational biology · 2020Article
- Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1.Molecular biology and evolution · 2019Article
- Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data.PLoS computational biology · 2019Article
- Survival analysis of DNA mutation motifs with penalized proportional hazards.The annals of applied statistics · 2019Article
- DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination.BMC bioinformatics · 2019Article
- Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Article
- Immunoglobulin gene analysis as a tool for investigating human immune responses.Immunological reviews · 2018Review
- The Bayesian optimist's guide to adaptive immune receptor repertoire analysis.Immunological reviews · 2018Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The antibody repertoire of each individual is continuously updated by the evolutionary process of B-cell receptor (BCR) mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B-cell sequence data, and then apply them to a very deep short-read dataset of BCRs. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on BCRs using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.
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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.