ArticleGenetics2017
A Phylogenetic Codon Substitution Model for Antibody Lineages.
Article in Genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
What it found
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Who cites it
55 citing papers in PubMed.
- Deletions in variable region 1 of the HIV envelope accelerate V3-glycan bNAb induction in SHIV-infected rhesus macaques.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- mRNA-based influenza vaccine expands the B cell response breadth in humans.Nature immunology · 2026Observational
- B cell αv integrin regulates tissue specialization and clonal expansion of lung germinal center and memory B cells after viral infection.Science advances · 2026Article
- Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.Science immunology · 2026Article
- A temporal and spatial atlas of adaptive immune responses in the lymph node following viral infection.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Profiling Allogeneic HLA-specific B-cell Responses Utilizing a 64-plex Single-HLA Reporter Cell Panel.bioRxiv : the preprint server for biology · 2026Article
- Functional Convergence of Genetically Diverse B-Cell Receptors in Simian-HIV Infected Rhesus Macaques.bioRxiv : the preprint server for biology · 2026Article
- Multifaceted B cell response to transient HIV viremia in elite controllers.PLoS pathogens · 2026Article
- Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.PLoS computational biology · 2025Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.bioRxiv : the preprint server for biology · 2025Article
- Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.Bioinformatics (Oxford, England) · 2025Article
- B cell αv integrin regulates tissue specialization and clonal expansion of lung germinal center and memory B cells after viral infection.bioRxiv : the preprint server for biology · 2025Article
- Article
- Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Discovery, recognized antigenic structures, and evolution of cross-serotype broadly neutralizing antibodies from porcine B-cell repertoires against foot-and-mouth disease virus.PLoS pathogens · 2024Article
- Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data.Cell genomics · 2024Article
- High affinity mAb infusion can enhance maximum affinity maturation during HIV Env immunization.iScience · 2024Article
- Lack of affinity signature for germinal center cells that have initiated plasma cell differentiation.Immunity · 2024Article
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Phylogenetic methods have shown promise in understanding the development of broadly neutralizing antibody lineages (bNAbs). However, the mutational process that generates these lineages, somatic hypermutation, is biased by hotspot motifs which violates important assumptions in most phylogenetic substitution models. Here, we develop a modified GY94-type substitution model that partially accounts for this context dependency while preserving independence of sites during calculation. This model shows a substantially better fit to three well-characterized bNAb lineages than the standard GY94 model. We also demonstrate how our model can be used to test hypotheses concerning the roles of different hotspot and coldspot motifs in the evolution of B-cell lineages. Further, we explore the consequences of the idea that the number of hotspot motifs, and perhaps the mutation rate in general, is expected to decay over time in individual bNAb lineages.
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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.