ArticleFrontiers in immunology2018
Benchmarking Tree and Ancestral Sequence Inference for B Cell Receptor Sequences.
Article in Frontiers in immunology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.bioRxiv : the preprint server for biology · 2025Article
- Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.Bioinformatics (Oxford, England) · 2025Article
- Increased immunogen valency improves the maturation of vaccine-elicited HIV-1 VRC01-like antibodies.PLoS pathogens · 2025Article
- Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- New generalized metric based on branch length distance to compare B cell lineage trees.Algorithms for molecular biology : AMB · 2024Article
- Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data.Cell genomics · 2024Article
- Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
- TRIBAL: Tree Inference of B cell Clonal Lineages.bioRxiv : the preprint server for biology · 2023Article
- Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser.bioRxiv : the preprint server for biology · 2023Article
- Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances.BMC bioinformatics · 2023Article
- Inference of B cell clonal families using heavy/light chain pairing information.PLoS computational biology · 2022Article
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- Phylogenetic analysis of migration, differentiation, and class switching in B cells.PLoS computational biology · 2022Article
- Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes.Bioinformatics advances · 2022Article
- A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.Frontiers in immunology · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
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- Using B cell receptor lineage structures to predict affinity.PLoS computational biology · 2020Article
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2 authors.
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Abstract
B cell receptor sequences evolve during affinity maturation according to a Darwinian process of mutation and selection. Phylogenetic tools are used extensively to reconstruct ancestral sequences and phylogenetic trees from affinity-matured sequences. In addition to using general-purpose phylogenetic methods, researchers have developed new tools to accommodate the special features of B cell sequence evolution. However, the performance of classical phylogenetic techniques in the presence of B cell-specific features is not well understood, nor how much the newer generation of B cell specific tools represent an improvement over classical methods. In this paper we benchmark the performance of classical phylogenetic and new B cell-specific tools when applied to B cell receptor sequences simulated from a forward-time model of B cell receptor affinity maturation toward a mature receptor. We show that the currently used tools vary substantially in terms of tree structure and ancestral sequence inference accuracy. Furthermore, we show that there are still large performance gains to be achieved by modeling the special mutation process of B cell receptors. These conclusions are further strengthened with real data using the rules of isotype switching to count possible violations within each inferred phylogeny.
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