ReviewFrontiers in immunology2018
Tracing Antibody Repertoire Evolution by Systems Phylogeny.
Review 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 16 papers.
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Who cites it
16 citing papers in PubMed, 35 citations in OpenAlex.
- deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning.Bioinformatics (Oxford, England) · 2025Article
- Mice carrying the full-length human immunoglobulin loci produce antigen-specific human antibodies with the lambda light chain.iScience · 2024Article
- Systematic evaluation of B-cell clonal family inference approaches.BMC immunology · 2024Article
- Genotype-phenotype landscapes for immune-pathogen coevolution.Trends in immunology · 2023Review
- Efficient human-like antibody repertoire and hybridoma production in trans-chromosomic mice carrying megabase-sized human immunoglobulin loci.Nature communications · 2022Article
- A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.Frontiers in immunology · 2022Article
- Trace Reconstruction Problems in Computational Biology.IEEE transactions on information theory · 2021Article
- Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes.NAR genomics and bioinformatics · 2021Article
- Single-cell immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system in mice.Proceedings. Biological sciences · 2021Article
- Novel metric for hyperbolic phylogenetic tree embeddings.Biology methods & protocols · 2021Article
- Review
- Optimizing immunization protocols to elicit broadly neutralizing antibodies.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- AncesTree: An interactive immunoglobulin lineage tree visualizer.PLoS computational biology · 2020Article
- Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.The Journal of experimental medicine · 2020Article
- Review
- Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antibody evolution studies have been traditionally limited to either tracing a single clonal lineage (B cells derived from a single V-(D)-J recombination) over time or examining bulk functionality changes (e.g., tracing serum polyclonal antibody proteins). Studying a single B cell disregards the majority of the humoral immune response, whereas bulk functional studies lack the necessary resolution to analyze the co-existing clonal diversity. Recent advances in high-throughput sequencing (HTS) technologies and bioinformatics have made it possible to examine multiple co-evolving antibody monoclonal lineages within the context of a single repertoire. A plethora of accompanying methods and tools have been introduced in hopes of better understanding how pathogen presence dictates the global evolution of the antibody repertoire. Here, we provide a comprehensive summary of the tremendous progress of this newly emerging field of systems phylogeny of antibody responses. We present an overview encompassing the historical developments of repertoire phylogenetics, state-of-the-art tools, and an outlook on the future directions of this fast-advancing and promising field.
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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.