ArticleNucleic acids research2012
Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 1 of them a synthesis that pooled it.
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Who cites it
132 citing papers in PubMed, 1 synthesis or guideline pooled it, 204 citations in OpenAlex.
- Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).PLoS computational biology · 2019Pooled it
- Rapid HIV Progression Is Associated with Extensive Ongoing Somatic Hypermutation.Journal of immunology (Baltimore, Md. : 1950) · 2020Trial
- Persistence and selection of an expanded B-cell clone in the setting of rituximab therapy for Sjögren's syndrome.Arthritis research & therapy · 2014Trial
- Transcriptomic characterization of transitional B cells reveals four subsets with perturbed activation profiles in scleroderma.iScience · 2026Article
- mRNA-based influenza vaccine expands the B cell response breadth in humans.Nature immunology · 2026Observational
- Immunoglobulin heavy chain locus duplication in bats.Science advances · 2026Article
- Atypical memory B cell clonal expansion and inflammatory programs associate with platelet-activating antibody development in COVID-19.JCI insight · 2026Article
- The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase.Nucleic acids research · 2026Article
- Germline based SARS-CoV-2 specific B cell repertoire motif identified with novel sequence based bioinformatic pipeline.Frontiers in immunology · 2026Article
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- TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.bioRxiv : the preprint server for biology · 2025Article
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- A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer-Encoder.Molecular biology and evolution · 2025Article
- BLIMP1 controls GC B cell expansion and exit through regulating cell cycle progression and key transcription factors BCL6 and IRF4.Cell reports · 2025Article
- B-cell Receptor Silencing Reveals the Origin and Dependencies of High-Grade B-cell Lymphomas with MYC and BCL2 Rearrangements.Blood cancer discovery · 2025Article
- Lung B cells in ectopic germinal centers undergo affinity maturation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The role of polyreactive memory B cells in systemic lupus erythematosus.International immunology · 2025Review
- Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus.Cell reports · 2024Article
- An unbiased comparison of immunoglobulin sequence aligners.Briefings in bioinformatics · 2024Article
- Combining mutation and recombination statistics to infer clonal families in antibody repertoires.eLife · 2024Article
72 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
High-throughput immunoglobulin sequencing promises new insights into the somatic hypermutation and antigen-driven selection processes that underlie B-cell affinity maturation and adaptive immunity. The ability to estimate positive and negative selection from these sequence data has broad applications not only for understanding the immune response to pathogens, but is also critical to determining the role of somatic hypermutation in autoimmunity and B-cell cancers. Here, we develop a statistical framework for Bayesian estimation of Antigen-driven SELectIoN (BASELINe) based on the analysis of somatic mutation patterns. Our approach represents a fundamental advance over previous methods by shifting the problem from one of simply detecting selection to one of quantifying selection. Along with providing a more intuitive means to assess and visualize selection, our approach allows, for the first time, comparative analysis between groups of sequences derived from different germline V(D)J segments. Application of this approach to next-generation sequencing data demonstrates different selection pressures for memory cells of different isotypes. This framework can easily be adapted to analyze other types of DNA mutation patterns resulting from a mutator that displays hot/cold-spots, substitution preference or other intrinsic biases.
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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.