ArticleBioinformatics (Oxford, England)2022
Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 14 citations in OpenAlex.
- The N-terminal region of malaria vaccine candidate asparagine-rich merozoite antigen is immunodominant and targeted by polyreactive antibodies.Disease models & mechanisms · 2026Article
- Iterative immunoprecipitation and phage pre-wash dramatically improve epitope-resolved serology by VirScan.Frontiers in virology (Lausanne, Switzerland) · 2026Article
- PhIP-Seq: unveiling the complexity of antibody repertoires in health and disease.Frontiers in immunology · 2026Review
- The N-terminal region of malaria vaccine candidatebioRxiv : the preprint server for biology · 2025Article
- Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides.Bioinformatics (Oxford, England) · 2024Article
- Comprehensive phage display viral antibody profiling using VirScan: potential applications in chronic immune-mediated disease.Journal of virology · 2024Review
- Physiological Mechanisms by Which the Functional Ingredients in Beer Impact Human Health.Molecules (Basel, Switzerland) · 2024Review
- PhIP-Seq: methods, applications and challenges.Frontiers in bioinformatics · 2024Review
- Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Ranking Antibody Binding Epitopes and Proteins Across Samples from Whole Proteome Tiled Linear Peptides.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
summaryBecause of their high abundance, easy accessibility in peripheral blood, and relative stability ex vivo, antibodies serve as excellent records of environmental exposures and immune responses. Phage Immuno-Precipitation Sequencing (PhIP-Seq) is the most efficient technique available for assessing antibody binding to hundreds of thousands of peptides at a cohort scale. PhIP-Seq is a high-throughput approach for assessing antibody reactivity to hundreds of thousands of candidate epitopes. Accurate detection of weakly reactive peptides is particularly important for characterizing the development and decline of antibody responses. Here, we present BEER (Bayesian Enrichment Estimation in R), a software package specifically developed for the quantification of peptide reactivity from PhIP-Seq experiments. BEER implements a hierarchical model and produces posterior probabilities for peptide reactivity and a fold change estimate to quantify the magnitude. BEER also offers functionality to infer peptide reactivity based on the edgeR package, though the improvement in speed is offset by slightly lower sensitivity compared to the Bayesian approach, specifically for weakly reactive peptides. AVAILABILITY AND IMPLEMENTATION: BEER is implemented in R and freely available from the Bioconductor repository at https://bioconductor.org/packages/release/bioc/html/beer.html.
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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.