{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T15:51:59Z","timestamp":1780415519337,"version":"3.54.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T00:00:00Z","timestamp":1660262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"United States National Institutes of General Medical Science NIGMS","award":["R01 GM136724"],"award-info":[{"award-number":["R01 GM136724"]}]},{"name":"Allergy and Infectious Diseases [NIAID","award":["R01 AI095068"],"award-info":[{"award-number":["R01 AI095068"]}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute [NCI","doi-asserted-by":"crossref","award":["P50 CA062924"],"award-info":[{"award-number":["P50 CA062924"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute [NCI","doi-asserted-by":"crossref","award":["NCI P30 CA006973"],"award-info":[{"award-number":["NCI P30 CA006973"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Because 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>BEER is implemented in R and freely available from the Bioconductor repository at https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/beer.html.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac555","type":"journal-article","created":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T12:46:57Z","timestamp":1660308417000},"page":"4647-4649","source":"Crossref","is-referenced-by-count":15,"title":["Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6900-2264","authenticated-orcid":false,"given":"Athena","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Kammers","sequence":"additional","affiliation":[{"name":"Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H Benjamin","family":"Larman","sequence":"additional","affiliation":[{"name":"Department of Pathology and the Institute for Cell Engineering, Johns Hopkins University School of Medicine , Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4702-2656","authenticated-orcid":false,"given":"Robert B","family":"Scharpf","sequence":"additional","affiliation":[{"name":"Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3278-6274","authenticated-orcid":false,"given":"Ingo","family":"Ruczinski","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,8,12]]},"reference":[{"key":"2023041408242236600_","author":"Chen","year":"2021"},{"key":"2023041408242236600_","author":"Chen","year":"2022"},{"key":"2023041408242236600_","author":"Langmead","year":"2010"},{"key":"2023041408242236600_","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/nbt.1856","article-title":"Autoantigen discovery with a synthetic human peptidome","volume":"29","author":"Larman","year":"2011","journal-title":"Nat. Biotechnol"},{"key":"2023041408242236600_","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.1038\/s41596-018-0025-6","article-title":"Phip-seq characterization of serum antibodies using oligonucleotide-encoded peptidomes","volume":"13","author":"Mohan","year":"2018","journal-title":"Nat. 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