Evidence map›Paper›PMID 39586680›Full record

ArticleCold Spring Harbor protocols2025

Antibody Data Analysis from Diverse Immune Libraries.

Ahmed S Fahad, Matías F Gutiérrez-Gonzalez, Bharat Madan, Brandon J DeKosky

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cold Spring Harbor protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Ahmed S Fahad *The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA.ORCID http://orcid.org/0000-0002-5088-9333
Matías F Gutiérrez-Gonzalez *The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA.ORCID http://orcid.org/0000-0002-9729-6850
Bharat MadanThe Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA.ORCID http://orcid.org/0000-0002-7376-9991
Brandon J DeKoskyThe Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA dekosky@mit.edu.ORCID http://orcid.org/0000-0001-6406-0836

Funding

Dissecting the mechanisms of HIV resistance in vivo to broadly neutralizing antibodiesU01AI169587 · NIAID · UNIVERSITY OF MINNESOTA · PI Priyamvada Acharya, Brandon James DeKosky · 2022 to 2026
$7.8M
Potent broadly neutralizing antibody development against the HIV-1 fusion peptide epitopeR01AI181684 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI Brandon James DeKosky · 2023 to 2026
$3.0M
Comprehensive analysis of human adaptive immune receptors to elucidate correlates of Epstein-Barr virus disease suppressionDP5OD023118 · OD · UNIVERSITY OF KANSAS LAWRENCE · PI DEKOSKY, BRANDON JAMES · 2016 to 2022
$2.2M
Rapid antibody screening systems to identify and engineer antiviral protectionR21AI166396 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI DEKOSKY, BRANDON JAMES · 2022 to 2023
$850k
Comprehensive molecular and functional analyses of anti-HIV-1 broadly neutralizing antibody repertoiresR21AI143407 · NIAID · UNIVERSITY OF KANSAS LAWRENCE · PI DEKOSKY, BRANDON JAMES, FORREST, MARCUS LAIRD · 2019 to 2020
$435k
NIAID NIH HHS R01 AI181684NIAID NIH HHS R21 AI143407NIAID NIH HHS R21 AI166396NIAID NIH HHS U01 AI169587NIH HHS DP5 OD023118
6 · The paper itself

Abstract

Antibody functional screening studies and next-generation sequencing require careful processing and interpretation of sequence data for optimal results. Here, we provide a detailed protocol for the functional analysis of antibody gene data, including antibody repertoire quantification and functional mapping of high-throughput screening data based on enrichment ratio values, which are a simple way to determine the enrichment of each sequenced antibody after sorting a display library against desired antigens. This protocol enables a user to apply a set of simple yet powerful bioinformatic tools for high-throughput analysis and interpretation of antibody data that is especially well suited for display library screening and for antibody discovery applications.

Indexed as

AntibodiesComputational BiologyData AnalysisGene LibraryHigh-Throughput Nucleotide SequencingAntibodies

Identifiers

PMID39586680
PMCPMC12043016

What OpenQuestion holds

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Registered trials

None linked

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.