ArticlemAbs
A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies.
Article in mAbs. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Computational mining of B cell receptor repertoires reveals antigen-specific and convergent responses to Ebola vaccination.Frontiers in immunology · 2024Trial
- AI-Driven BCR Modeling for Precision Immunology.International journal of molecular sciences · 2026Review
- Contrastive learning enables epitope overlap predictions for targeted antibody discovery.Patterns (New York, N.Y.) · 2026Article
- LM-QASAS: reference-free identification of antigen-specific sequences from the BCR repertoire using antibody language models.Frontiers in immunology · 2026Article
- Is the vaccination-induced B cell receptor repertoire predictable?Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.PLoS computational biology · 2025Article
- Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining.Nature communications · 2024Article
- Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors.Briefings in bioinformatics · 2024Article
- Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications.Frontiers in molecular biosciences · 2024Article
- Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences.mSystems · 2023Article
- Convergent evolution and B-cell recirculation in germinal centers in a human lymph node.Life science alliance · 2023Article
- KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies.Scientific reports · 2023Article
- Leveraging deep learning to improve vaccine design.Trends in immunology · 2023Review
- Article
- Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope.Frontiers in molecular biosciences · 2023Article
- Structural modeling of antibody variable regions using deep learning-progress and perspectives on drug discovery.Frontiers in molecular biosciences · 2023Review
- Antibodies as drugs-a Keystone Symposia report.Annals of the New York Academy of Sciences · 2023Article
- Functional antibodies exhibit light chain coherence.Nature · 2022Article
- Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery.Briefings in bioinformatics · 2022Review
- Deciphering the language of antibodies using self-supervised learning.Patterns (New York, N.Y.) · 2022Article
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Authors and funding
8 authors.
Funding
Abstract
Due to their shared genetic history, antibodies from the same clonotype often bind to the same epitope. This knowledge is used in immune repertoire mining, where known binders are used to search bulk sequencing repertoires to identify new binders. However, current computational methods cannot identify epitope convergence between antibodies from different clonotypes, limiting the sequence diversity of antigen-specific antibodies that can be identified. We describe how the antibody binding site, the paratope, can be used to cluster antibodies with common antigen reactivity from different clonotypes. Our method, paratyping, uses the predicted paratope to identify these novel cross clonotype matches. We experimentally validated our predictions on a pertussis toxoid dataset. Our results show that even the simplest abstraction of the antibody binding site, using only the length of the loops involved and predicted binding residues, is sufficient to group antigen-specific antibodies and provide additional information to conventional clonotype analysis.
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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.