ArticlePLoS computational biology2022
Inference of B cell clonal families using heavy/light chain pairing information.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 32 citations in OpenAlex.
- A single-cell atlas of porcine hematopoietic development.Nature communications · 2026Article
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- Large-scale paired chain BCR analysis reveals antibody clonal family inference bias and enhances resolution with machine learning.PLoS computational biology · 2026Article
- Deep generative modeling captures maturation-dependent pairing patterns in human antibodies.iScience · 2026Article
- Decoding autoimmune disease with single-cell immune repertoire and transcriptome sequencing: mechanisms and therapeutic opportunities.Frontiers in immunology · 2026Review
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.PLoS computational biology · 2025Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.bioRxiv : the preprint server for biology · 2025Article
- Separating selection from mutation in antibody language models.bioRxiv : the preprint server for biology · 2025Article
- Conserved heavy/light contacts and germline preferences revealed by a large-scale analysis of natively paired human antibody sequences and structural data.Communications biology · 2025Article
- Increased immunogen valency improves the maturation of vaccine-elicited HIV-1 VRC01-like antibodies.PLoS pathogens · 2025Article
- Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.PLoS computational biology · 2025Article
- Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.Nucleic acids research · 2025Article
- Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses.PLoS pathogens · 2024Article
- Computational detection of antigen-specific B cell receptors following immunization.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Combining mutation and recombination statistics to infer clonal families in antibody repertoires.eLife · 2024Article
- The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2.PLoS pathogens · 2024Article
- Evaluating methods for B-cell clonal family assignment.bioRxiv : the preprint server for biology · 2024Article
- Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.
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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.