ArticleNucleic acids research2021
Alignment free identification of clones in B cell receptor repertoires.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- Anchor Clustering for million-scale immune repertoire sequencing data.BMC bioinformatics · 2024Pooled it
- Fine-tuned protein language model identifies antigen-specific B cell receptors from immune repertoires.bioRxiv : the preprint server for biology · 2025Article
- deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning.Bioinformatics (Oxford, England) · 2025Article
- Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning.Nucleic acids research · 2025Article
- Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.PLoS computational biology · 2025Article
- Bats generate lower affinity but higher diversity antibody responses than those of mice, but pathogen-binding capacity increases if protein is restricted in their diet.PLoS biology · 2024Article
- Combining mutation and recombination statistics to infer clonal families in antibody repertoires.eLife · 2024Article
- Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.Briefings in bioinformatics · 2024Article
- Systematic evaluation of B-cell clonal family inference approaches.BMC immunology · 2024Article
- Convergent evolution and B-cell recirculation in germinal centers in a human lymph node.Life science alliance · 2023Article
- Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires.Frontiers in immunology · 2023Article
- Lineage Reconstruction of In Vitro Identified Antigen-Specific Autoreactive B Cells from Adaptive Immune Receptor Repertoires.International journal of molecular sciences · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
Following antigenic challenge, activated B cells rapidly expand and undergo somatic hypermutation, yielding groups of clonally related B cells with diversified immunoglobulin receptors. Inference of clonal relationships based on the receptor sequence is an essential step in many adaptive immune receptor repertoire sequencing studies. These relationships are typically identified by a multi-step process that involves: (i) grouping sequences based on shared V and J gene assignments, and junction lengths and (ii) clustering these sequences using a junction-based distance. However, this approach is sensitive to the initial gene assignments, which are error-prone, and fails to identify clonal relatives whose junction length has changed through accumulation of indels. Through defining a translation-invariant feature space in which we cluster the sequences, we develop an alignment free clonal identification method that does not require gene assignments and is not restricted to a fixed junction length. This alignment free approach has higher sensitivity compared to a typical junction-based distance method without loss of specificity and PPV. While the alignment free procedure identifies clones that are broadly consistent with the junction-based distance method, it also identifies clones with characteristics (multiple V or J gene assignments or junction lengths) that are not detectable with the junction-based distance method.
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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.