ArticleBioinformatics (Oxford, England)2018
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Anchor Clustering for million-scale immune repertoire sequencing data.BMC bioinformatics · 2024Pooled it
- Central nervous system B cell multiomics reveals a legacy of immune dysregulation in long-term treated HIV infection.Science advances · 2026Article
- Maternal vaccination timing shapes the composition and maturation of antibody clonotypes transferred to the newborn.bioRxiv : the preprint server for biology · 2026Article
- Pathogenesis and host response to a novel Tacaribe virus isolate in experimentally-infected Jamaican fruit bats.bioRxiv : the preprint server for biology · 2026Article
- Heavy-chain immune repertoire sequencing enables language-model prediction of antigen-specific antibodies.Research square · 2026Article
- RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis.bioRxiv : the preprint server for biology · 2026Article
- Granzyme B-expressing regulatory B cells share the same origin as conventional blood B cells.Biochemistry and biophysics reports · 2026Article
- A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.Nature immunology · 2026Article
- SARS-CoV-2 infection and vaccination elicit distinct pharyngeal mucosal B cell responses in children.Nature communications · 2026Article
- Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs.Journal of neuroinflammation · 2026Article
- Large-scale paired chain BCR analysis reveals antibody clonal family inference bias and enhances resolution with machine learning.PLoS computational biology · 2026Article
- Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.JCI insight · 2026Article
- Robust effector memory features of human T-betiScience · 2026Article
- Immunoglobulin germline reference sequences enable investigations and reveal insights into bat-specific immunity.iScience · 2025Article
- Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus.Genome research · 2025Article
- SARS-CoV-2 infection and vaccination elicit distinct pharyngeal mucosal B cell responses in children.Research square · 2025Article
- deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning.Bioinformatics (Oxford, England) · 2025Article
- B- and T cell receptor sequencing elucidates characteristics of lymphocyte depletion by ocrelizumab.iScience · 2025Article
- Mature tertiary lymphoid structures evoke intra-tumoral T and B cell responses via progenitor exhausted CD4Nature communications · 2025Article
- Systemic 4-1BB stimulation augments extrafollicular memory B cell formation and recall responses during Plasmodium infection.Cell reports · 2025Article
4 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Motivation: B cells derive their antigen-specificity through the expression of Immunoglobulin (Ig) receptors on their surface. These receptors are initially generated stochastically by somatic re-arrangement of the DNA and further diversified following antigen-activation by a process of somatic hypermutation, which introduces mainly point substitutions into the receptor DNA at a high rate. Recent advances in next-generation sequencing have enabled large-scale profiling of the B cell Ig repertoire from blood and tissue samples. A key computational challenge in the analysis of these data is partitioning the sequences to identify descendants of a common B cell (i.e. a clone). Current methods group sequences using a fixed distance threshold, or a likelihood calculation that is computationally-intensive. Here, we propose a new method based on spectral clustering with an adaptive threshold to determine the local sequence neighborhood. Validation using simulated and experimental datasets demonstrates that this method has high sensitivity and specificity compared to a fixed threshold that is optimized for these measures. In addition, this method works on datasets where choosing an optimal fixed threshold is difficult and is more computationally efficient in all cases. The ability to quickly and accurately identify members of a clone from repertoire sequencing data will greatly improve downstream analyses. Clonally-related sequences cannot be treated independently in statistical models, and clonal partitions are used as the basis for the calculation of diversity metrics, lineage reconstruction and selection analysis. Thus, the spectral clustering-based method here represents an important contribution to repertoire analysis. Availability and implementation: Source code for this method is freely available in the SCOPe (Spectral Clustering for clOne Partitioning) R package in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 license. Supplementary information: Supplementary data are available at Bioinformatics online.
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