ArticleScientific reports2016
Clonify: unseeded antibody lineage assignment from next-generation sequencing data.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Anchor Clustering for million-scale immune repertoire sequencing data.BMC bioinformatics · 2024Pooled it
- Vaccination induces HIV broadly neutralizing antibody precursors in humans.Science (New York, N.Y.) · 2022Trial
- Trial
- Longitudinal analysis of drift in the circulating human antibody repertoire over four years.Scientific reports · 2026Article
- Combining mutation and recombination statistics to infer clonal families in antibody repertoires.eLife · 2024Article
- Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications.Frontiers in molecular biosciences · 2024Article
- Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.PLoS pathogens · 2023Article
- Dependence on a variable residue limits the breadth of an HIV MPER neutralizing antibody, despite convergent evolution with broadly neutralizing antibodies.PLoS pathogens · 2022Article
- Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM.BMC immunology · 2022Article
- Efficient isolation of rare B cells using next-generation antigen barcoding.Frontiers in cellular and infection microbiology · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity.JCI insight · 2021Article
- B cell engagement with HIV-1 founder virus envelope predicts development of broadly neutralizing antibodies.Cell host & microbe · 2021Article
- Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.PLoS computational biology · 2021Article
- Alignment free identification of clones in B cell receptor repertoires.Nucleic acids research · 2021Article
- PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST.BMC bioinformatics · 2020Article
- AncesTree: An interactive immunoglobulin lineage tree visualizer.PLoS computational biology · 2020Article
- Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults.Frontiers in immunology · 2020Observational
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- Article
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Authors and funding
4 authors.
Funding
Abstract
Defining the dynamics and maturation processes of antibody clonal lineages is crucial to understanding the humoral response to infection and immunization. Although individual antibody lineages have been previously analyzed in isolation, these studies provide only a narrow view of the total antibody response. Comprehensive study of antibody lineages has been limited by the lack of an accurate clonal lineage assignment algorithm capable of operating on next-generation sequencing datasets. To address this shortcoming, we developed Clonify, which is able to perform unseeded lineage assignment on very large sets of antibody sequences. Application of Clonify to IgG+ memory repertoires from healthy individuals revealed a surprising lack of influence of large extended lineages on the overall repertoire composition, indicating that this composition is driven less by the order and frequency of pathogen encounters than previously thought. Clonify is freely available at www.github.com/briney/clonify-python.
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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.