ArticleFrontiers in immunology2016
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts.
Article in Frontiers in immunology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
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- Deletions in variable region 1 of the HIV envelope accelerate V3-glycan bNAb induction in SHIV-infected rhesus macaques.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Signatures of the neutralizing dengue virus-reactive memory B cell repertoire identified by multiplexed envelope dimer probes.medRxiv : the preprint server for health sciences · 2026Article
- Potent type-specific de novo antibodies complement broadly reactive imprinted antibodies in immune responses to SARS-CoV-2 variants.Nature immunology · 2026Article
- Induction of broadly neutralizing HIV antibodies by a two-step mechanism informs vaccine design.Science (New York, N.Y.) · 2026Article
- The vaccine platform used for COVID-19 primary immunization shapes the quality of the human B cell response to a vaccine boost.Science translational medicine · 2026Article
- Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.Science immunology · 2026Article
- Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies.The Journal of experimental medicine · 2025Article
- Consistent Induction of Broadly Neutralizing HIV Antibodies by a Novel Two-Step Mechanism Informs Immunogen Design.bioRxiv : the preprint server for biology · 2025Article
- Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.Bioinformatics (Oxford, England) · 2025Article
- Transient glycan shield reduction induces CD4-binding site broadly neutralizing antibodies in SHIV-infected macaques.Cell reports · 2025Article
- Isolation and structure of broad SIV-neutralizing antibodies reveal a proximal helical MPER epitope recognized by a rhesus multi-donor class.Cell reports · 2025Article
- Frequency-potency analysis of IgG+ memory B cells delineates neutralizing antibody responses at single-cell resolution.Cell reports · 2024Article
- Novel rhesus macaque immunoglobulin germline genes identified by three sequencing approaches.Frontiers in immunology · 2024Article
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
- Interaction dynamics between innate and adaptive immune cells responding to SARS-CoV-2 vaccination in non-human primates.Nature communications · 2023Article
- Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking.Immunity · 2023Article
- Article
- Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones.Nature communications · 2022Article
- Dependence on a variable residue limits the breadth of an HIV MPER neutralizing antibody, despite convergent evolution with broadly neutralizing antibodies.PLoS pathogens · 2022Article
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Authors and funding
6 authors.
Funding
Abstract
The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity-divergence plots and longitudinal phylogenetic "birthday" trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/.
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