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Article
Open AccessPremature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants
While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Her...
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Protocol
Data Sharing and Reuse: A Method by the AIRR Community
of (AIRR, i.e., IG and TR ) has revolutionized the ability to study the adaptive immune response via large-scale experiments. Since 2009, AIRR sequencing (AIRR-seq) has been widely applied to survey the im...
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Article
Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening
CD4+ T cells are critical to fighting pathogens, but a comprehensive analysis of human T-cell specificities is hindered by the diversity of HLA alleles (>20,000) and the complexity of many pathogen genomes. We pr...
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Article
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data
High-throughput sequencing of B and T cell receptors is routinely being applied in studies of adaptive immunity. The Adaptive Immune Receptor Repertoire (AIRR) Community was formed in 2015 to address issues in...
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Article
Open AccessVDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data
Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perfor...
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Article
Identifying specificity groups in the T cell receptor repertoire
The authors devise an algorithm that can cluster T cell receptor (TCR) sequences sharing the same specificity, predict the HLA restriction of these TCR clusters on the basis of subjects’ genotypes and help to ...
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Article
Open AccessThe Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires
The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoi...
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Article
Open AccessVDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each develo** lymphocyte by a process called V(D)J reco...
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Article
Open AccessIndividual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells
The adaptive immune system’s capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these re...
