Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

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The Relation between Evenness and Diversity

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pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

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Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

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Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

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High-Throughput Sequencing of the Zebrafish Antibody Repertoire

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Towards error-free profiling of immune repertoires

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Reference values for B cell subpopulations from infancy to adulthood

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Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

Shi, W., Liao, Y., Willis, S. N., Taubenheim, N., Inouye, M., Tarlinton, D. M., Smyth, G. K., Hodgkin, P. D., Nutt, S. L., & Corcoran, L. M. (2015) · Nature Immunology · doi:10.1038/ni.3154 · Cited by 397

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

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Overlap and Effective Size of the Human CD8 + T Cell Receptor Repertoire

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Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

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Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypesPreprint

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Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

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Maximum entropy models for antibody diversity

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Functional heterogeneity of human memory CD4 + T cell clones primed by pathogens or vaccines

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Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells

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Statistical inference of the generation probability of T-cell receptors from sequence repertoires

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Convergent Antibody Signatures in Human Dengue

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T cell repertoire following autologous stem cell transplantation for multiple sclerosis

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Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

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Rep‐Seq: uncovering the immunological repertoire through next‐generation sequencing

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Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

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Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data

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Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota

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IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling

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Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation

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High-throughput pairing of T cell receptor α and β sequences

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Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach

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Characterizing immune repertoires by high throughput sequencing: strategies and applications

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Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

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Inferring processes underlying B-cell repertoire diversity

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The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies

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A proteomics approach for the identification and cloning of monoclonal antibodies from serum

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A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

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Estimating the Diversity, Completeness, and Cross-Reactivity of the T Cell Repertoire

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Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires

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Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery

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Detecting and correcting systematic variation in large-scale RNA sequencing data

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A Mechanism for TCR Sharing between T Cell Subsets and Individuals Revealed by Pyrosequencing

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MiTCR: software for T-cell receptor sequencing data analysis

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High-resolution antibody dynamics of vaccine-induced immune responses

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T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunityPreprint

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Next generation sequencing for TCR repertoire profiling: Platform‐specific features and correction algorithms

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Quantifying selection in immune receptor repertoires

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Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populationsPreprint

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αβ T cell receptors as predictors of health and disease

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Mining the antibodyome for HIV-1–neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains

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Aging and developmental transitions in the B cell lineage

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The analysis of clonal expansions in normal and autoimmune B cell repertoires

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Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes

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