Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

(2021) Louis du Plessis et al.   SCIENCE

Distinct clonal evolution of B-cells in HIV controllers with neutralizing antibody breadth

(2021) Deniz Cizmeci et al.   eLife

Rapid HIV Progression Is Associated with Extensive Ongoing Somatic Hypermutation

(2020) Ben S. Wendel et al.   JOURNAL OF IMMUNOLOGY

Earliest infections predict the age distribution of seasonal influenza A cases

(2020) Philip Arevalo et al.   eLife

Single-cell repertoire tracing identifies rituximab-resistant B cells during myasthenia gravis relapses

(2020) Ruoyi Jiang et al.   JCI Insight

Human germinal centres engage memory and naive B cells after influenza vaccination

(2020) Jackson S. Turner et al.   NATURE

Thymus-derived B cell clones persist in the circulation after thymectomy in myasthenia gravis

(2020) Ruoyi Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shaping of infant B cell receptor repertoires by environmental factors and infectious disease

(2019) Sandra C. A. Nielsen et al.   Science Translational Medicine

Longitudinal Analysis of the Human B Cell Response to Ebola Virus Infection

(2019) Carl W. Davis et al.   CELL

Fierce selection and interference in B-cell repertoire response to chronic HIV-1

(2019) Armita Nourmohammad et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships

(2019) Julian Q. Zhou et al.   JOURNAL OF IMMUNOLOGY

Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination

(2019) Kenneth B. Hoehn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Restricted Clonality and Limited Germinal Center Reentry Characterize Memory B Cell Reactivation by Boosting

(2019) Luka Mesin et al.   CELL

Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection

(2018) Ian Setliff et al.   Cell Host & Microbe

Selection and Neutral Mutations Drive Pervasive Mutability Losses in Long-Lived Anti-HIV B-Cell Lineages

(2018) Marcos C Vieira et al.   MOLECULAR BIOLOGY AND EVOLUTION

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

(2018) Aleksandr Kovaltsuk et al.   JOURNAL OF IMMUNOLOGY

Sequencing HIV-neutralizing antibody exons and introns reveals detailed aspects of lineage maturation

(2018) Erik L. Johnson et al.   Nature Communications

Benchmarking Tree and Ancestral Sequence Inference for B Cell Receptor Sequences

(2018) Kristian Davidsen et al.   Frontiers in Immunology

A Phylogenetic Codon Substitution Model for Antibody Lineages

(2017) Kenneth B. Hoehn et al.   GENETICS

HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage

(2017) Elise Landais et al.   IMMUNITY

Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data

(2017) Namita T. Gupta et al.   JOURNAL OF IMMUNOLOGY

A Phylogenetic Codon Substitution Model for Antibody Lineages

(2017) Kenneth B. Hoehn et al.   GENETICS

Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth

(2016) Jinghe Huang et al.   IMMUNITY

Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy

(2016) Mattias Levin et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination

(2016) Ali H Ellebedy et al.   NATURE IMMUNOLOGY

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation

(2016) Jacob D. Galson et al.   Genome Medicine

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

(2016) Zizhang Sheng et al.   PLoS Computational Biology

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

(2015) Namita T. Gupta et al.   BIOINFORMATICS

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

(2015) Xueling Wu et al.   CELL

BCR repertoire sequencing: different patterns of B-cell activation after two Meningococcal vaccines

(2015) Jacob D Galson et al.   IMMUNOLOGY AND CELL BIOLOGY

Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing

(2015) Konstantinos Tsioris et al.   Integrative Biology

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales

(2015) Gur Yaari et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2015) Daniel Gadala-Maria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effect of genetic structure on molecular dating and tests for temporal signal

(2015) Gemma G. R. Murray et al.   Methods in Ecology and Evolution

Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences

(2015) Jacob D. Galson et al.   EBioMedicine

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

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

Generation of memory B cells inside and outside germinal centers

(2014) Toshitada Takemori et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

(2014) Nicole A. Doria-Rose et al.   NATURE

High-Throughput Sequencing of Human Immunoglobulin Variable Regions with Subtype Identification

(2014) Merle Schanz et al.   PLoS One

High-resolution antibody dynamics of vaccine-induced immune responses

(2014) Uri Laserson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) C. Wang et al.   JOURNAL OF IMMUNOLOGY

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

(2013) Hua-Xin Liao et al.   NATURE

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Gur Yaari et al.   Frontiers in Immunology

Germinal Centers

(2012) Gabriel D. Victora et al.   Annual Review of Immunology

Germinal center selection and the development of memory B and plasma cells

(2012) Mark J. Shlomchik et al.   IMMUNOLOGICAL REVIEWS

A germinal center–independent pathway generates unswitched memory B cells early in the primary response

(2012) Justin J. Taylor et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

(2012) Gur Yaari et al.   NUCLEIC ACIDS RESEARCH

Detecting selection in immunoglobulin sequences

(2011) M. Uduman et al.   NUCLEIC ACIDS RESEARCH

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

(2011) X. Wu et al.   SCIENCE

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Rapid cloning of high-affinity human monoclonal antibodies against influenza virus

(2008) Jens Wrammert et al.   NATURE

JANEWAY'S IMMUNOBIOLOGY, 7TH EDITION

(2008) Denise Chee Hsu   SHOCK