A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies

Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics

(2020) Felix Horns et al.   Cell Reports

CoV-AbDab: the Coronavirus Antibody Database

(2020) Matthew I J Raybould et al.   BIOINFORMATICS

Commonality despite exceptional diversity in the baseline human antibody repertoire

(2019) Bryan Briney et al.   NATURE

Five computational developability guidelines for therapeutic antibody profiling

(2019) Matthew I. J. Raybould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High frequency of shared clonotypes in human B cell receptor repertoires

(2019) Cinque Soto et al.   NATURE

Immune repertoire mining for rapid affinity optimization of mouse monoclonal antibodies

(2019) Yi-Chun Hsiao et al.   mAbs

Therapeutic Monoclonal Antibodies for Ebola Virus Infection Derived from Vaccinated Humans

(2019) Pramila Rijal et al.   Cell Reports

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

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

Analysis of the B cell receptor repertoire in six immune-mediated diseases

(2019) R. J. M. Bashford-Rogers et al.   NATURE

Thera-SAbDab: the Therapeutic Structural Antibody Database

(2019) Matthew I J Raybould et al.   NUCLEIC ACIDS RESEARCH

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

(2019) Erand Smakaj et al.   BIOINFORMATICS

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

(2018) Edgar Liberis et al.   BIOINFORMATICS

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Antibody repertoire analysis in polygenic autoimmune diseases

(2018) Rachael J. M. Bashford-Rogers et al.   IMMUNOLOGY

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

(2018) Ida Lindeman et al.   NATURE METHODS

Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding

(2018) Sara D’Angelo et al.   Frontiers in Immunology

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

(2018) Aleksandr Kovaltsuk et al.   JOURNAL OF IMMUNOLOGY

High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease

(2017) Bishnudeo Roy et al.   JOURNAL OF IMMUNOLOGY

Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen

(2017) Lorenzo Di Rienzo et al.   Scientific Reports

Novel Structural Parameters of Ig–Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity

(2017) Simon Marillet et al.   Frontiers in Immunology

Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses

(2016) M. Gordon Joyce et al.   CELL

ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation

(2016) Jinwoo Leem et al.   mAbs

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

ANARCI: antigen receptor numbering and receptor classification

(2015) James Dunbar et al.   BIOINFORMATICS

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

(2015) Namita T. Gupta et al.   BIOINFORMATICS

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 analysis of clonal expansions in normal and autoimmune B cell repertoires

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

IgH sequences in common variable immune deficiency reveal altered B cell development and selection

(2015) Krishna M. Roskin et al.   Science Translational Medicine

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

(2015) Victor Greiff et al.   TRENDS IN IMMUNOLOGY

Practical guidelines for B-cell receptor repertoire sequencing analysis

(2015) Gur Yaari et al.   Genome Medicine

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

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

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

(2014) Katherine J.L. Jackson et al.   Cell Host & Microbe

The promise and challenge of high-throughput sequencing of the antibody repertoire

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery

(2014) E-Chiang Lee et al.   NATURE BIOTECHNOLOGY

Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery

(2014) William H. Robinson   Nature Reviews Rheumatology

B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes

(2014) J. N. H. Stern et al.   Science Translational Medicine

Studying the antibody repertoire after vaccination: practical applications

(2014) Jacob D. Galson et al.   TRENDS IN IMMUNOLOGY

Immunosequencing: applications of immune repertoire deep sequencing

(2013) Harlan Robins   CURRENT OPINION IN IMMUNOLOGY

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

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

(2013) J. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts

(2013) J. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) N. Jiang et al.   Science Translational Medicine

Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens

(2012) Gopalan Raghunathan et al.   JOURNAL OF MOLECULAR RECOGNITION

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

(2011) J. F. Scheid et al.   SCIENCE

A New Clustering of Antibody CDR Loop Conformations

(2010) Benjamin North et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2010) Sai T Reddy et al.   NATURE BIOTECHNOLOGY

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

(2009) S. D. Boyd et al.   Science Translational Medicine