B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV

Maturation and persistence of the anti-SARS-CoV-2 memory B cell response

(2021) Aurélien Sokal et al.   CELL

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

(2021) Zijun Wang et al.   NATURE

Serum Neutralizing Activity Elicited by mRNA-1273 Vaccine — Preliminary Report

(2021) Kai Wu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Neutralizing Activity of BNT162b2-Elicited Serum

(2021) Yang Liu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

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

(2020) Felix Horns et al.   Cell Reports

Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody

(2020) Xiaolong Tian et al.   Emerging Microbes & Infections

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

(2020) Dora Pinto et al.   NATURE

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

(2020) Yan Wu et al.   SCIENCE

Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays

(2020) Katharine H. D. Crawford et al.   Viruses-Basel

Transcriptional and clonal characterization of B cell plasmablast diversity following primary and secondary natural DENV infection

(2020) Adam T. Waickman et al.   EBioMedicine

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

(2020) Christopher O. Barnes et al.   CELL

Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells

(2020) Yunlong Cao et al.   CELL

Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses

(2020) Fabian Schmidt et al.   JOURNAL OF EXPERIMENTAL MEDICINE

SARS-CoV-2-specific ELISA development

(2020) Vicky Roy et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

(2020) Davide F. Robbiani et al.   NATURE

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

(2020) Bo Li et al.   NATURE METHODS

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes

(2020) Ching-Lin Hsieh et al.   SCIENCE

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail

(2020) Johanna Hansen et al.   SCIENCE

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody

(2020) Zhe Lv et al.   SCIENCE

Structural basis of a shared antibody response to SARS-CoV-2

(2020) Meng Yuan et al.   SCIENCE

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

(2020) Luca Piccoli et al.   CELL

Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses

(2020) Jenna J. Guthmiller et al.   IMMUNITY

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

(2020) M. Alejandra Tortorici et al.   SCIENCE

An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain

(2020) Nicholas C. Wu et al.   Cell Reports

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2

(2020) Takuya Tada et al.   Cell Reports

The Multifaceted B Cell Response to Influenza Virus

(2019) Jonathan H. Lam et al.   JOURNAL OF IMMUNOLOGY

VH1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design

(2019) Fang Chen et al.   Current Opinion in Virology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data

(2018) Nima Nouri et al.   BIOINFORMATICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Establishing Correlates of Protection for Vaccine Development: Considerations for the Respiratory Syncytial Virus Vaccine Field

(2018) Prasad S. Kulkarni et al.   VIRAL IMMUNOLOGY

Conformational Plasticity in Broadly Neutralizing HIV-1 Antibodies Triggers Polyreactivity

(2018) Julie Prigent et al.   Cell Reports

Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination

(2018) Karlynn E. Neu et al.   JOURNAL OF CLINICAL INVESTIGATION

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

(2018) Thomas C. Terwilliger et al.   NATURE METHODS

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Inherited CD70 deficiency in humans reveals a critical role for the CD70–CD27 pathway in immunity to Epstein-Barr virus infection

(2016) Kazushi Izawa et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

SARS and MERS: recent insights into emerging coronaviruses

(2016) Emmie de Wit et al.   NATURE REVIEWS MICROBIOLOGY

Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site

(2016) Harry B Gristick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site

(2016) Harry B Gristick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2015) Namita T. Gupta et al.   BIOINFORMATICS

Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory

(2015) Anne Chao et al.   ECOLOGY

Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus

(2015) Davide Corti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microneutralization Assay Titres Correlate with Protection against Seasonal Influenza H1N1 and H3N2 in Children

(2015) Chris P. Verschoor et al.   PLoS One

Passive transfer of modest titers of potent and broadly neutralizing anti-HIV monoclonal antibodies block SHIV infection in macaques

(2014) Masashi Shingai et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype

(2014) Griselda V Zuccarino-Catania et al.   NATURE IMMUNOLOGY

IMGT®, the international ImMunoGeneTics information system® 25 years on

(2014) Marie-Paule Lefranc et al.   NUCLEIC ACIDS RESEARCH

Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution

(2014) X.-C. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Broadly Neutralizing Antiviral Antibodies

(2013) Davide Corti et al.   Annual Review of Immunology

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Restricting HIV-1 pathways for escape using rationally designed anti–HIV-1 antibodies

(2013) Ron Diskin et al.   JOURNAL OF EXPERIMENTAL MEDICINE

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

HIV-1 suppression and durable control by combining single broadly neutralizing antibodies and antiretroviral drugs in humanized mice

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

Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues

(2013) A. P. West et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germinal Centers

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

A strategy for risk mitigation of antibodies with fast clearance

(2012) Isidro Hötzel et al.   mAbs

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

(2012) Gur Yaari et al.   NUCLEIC ACIDS RESEARCH

Onset of Immune Senescence Defined by Unbiased Pyrosequencing of Human Immunoglobulin mRNA Repertoires

(2012) Florian Rubelt et al.   PLoS One

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Costimulatory Molecule CD27 Maintains Clonally Diverse CD8+ T Cell Responses of Low Antigen Affinity to Protect against Viral Variants

(2011) Klaas P.J.M. van Gisbergen et al.   IMMUNITY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

(2011) J. F. Scheid et al.   SCIENCE

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation

(2010) Hugo Mouquet et al.   NATURE

Few and Far Between: How HIV May Be Evading Antibody Avidity

(2010) Joshua S. Klein et al.   PLoS Pathogens

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Evaluation of CD4-CD4i Antibody Architectures Yields Potent, Broadly Cross-Reactive Anti-Human Immunodeficiency Virus Reagents

(2009) A. P. West et al.   JOURNAL OF VIROLOGY

Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals

(2009) Johannes F. Scheid et al.   NATURE

Evidence for HIV-associated B cell exhaustion in a dysfunctional memory B cell compartment in HIV-infected viremic individuals

(2008) Susan Moir et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Structural Basis for Potent Cross-Neutralizing Human Monoclonal Antibody Protection against Lethal Human and Zoonotic Severe Acute Respiratory Syndrome Coronavirus Challenge

(2008) B. Rockx et al.   JOURNAL OF VIROLOGY

Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning

(2007) Thomas Tiller et al.   JOURNAL OF IMMUNOLOGICAL METHODS