Y. Safonova

Germline-targeting chimpanzee SIV Envelopes induce V2-apex broadly neutralizing-like B cell precursors in a rhesus macaque infection model

This study shows that germline-targeting SCIVs can activate and expand B cells expressing V2-apex bnAb-like precursors in rhesus macaques.

Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift

The paper identifies broadly neutralizing antibodies against SARS-CoV-2 that target conserved regions on the spike RBD, showing resistance to antigenic drift and suggesting potential vaccine targets.

Analyzing patterns of tyrosine sulfation in naive antibody repertoires

The paper analyzes human naive antibody repertoires to identify VDJ recombination patterns generating CDR3s with sulfated tyrosines and anionic motifs, finding they are common in specific D gene families.

Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains

The paper catalogs germline immunoglobulin light chain variable genes in 18 mouse strains, finding extensive undocumented diversity not present in IMGT.

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease

The paper identifies broadly neutralizing antibodies targeting the S2 region of betacoronavirus spikes that protect against SARS-CoV-1, SARS-CoV-2, and MERS-CoV.

Targeted isolation of panels of diverse human protective broadly neutralizing antibodies against SARS-like viruses

This study isolates a panel of broadly neutralizing antibodies against SARS-like viruses from donors, showing effectiveness against multiple variants including Omicron.

Revealing how variations in antibody repertoires correlate with vaccine responses

The paper analyzes antibody repertoire variations in vaccinated calves to identify genetic factors influencing vaccine efficacy against bovine respiratory disease.

Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques

This study shows that rhesus macaques can be immunized to produce broadly neutralizing antibodies against multiple SARS-related viruses, highlighting differences in B cell repertoires between humans and macaques.

Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naive human B cells

The paper screens naive B cells for VRC01-class broadly neutralizing antibody precursors using a germline-targeting immunogen and single-cell BCR sequencing, finding common germline variation affecting gene usage.

Scalable Models of Antibody Evolution and Benchmarking of Clonal Tree Reconstruction Methods

This paper benchmarks clonal tree reconstruction methods using a scalable model of antibody evolution and finds that simple postprocessing improves accuracy over alternative methods.

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

The paper identifies a compact vocabulary of paratope-epitope interaction motifs that enables machine learning prediction of antibody-antigen binding.

IgEvolution: clonal analysis of antibody repertoires

IgEvolution constructs antibody repertoires and clonal trees together, improving accuracy by identifying mutable positions linked to antigen-binding sites.