F. A. Matsen

The paper maps how HA mutations affect neutralization by serum from different age groups, showing age-dependent antigenic effects and implications for viral evolution.

The paper uses single-cell transcriptomics to identify new broadly neutralizing antibodies against flaviviruses, including an IgA1 isotype with unique neutralizing properties.

The paper compares SARS-CoV-2 antibody responses between infants and mothers, finding higher binding and functional antibody levels in infants, particularly in the fusion peptide region.

The paper uses a probabilistic model to analyze TCRβ repertoire data and identifies sequence features that predict nucleotide trimming during V(D)J recombination.

This paper introduces a biophysical model to predict viral escape from polyclonal antibodies by analyzing how mutations affect antibody activity against specific epitopes.

This study examines antibody responses to endemic coronaviruses before and after SARS-CoV-2 infection in Kenyan mothers and infants, finding increased eHCoV antibodies in mothers but not infants post-infection.

This study compares SARS-CoV-2 Spike antibody responses between macaques and humans after vaccination or infection, identifying shared and distinct epitope recognition patterns and escape pathways.

The paper infers genetic loci influencing V(D)J recombination probabilities by combining TCR repertoires and genome-wide genotypes from a human cohort.

This study identifies antibody escape pathways for SARS-CoV-2 spike protein using Phage-DMS, revealing variable escape mutations in immunodominant regions and individual epitope targeting differences.

This study maps SARS-CoV-2 antibody epitopes and identifies cross-reactive sequences with endemic HCoVs in COVID-19 patients.

This study reconstructs the developmental pathways of HIV-specific ADCC antibodies and identifies mutations required for antigen binding and ADCC function.

sumrep is an R package for analyzing and comparing immune receptor repertoires, showing that recombination features are more discriminative than amino acid composition summaries and that generative models capture some but not all repertoire properties.

This study reconstructs the developmental lineage of an infant-derived HIV-1 broadly neutralizing antibody, showing a rapid evolution with fewer mutations compared to adult antibodies.

The paper analyzes TCR repertoire data to uncover associations between MHC alleles, immune exposures, and TCR sequences in a human cohort, revealing patterns linked to pathogen exposure and genetic background.