V. Greiff

Using TCR and BCR sequencing to unravel the role of T and B cells in abdominal aortic aneurysm

This study uses scRNA TCR and BCR sequencing to analyze T and B cell responses in murine AAA, finding no clonal expansion of TCRs or BCRs.

Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling

This study benchmarks and integrates bulk and single-cell BCR sequencing with antibody peptide sequencing to understand the humoral immune response.

Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status

The paper develops AIRRTM, a generative model that identifies and generates disease-associated adaptive immune receptor sequences using only repertoire-level immune status data.

Atypical memory B cells form a pre-plasmacellular reservoir for steady-state IgD responses to common nasopharyngeal antigens

The paper identifies a new subset of tonsillar memory B cells that serve as precursors for IgD-secreting plasma cells, contributing to steady-state IgD responses to common antigens.

High-resolution mapping of cell-cycle dynamics during T-cell development and regeneration in vivo

This study maps cell-cycle dynamics during T-cell development and regeneration using in vivo labeling and modeling, revealing phase adjustments that maintain homeostasis.

Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes

Echidna simulates single-cell immune receptor repertoires and transcriptomes, enabling benchmarking of clonotyping and phylogenetic analysis tools.

In silico proof of principle of machine learning-based antibody design at unconstrained scale

This paper demonstrates that deep generative models can design high-affinity, developable antibodies at scale using synthetic data and transfer learning.

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction

The paper introduces Absolut!, a software suite generating synthetic antibody-antigen structures to benchmark machine learning methods for antibody specificity prediction.

Individualized VDJ recombination predisposes the available Ig sequence space

The paper shows that VDJ recombination rules vary between individuals, leading to individual-specific Ig sequence spaces.

Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies

Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses.

The paper analyzes single-cell BCR and transcriptome data from influenza-infected mice to reveal organ-specific B cell dynamics and clonal responses.

Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection

This study compares IgM antibody repertoires in blood and bone marrow plasma cells of mice after viral infection, finding that they are mouse-specific but not infection-specific.

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.

Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow

The paper identifies discrete populations of isotype-switched memory B cells in murine spleen and bone marrow, with distinct locations and characteristics.

Resident memory CD8 T cells persist for years in human small intestine

The paper identifies that most CD8 T cells in the human small intestine are resident memory cells that persist for over a year and maintain a stable TCR repertoire.

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

This paper develops a high-throughput method for antibody engineering in mammalian cells using CRISPR/Cas9-mediated homology-directed mutagenesis, demonstrating improved efficiency and applicability for variant discovery and optimization.