T. Dupic

Protein sequence landscapes are not so simple: on reference-free versus reference-based inference

The paper shows that reference-free analysis is equivalent to reference-based methods, leading to identical landscapes but different interpretations of epistasis.

Computational detection of antigen specific B cell receptors following immunization

This study presents a computational method to identify antigen-specific BCRs from immune repertoires using sequence similarity and validates it with human data post-vaccination and infection.

Combining mutation and recombination statistics to infer clonal families in antibody repertoires

The paper introduces HILARy, a method to identify clonal families in antibody repertoires by combining mutation and recombination statistics, finding evolutionary properties are independent of junction length and revealing broad selection pressures.

Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

This study characterizes the hierarchical epistasis between heavy and light chain mutations in an anti-influenza bnAb, showing how such interactions shape the evolution of broad antigen affinity.

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

The paper maps how mutations in the SARS-CoV-2 Omicron BA.1 RBD affect antibody binding affinity through systematic analysis of 32,768 genotypes against four monoclonal antibodies.

Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1

This study identifies compensatory epistasis in SARS-CoV-2 Omicron BA.1 that maintains ACE2 affinity despite antibody-escape mutations.

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

This study measures binding affinity landscapes of two influenza bnAbs to understand their evolutionary pathways and how they acquire breadth.

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in non-small cell lung cancer patients

The paper identifies two CD8+ TIL subpopulations in NSCLC, one circulating and one resident, which transition into terminally differentiated cells through a unique state.

Population variability in the generation and thymic selection of T-cell repertoires

The paper introduces SONIA, a tool to analyze TCR repertoire variability, finding that most variability stems from VDJ generation and that inter-individual variance is small compared to intra-individual variance.

Genesis of the αβ T-cell receptor

The paper quantitatively characterizes the β T-cell receptor generation process using high-throughput sequencing and computational experiments, revealing correlations and diversity properties.