Daphne van Ginneken

AntibodyForests quantifies inter- and intra-antibody repertoire evolution using protein language models and structure analysis.

The paper characterizes clonal dynamics of antibody-secreting cells in bone marrow following influenza infection, finding that IgG ASCs preferentially target nucleoprotein regardless of infection type.

This study shows that protein language model pseudolikelihoods correlate with B cell selection features like SHM and isotype usage, but not binding affinity, in vivo.

scMitoMut is an R package that improves mitochondrial mutation calling in single cells by using statistical methods, showing better sensitivity and precision than existing tools.