Will Dumm

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

This study uses deep learning to detect entrenchment in antibody germline genes, revealing epistatic constraints from both intra-chain and genetically uncoupled partners.

This paper introduces a model that separates mutation and selection processes in antibody language models to improve prediction of mutation effects on antibody function.

This study examines how SARS-CoV-2 evolved to escape 1,603 antibodies by analyzing mutation dynamics and selective pressures over 3.5 years of the pandemic.

The paper introduces larch, a tool that explores the space of optimal phylogenetic trees to find more parsimonious trees and increase diversity in the set of optimal solutions.

The paper develops 'thrifty' models of somatic hypermutation using convolutions on 3-mer embeddings, showing they outperform 5-mer models with fewer parameters.