12 papers
Surveying the adaptive landscapes of 10,000 antibodies
Daniel PGH Wong, Aleksandra M. Walczak, Thierry Mora
Affinity maturation is the Darwinian process by which antibodies improve antigen binding through somatic hypermutation and selection. The adaptive landscape, which defines the set…
Neutralization titers reveal the structure of polyclonal antibody responses
Henry Alston, Thierry Mora, Aleksandra M. Walczak
The composition of a polyclonal antibody response is hard to measure experimentally but contains vital information about the robustness of immunity. Here, we argue that the statist…
Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics
Leonardo Di Bari, Thierry Mora, Andrea Pagnani +3
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics…
Dynamics of memory B cells and plasmablasts in healthy individuals
Andrea Mazzolini, Aleksandra M. Walczak, Thierry Mora
Our adaptive immune system relies on the persistence over long times of a diverse set of antigen-experienced B cells to encode our memories of past infections and to protect us aga…
Theoretical limits for sensing through phase separation
Henry Alston, Mason Rouches, Arvind Murugan +2
Biomolecular condensates form on timescales of seconds in cells upon environmental or compositional changes. Condensate formation is thus argued to act as a mechanism for sensing s…
Paraplume: A fast and accurate paratope prediction method provides insights into repertoire-scale binding dynamics
Gabriel Athènes, Adam Woolfe, Thierry Mora +1
The specific region of an antibody responsible for binding to an antigen, known as the paratope, is essential for immune recognition. Accurate identification of this small yet crit…