As organisms evolve, the effects of mutations change as a result of epistatic interactions with
other mutations accumulated along the line of descent. This can lead to shifts in adaptability …

Substitutions that fix between SARS-CoV-2 variants can transform the mutational landscape
of future evolution via epistasis. For example, large epistatic shifts in mutational effects …

Our immune systems constantly coevolve with the pathogens that challenge them, as
pathogens adapt to evade our defense responses, with our immune repertoires shifting in …

A protein's genetic architecture–the set of causal rules by which its sequence produces its
functions–also determines its possible evolutionary trajectories. Prior research has …

The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and
convenient therapies, especially for outpatient settings. We have previously developed …

Antigen-specific B-cell ELISPOT and multicolor FluoroSpot assays, in which the membrane-
bound antigen itself serves as the capture reagent for the antibodies that B cells secrete …

The affinity distribution of the antigen-specific memory B cell (Bmem) repertoire in the body
is a critical variable that defines an individual's ability to rapidly generate high-affinity …

The recent advances in artificial intelligence (AI) and machine learning have driven the
design of new expert systems and automated workflows that are able to model complex …

Despite breakthroughs achieved in protein sequence-to-structure and function-to-sequence
predictions, the affinity-to-mutation prediction problem remains unsolved. Such a problem is …

Fig. 1. Conformations of the SARS-CoV2 spike protein. The spike protein forms a trimer, and
the receptor-binding domain (RBD) for each protein in the trimer can be in either the down or …