Potts Hamiltonian models of protein sequence co-variation are statistical models constructed
from the pair correlations observed in a multiple sequence alignment (MSA) of a protein …

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is
mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors …

This is an exciting time for immunology because the future promises to be replete with
exciting new discoveries that can be translated to improve health and treat disease in novel …

HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still
not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected …

The design of synthetic proteins with the desired function is a long-standing goal in
biomolecular science, with broad applications in biochemical engineering, agriculture …

Direct-acting antiviral agents (DAAs) provide efficacious therapeutic treatments for chronic
Hepatitis C virus (HCV) infection. However, emergence of drug resistance mutations (DRMs) …

Vaccination has essentially eradicated poliovirus. Yet, its mutation rate is higher than that of
viruses like HIV, for which no effective vaccine exists. To investigate this, we infer a fitness …

Understanding the complex mutation patterns that give rise to drug resistant viral strains
provides a foundation for developing more effective treatment strategies for HIV/AIDS …

The development of drug resistance in HIV is the result of primary mutations whose effects
on viral fitness depend on the entire genetic background, a phenomenon called 'epistasis' …

We introduce a model of amino acid sequence evolution that accounts for the statistical
behavior of real sequences induced by epistatic interactions. We base the model dynamics …