Mahan Ghafari

The paper identifies a bias in phylogenetic branch lengths when using the discrete Gamma model and recommends replacing it with the FreeRate model.

This study traces how natural selection on SARS-CoV-2 has shifted during the pandemic, favoring antibody escape and ACE2 binding, with dynamic pressures across antibody classes.

This study analyzes HCV within-host dynamics post-DAA treatment failure, finding persistent viral subpopulations and lineage-specific evolutionary rates.

This study uses deep-learning structural modeling and divergence dating to analyze RdRps from plant and fungal viruses, revealing a recent divergence of sobelivirads and suggesting cross-kingdom host shifts in their evolutionary history.

This study applies a mechanistic model to correct for time-dependent rate phenomena in plant viruses, revealing an ancient origin for sobemoviruses over four million years ago.