Pierre Barrat-Charlaix

This paper introduces a coevolution-aware ancestral sequence reconstruction framework that improves reconstruction by incorporating residue-residue constraints from extant protein families.

The paper introduces a continuous-time generative model for protein evolution that captures epistatic effects and reveals how epistasis influences evolutionary dynamics and distance estimation.

This paper introduces a method using autoregressive generative models to reconstruct ancestral protein sequences while accounting for epistasis, outperforming existing methods in simulations and experimental data.

TreeKnit infers ancestral reassortment graphs from segment trees of influenza viruses, showing high accuracy and speed compared to Bayesian methods.