Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). - Gabriel Foley; Ariane Mora; Connie M. Ross; Scott Bottoms; Leander Sützl; Marnie L. Lamprecht; Julian Zaugg; Alexandra Essebier; Brad Balderson; Rhys Newell; Raine E. S. Thomson; Bostjan Kobe; et al. (PLoS Comput. Biol., 2022)

Do protein language models learn phylogeny? - Sanjana Tule; Gabriel Foley; Mikael Bodén (Briefings Bioinform., 2024)

Optimal phylogenetic reconstruction of insertion and deletion events. - Sanjana Tule; Gabriel Foley; Chongting Zhao; Michael Forbes; Mikael Bodén (Bioinform., 2024)