François D. Rouleau

This paper trains a machine learning model to predict antifolate resistance mutations in Pneumocystis jirovecii using experimental data and computational modeling, finding mutations that confer resistance to trimethoprim-sulfamethoxazole.

The paper curates AMR mutations in fungi to create FungAMR, identifies universal resistance mutations, and provides a tool to screen genomes for AMR mutations.

The paper identifies 355 resistance mutations in P. jirovecii DHFR to methotrexate using deep mutational scanning, revealing an allosteric mechanism at position F199.

Toeholder is a software tool for automated design and in silico validation of toehold riboswitches, incorporating experimental data and molecular dynamics simulations.

BFG-PCA is a high-throughput method for discovering binary protein interactions using DHFR-PCA, showing high sensitivity and specificity across human and yeast protein pairs.