Bernard De Baets

May 22, 2024 | nature.com | Dimitri Boeckaerts |Michiel Stock |Celia Ferriol-Gonzalez |Rafael Sanjuán |Pilar Domingo-Calap |Bernard De Baets

AbstractPhages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging to find matching phages against bacteria of interest. Current computational tools do not accurately predict interactions at the strain level in a way that is relevant and properly evaluated for practical use.

Jan 17, 2024 | biorxiv.org | Robby Concha-Eloko |Michiel Stock |Bernard De Baets |Yves Briers

AbstractBacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool that combines a fine-tuned ESM-2 model with a convolutional neural network to precisely identify depolymerase sequences and their enzymatic domains.