Michiel Stock

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.

Apr 29, 2024 | nature.com | Simeon D. Castle |Michiel Stock |Thomas E Gorochowski

AbstractCareful consideration of how we approach design is crucial to all areas of biotechnology. However, choosing or developing an effective design methodology is not always easy as biology, unlike most areas of engineering, is able to adapt and evolve. Here, we put forward that design and evolution follow a similar cyclic process and therefore all design methods, including traditional design, directed evolution, and even random trial and error, exist within an evolutionary design spectrum.

Jan 19, 2024 | science.org | Jian-Ting Li |Grace Brown |Chiho Kim |Michiel Stock

ReviewSYSTEMS BIOLOGYMichiel Stock https://orcid.org/0000-0003-0903-6061 [email protected] and Thomas E. Gorochowski https://orcid.org/0000-0003-1702-786XAuthors Info & AffiliationsAbstractDesign in synthetic biology is typically goal oriented, aiming to repurpose or optimize existing biological functions, augmenting biology with new-to-nature capabilities, or creating life-like systems from scratch.

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.