Rate My Professor Andre Ribeiro

Ribeiro's academic interests span gene expression dynamics, gene regulatory networks, models and simulators of biological processes, systems microbiology, signal processing of biological systems, single-cell biology, biophysics, information in biosystems, synthetic biology, and learning and behaviour biology. The Laboratory of Biosystem Dynamics examines the in vivo dynamics and regulatory mechanisms of bacterial gene networks during health and stress conditions, such as antibiotic exposure. The research employs experimental methods including time-lapse microscopy, flow-cytometry, RNA-seq, and synthetic biology, alongside multi-scale stochastic models, network theory, and signal processing techniques, to explore relationships between gene network structure and dynamics for potential therapeutic and biotechnological applications. Ribeiro has earned the Best Paper Award at BIOTECHNO 2016 (with S. Matos da Costa), a prize at the 6th Global Summit on Artificial Intelligence and Neural Networks (2018) for studying Z-ring formation in Escherichia coli, a prize at the 1st International BioDesign Research Conference (2020) for regulatory mechanisms of promoter dynamics, and an honorable mention for the best publication of the year from the Faculty of Medicine and Health Technology (2022). Key publications include "Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses" (PLoS Computational Biology, 2025), "Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters" (Science Advances, 2025), "Effects of cooling on E. coli’s DNA organization, structure, and gene expression" (Microbiology and Molecular Biology Reviews, 2025), and "A library of reporters of the global regulators of gene expression in Escherichia coli" (mSystems, 2024).