Rate My Professor Andre Ribeiro

Andre Sanches Ribeiro is a tenured Professor of Computational Systems Biology in the Faculty of Medicine and Health Technology, Biosciences, at Tampere University, appointed on July 1, 2017. He is the Principal Investigator and Head of the Laboratory of Biosystem Dynamics, which he founded in 2008 in the Department of Signal Processing at the former Tampere University of Technology. His prior appointments include Associate Professor in Signal Processing for Systems and Molecular Biology in 2017 and Associate Professor in the Signal Processing Department from 2012 to 2017. Ribeiro obtained a degree in physics from the University of Lisbon and a Doctor of Science (Technology) in network theory from the Technical University of Lisbon, awarded on July 29, 2004. He subsequently held a postdoctoral position at the University of Calgary in Canada, where he developed large-scale stochastic models of gene networks.

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).